diff --git a/beast-base/src/assembly/package.xml b/beast-base/src/assembly/package.xml
index 3b01d986..a87e43c7 100644
--- a/beast-base/src/assembly/package.xml
+++ b/beast-base/src/assembly/package.xml
@@ -45,7 +45,7 @@
             <outputDirectory>examples</outputDirectory>
             <includes>
                 <include>*.xml</include>
-                <include>spec/*.xml</include>
+                <include>fasta/**</include>
                 <include>nexus/**</include>
             </includes>
         </fileSet>
diff --git a/beast-base/src/test/java/beast/base/spec/beast2vs1/TestFramework.java b/beast-base/src/test/java/beast/base/spec/beast2vs1/TestFramework.java
index c6345da8..3f5795c6 100644
--- a/beast-base/src/test/java/beast/base/spec/beast2vs1/TestFramework.java
+++ b/beast-base/src/test/java/beast/base/spec/beast2vs1/TestFramework.java
@@ -32,7 +32,7 @@ public TestFramework() {
     }
 
     public static File readTestXML(String xmlName) throws URISyntaxException {
-        String fullPath = "/beast.base/examples/spec/beast2vs1/" + xmlName;
+        String fullPath = "/beast.base/examples/beast2vs1/" + xmlName;
         var url = TestFramework.class.getResource(fullPath);
         if (url == null)
             throw new IllegalArgumentException("Test XML not found on classpath: " + fullPath);
diff --git a/beast-base/src/test/resources/beast.base/examples/README.md b/beast-base/src/test/resources/beast.base/examples/README.md
index 1ac27ff6..e0015a2c 100644
--- a/beast-base/src/test/resources/beast.base/examples/README.md
+++ b/beast-base/src/test/resources/beast.base/examples/README.md
@@ -1,5 +1,7 @@
 # XML examples
 
-The converted XML examples for BEAST3 are available under beast-base/src/test/resources/beast.base/examples/spec/
+The BEAST3 XML examples for release are directly under `beast-base/src/test/resources/beast.base/examples/` (i.e., `examples/*.xml`).
 
+Long-run beast2-vs-1 comparison XMLs are under `examples/beast2vs1/` (not for release).
 
+All BEAST2 XMLs are hosted under `examples/legacy/` (not for release).
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testBSP1.xml b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testBSP1.xml
index ccaaf232..07067317 100644
--- a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testBSP1.xml
+++ b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testBSP1.xml
@@ -1,6 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
+       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
+       beast.base.evolution.operator:beast.base.spec.inference.operator:
+       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
+       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
+       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
 
     <!-- 17 taxa, 1485 sites, 138 patterns -->
     <data dataType="nucleotide" id="alignment">
@@ -74,7 +79,7 @@
         </sequence>
     </data>
 
-    <tree spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+    <tree spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
         <trait spec='beast.base.evolution.tree.TraitSet' traitname='date-forward' units='year'
                value='
 		D4Brazi82  = 1982,
@@ -101,50 +106,43 @@
 
     <distribution spec="CompoundDistribution" id="posterior">
         <distribution spec="CompoundDistribution" id="prior">
-<!--	
-            <distribution id="hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@hky.kappa">
-                <distr id="LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false"
-                              spec="beast.base.inference.distribution.LogNormalDistributionModel"/>
-            </distribution>
-            <distribution id="hky.frequencies.prior" spec="beast.base.inference.distribution.Prior" x="@hky.frequencies">
-                <distr id="Uniform" lower="0.0" upper="1.0" spec="beast.base.inference.distribution.Uniform"/>
-            </distribution>
--->
 
-            <distribution spec="BayesianSkyline" id='skyline'>
+            <distribution spec="beast.base.spec.evolution.tree.coalescent.BayesianSkyline" id='skyline'>
                 <popSizes idref="skyline.popSize"/>
                 <groupSizes idref='skyline.groupSize'/>
                 <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
                     <tree idref="tree"/>
                 </treeIntervals>
             </distribution>
-            
-            <distribution id='eml1' spec="beast.base.inference.distribution.MarkovChainDistribution"
-				jeffreys="true"
-				parameter="@skyline.popSize"/>
+
+            <distribution id='eml1' spec="beast.base.spec.inference.distribution.MarkovChainDistribution"
+				jeffreys="true" param="@skyline.popSize"/>
         </distribution>
 
 		<distribution spec='TreeLikelihood' id="likelihood">
 		    <data idref="alignment"/>
 		    <tree idref="tree"/>
 			<siteModel spec='SiteModel' id="siteModel" gammaCategoryCount="4">
-				<parameter id='siteModel.alpha' name='shape' value="5.40372E-2" lower="0.0" upper="100.0"/>
+                <parameter id='siteModel.alpha' name='shape' spec="RealScalarParam" domain="PositiveReal" value="5.40372E-2"/>
 
-				<substModel spec='HKY' id="hky">
-					<parameter name='kappa' id="hky.kappa" value="21.5056" lower="0.0" upper="100.0"/>
-					<frequencies id='freqs' spec='Frequencies' data="@alignment"/>
-				</substModel>
+                <substModel spec='HKY' id="hky">
+                    <kappa id="hky.kappa" spec="RealScalarParam" domain="PositiveReal" value="21.5056"/>
+                    <frequencies id='freqs' spec='Frequencies' data="@alignment"/>
+                </substModel>
 			</siteModel>
-			<branchRateModel spec='beast.base.evolution.branchratemodel.StrictClockModel' id="branchRates">
-				<parameter name='clock.rate' id='clock.rate' value="8.8579E-4" lower="0.0" upper="100.0"/>
+			<branchRateModel spec='beast.base.spec.evolution.branchratemodel.StrictClockModel' id="branchRates">
+				<parameter id="clock.rate" name='clock.rate' spec="RealScalarParam" domain="PositiveReal" value="8.8579E-4"/>
 			</branchRateModel>
 		</distribution>
     </distribution>
 
     <run spec="MCMC" id="mcmc" chainLength="5000000">
         <state>
-			<parameter name='stateNode' id="skyline.popSize" dimension="5" value="380.0" lower="0.0" upper="38000.0"/>
-			<stateNode spec='parameter.IntegerParameter' id='skyline.groupSize' dimension="5" value="0"/>
+            <stateNode id="skyline.popSize" spec='beast.base.spec.inference.parameter.RealVectorParam'
+                       domain="PositiveReal" dimension="5" value="380.0"/>
+            <!--  Note: for group size of BSP, need to set domain="PositiveInt" -->
+            <stateNode id='skyline.groupSize' spec='beast.base.spec.inference.parameter.IntSimplexParam'
+                       domain="PositiveInt" dimension="5" value="1"/>
             <stateNode idref="hky.kappa"/>
             <stateNode idref="tree"/>
             <stateNode idref="clock.rate"/>
@@ -152,20 +150,24 @@
         </state>
 
         <distribution idref="posterior"/>
-        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="1" parameter="@hky.kappa"/>
-        <operator id='clockRateScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@clock.rate"/>
-        <operator id='shapeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="1" parameter="@siteModel.alpha"/>
-        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree"/>
-        <operator spec='Uniform' weight="30" tree="@tree"/>
+        <operator id='kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.75" weight="1" parameter="@hky.kappa"/>
+        <operator id='clockRateScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.75" weight="3" parameter="@clock.rate"/>
+        <operator id='shapeScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.75" weight="1" parameter="@siteModel.alpha"/>
+
+<!--        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree"/>-->
+        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator'
+                  scaleFactor="0.75" weight="3" tree="@tree"/>
+        <operator spec='beast.base.evolution.operator.Uniform' weight="30" tree="@tree"/>
         <operator spec='SubtreeSlide' weight="15" gaussian="true" tree="@tree"/>
         <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree"/>
         <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree"/>
         <operator spec='WilsonBalding' weight="3" tree="@tree"/>
-        <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" up="@clock.rate" down="@tree"/>
+        <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3"
+                  up="@clock.rate" down="@tree"/>
 
-        <operator id='popSizesScaler' spec='ScaleOperator' scaleFactor="0.75" weight="15" parameter="@skyline.popSize"/>
-        <operator id='groupSizesDelta' spec='DeltaExchangeOperator' delta="1" weight="6" integer="true"
-                  intparameter="@skyline.groupSize"/>
+        <operator id='popSizesScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.75" weight="15" parameter="@skyline.popSize"/>
+        <operator id='groupSizesDelta' spec='beast.base.spec.inference.operator.DeltaExchangeOperator'
+                  delta="1" weight="6" ivparameter="@skyline.groupSize"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
             <log idref="posterior"/>
@@ -195,3 +197,62 @@
     </run>
 </beast>
 
+<!--        posterior : -3865.9542466284047 +- 0.0961389601876614, ESS = 3492.604498800299, expectation is -3865.3635 +- 0.082236-->
+<!--        prior : -92.83210229903075 +- 0.08003083882360096, ESS = 3526.0536725304587, expectation is -92.178 +- 0.075174-->
+<!--        siteModel.alpha : 0.05497788953106609 +- 5.299331110248909E-4, ESS = 4359.688517553307, expectation is 0.054354 +- 5.2519E-4-->
+<!--        clock.rate : 9.458175044728434E-4 +- 2.0321064507817452E-6, ESS = 3931.1423167686116, expectation is 9.4858E-4 +- 1.9706E-6-->
+<!--        skyline.popSize.1 : 173.76402579265374 +- 29.860420930332154, ESS = 3790.3791104367774, expectation is 67.8827 +- 2.2639-->
+<!--        skyline.popSize.2 : 72.87159412926472 +- 30.305852200599514, ESS = 4293.640695139613, expectation is 25.4281 +- 0.3165-->
+<!--        skyline.popSize.3 : 39.87848820895047 +- 3.462081443420053, ESS = 4260.583420175925, expectation is 31.9271 +- 0.3819-->
+<!--        skyline.popSize.4 : 37.32718252996777 +- 0.4472310626854941, ESS = 4097.472800164088, expectation is 41.6596 +- 0.3976-->
+<!--        skyline.popSize.5 : 33.55786864929906 +- 0.550735781840017, ESS = 4057.284272072856, expectation is 33.5967 +- 0.3554-->
+<!--        skyline.groupSize.1 : 2.7127305043323706 +- 0.06306608837776836, ESS = 2398.929431240526, expectation is 2.4686 +- 0.040465-->
+<!--        skyline.groupSize.2 : 3.3061541879582315 +- 0.05994709875781661, ESS = 2772.55083764436, expectation is 3.3671 +- 0.039454-->
+<!--        skyline.groupSize.3 : 3.5143301488558096 +- 0.05338807957250786, ESS = 3592.6273024874827, expectation is 3.181 +- 0.033807-->
+<!--        skyline.groupSize.4 : 3.4534547878249278 +- 0.06293620983239555, ESS = 2705.219849449633, expectation is 3.723 +- 0.050187-->
+<!--        skyline.groupSize.5 : 3.01333037102866 +- 0.06597484934953088, ESS = 2423.979975652484, expectation is 3.2603 +- 0.059824-->
+<!--        hky.kappa : 21.61103060838405 +- 0.06324776408653743, ESS = 4501.000000000001, expectation is 21.6911 +- 0.052142-->
+<!--        likelihood : -3773.1221443293744 +- 0.05486169919391575, ESS = 3815.825171853874, expectation is -3773.1854 +- 0.039474-->
+<!--        skyline : -70.2720392679962 +- 0.055065315407511715, ESS = 3360.9793129247732, expectation is -69.725 +- 0.05435-->
+<!--        eml1 : -22.560063031034492 +- 0.052431171754551725, ESS = 2963.8139809178087, expectation is -22.453 +- 0.031115-->
+
+
+<!-- Uniform prior-->
+<!--        posterior : -3918.723673298291 +- 0.09293307120140108, ESS = 3737.03597399822, expectation is -3865.3635 +- 0.082236-->
+<!--        prior : -145.592239548388 +- 0.08139134407857418, ESS = 3330.253918111081, expectation is -92.178 +- 0.075174-->
+<!--        siteModel.alpha : 0.05575303704611519 +- 5.944657534632992E-4, ESS = 3362.732291389403, expectation is 0.054354 +- 5.2519E-4-->
+<!--        clock.rate : 9.47976581828431E-4 +- 2.1266182866295015E-6, ESS = 3444.6362179749535, expectation is 9.4858E-4 +- 1.9706E-6-->
+<!--        skyline.popSize.1 : 163.1044085425222 +- 22.593891532033254, ESS = 2321.735979191498, expectation is 67.8827 +- 2.2639-->
+<!--        skyline.popSize.2 : 50.939151229419615 +- 9.07633634051999, ESS = 1467.111240235273, expectation is 25.4281 +- 0.3165-->
+<!--        skyline.popSize.3 : 41.0104252266342 +- 4.718937661308659, ESS = 3855.6620005064383, expectation is 31.9271 +- 0.3819-->
+<!--        skyline.popSize.4 : 37.135462041283105 +- 0.4462350613992348, ESS = 3731.988309847787, expectation is 41.6596 +- 0.3976-->
+<!--        skyline.popSize.5 : 34.17745448837122 +- 0.5473854560669065, ESS = 4016.578695468486, expectation is 33.5967 +- 0.3554-->
+<!--        skyline.groupSize.1 : 2.4890024439013554 +- 0.0564806436428423, ESS = 2657.0167213248005, expectation is 2.4686 +- 0.040465-->
+<!--        skyline.groupSize.2 : 3.282159520106643 +- 0.05647092935103854, ESS = 3070.85720372171, expectation is 3.3671 +- 0.039454-->
+<!--        skyline.groupSize.3 : 3.4034658964674516 +- 0.05133295951550351, ESS = 3614.4717293796266, expectation is 3.181 +- 0.033807-->
+<!--        skyline.groupSize.4 : 3.597200622083981 +- 0.0636065492027155, ESS = 2714.9046234601724, expectation is 3.723 +- 0.050187-->
+<!--        skyline.groupSize.5 : 3.2281715174405687 +- 0.07138178790261579, ESS = 2225.0890477043995, expectation is 3.2603 +- 0.059824-->
+<!--        hky.kappa : 21.706993859867826 +- 0.06519983739530205, ESS = 4421.030218272883, expectation is 21.6911 +- 0.052142-->
+<!--        likelihood : -3773.131433749916 +- 0.05689918245086899, ESS = 3710.0809574936966, expectation is -3773.1854 +- 0.039474-->
+<!--        skyline : -70.1887676852798 +- 0.052847791629031235, ESS = 3547.545071612453, expectation is -69.725 +- 0.05435-->
+<!--        eml1 : -22.676764801144497 +- 0.05522848188228343, ESS = 2636.96968956787, expectation is -22.453 +- 0.031115-->
+
+
+<!--        posterior : -3917.9498143004666 +- 0.08565826258812939, ESS = 3915.6596753020604, expectation is -3865.3635 +- 0.082236-->
+<!--        prior : -144.92219722155576 +- 0.0716846034994167, ESS = 3702.4421228085616, expectation is -92.178 +- 0.075174-->
+<!--        siteModel.alpha : 0.05409879470678472 +- 5.083947725398481E-4, ESS = 4404.751737929933, expectation is 0.054354 +- 5.2519E-4-->
+<!--        clock.rate : 9.490971564476442E-4 +- 2.2088548142697736E-6, ESS = 3176.895074955792, expectation is 9.4858E-4 +- 1.9706E-6-->
+<!--        skyline.popSize.1 : 63.81156608863796 +- 1.6921469269889846, ESS = 4236.376838314304, expectation is 67.8827 +- 2.2639-->
+<!--        skyline.popSize.2 : 25.434787606102066 +- 0.3636549889452317, ESS = 3545.580404779142, expectation is 25.4281 +- 0.3165-->
+<!--        skyline.popSize.3 : 32.40195192030104 +- 0.3965431307420086, ESS = 3730.674552441753, expectation is 31.9271 +- 0.3819-->
+<!--        skyline.popSize.4 : 40.870729251940446 +- 0.406585858420294, ESS = 3810.877649501971, expectation is 41.6596 +- 0.3976-->
+<!--        skyline.popSize.5 : 33.87653529388686 +- 0.44469436767918263, ESS = 3962.1583904865975, expectation is 33.5967 +- 0.3554-->
+<!--        skyline.groupSize.1 : 2.512108420351033 +- 0.039466698140399714, ESS = 2797.7482686302988, expectation is 2.4686 +- 0.040465-->
+<!--        skyline.groupSize.2 : 3.374805598755832 +- 0.036870783125188336, ESS = 3467.728566706139, expectation is 3.3671 +- 0.039454-->
+<!--        skyline.groupSize.3 : 3.2448344812263943 +- 0.03324235155534377, ESS = 3958.7444794721573, expectation is 3.181 +- 0.033807-->
+<!--        skyline.groupSize.4 : 3.6665185514330147 +- 0.04135488020523446, ESS = 3399.502449281693, expectation is 3.723 +- 0.050187-->
+<!--        skyline.groupSize.5 : 3.201732948233726 +- 0.04660359139697981, ESS = 2798.2478556787314, expectation is 3.2603 +- 0.059824-->
+<!--        hky.kappa : 21.589261203122547 +- 0.06314340352206708, ESS = 4488.708350190953, expectation is 21.6911 +- 0.052142-->
+<!--        likelihood : -3773.0276170789084 +- 0.056627001899388164, ESS = 3782.5079405522606, expectation is -3773.1854 +- 0.039474-->
+<!--        skyline : -69.77661896471284 +- 0.052313445818236035, ESS = 3885.3498389520378, expectation is -69.725 +- 0.05435-->
+<!--        eml1 : -22.41887119487888 +- 0.032732487520717904, ESS = 3976.6606751683016, expectation is -22.453 +- 0.031115-->
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testBSPNoClock.xml b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testBSPNoClock.xml
index 94691f06..cb337366 100644
--- a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testBSPNoClock.xml
+++ b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testBSPNoClock.xml
@@ -1,6 +1,10 @@
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter'>
-
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
+       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
+       beast.base.evolution.operator:beast.base.spec.inference.operator:
+       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
+       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
+       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
 
     <!-- The sequence alignment (each sequence refers to a taxon above).         -->
     <!-- ntax=6 nchar=768                                                        -->
@@ -44,14 +48,16 @@
         <siteModel idref="siteModel"/>
     </input>
 
-    <input spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+    <input spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
         <taxa idref='alignment'/>
     </input>
 
-    <parameter id="hky.kappa" value="2.0" lower="0.0"/>
-    <parameter id="hky.frequencies" value="0.25" dimension="4" lower='0.0'/>
-    <parameter id="popSizes" dimension="3" value="380.0" lower="0.0" upper="38000.0"/>
-    <input name="groupSizes" spec='IntegerParameter' id='groupSizes' dimension="3" value="0" lower='0'/>
+    <parameter id="hky.kappa" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
+    <parameter id="hky.frequencies" dimension="4" value="0.25" spec="SimplexParam"/>
+    <parameter id="popSizes" dimension="3" value="380.0" spec="RealVectorParam" domain="PositiveReal"/>
+<!--  groupSizes 0 ?  -->
+    <parameter id="groupSizes" dimension="3" value="1"
+               spec='beast.base.spec.inference.parameter.IntSimplexParam' domain="PositiveInt"/>
 
     <run spec="MCMC" id="mcmc" chainLength="10000000"> <!--autoOptimize="true"-->
         <state>
@@ -64,42 +70,52 @@
 
         <distribution spec="CompoundDistribution" id="posterior">
             <distribution spec="CompoundDistribution" id="prior">
-                <distribution id="hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@hky.kappa">
-                    <distr id="LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false"
-                           spec="beast.base.inference.distribution.LogNormalDistributionModel"/>
+                <distribution id="hky.kappa.prior" spec="LogNormal" param="@hky.kappa">
+                    <M spec="RealScalarParam" domain="Real" value="1.0"/>
+                    <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>
                 </distribution>
-                <distribution id="hky.frequencies.prior" spec="beast.base.inference.distribution.Prior" x="@hky.frequencies">
-                    <distr id="Uniform" lower="0.0" upper="1.0" spec="beast.base.inference.distribution.Uniform"/>
+
+                <!-- frequencies prior -->
+                <distribution id="hky.frequencies.prior" spec="beast.base.spec.inference.distribution.IID"
+                              param="@hky.frequencies">
+                    <distr spec="beast.base.spec.inference.distribution.Uniform">
+                        <lower spec="RealScalarParam" domain="Real" value="0.0"/>
+                        <upper spec="RealScalarParam" domain="Real" value="1.0"/>
+                    </distr>
                 </distribution>
 
-                <distribution spec="BayesianSkyline" id='skyline'>
+                <!-- Bayesian Skyline -->
+                <distribution id="skyline" spec="beast.base.spec.evolution.tree.coalescent.BayesianSkyline">
                     <popSizes idref="popSizes"/>
-                    <groupSizes idref='groupSizes'/>
-                    <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
+                    <groupSizes idref="groupSizes"/>
+                    <treeIntervals spec="beast.base.evolution.tree.TreeIntervals">
                         <tree idref="tree"/>
                     </treeIntervals>
                 </distribution>
-
-                <distribution id='eml1' spec="beast.base.inference.distribution.MarkovChainDistribution"
-				jeffreys="true"
-				parameter="@popSizes"/>
+                <!-- Jeffrey’s prior on popSizes -->
+                <distribution id="eml1" spec="beast.base.spec.inference.distribution.MarkovChainDistribution"
+                              jeffreys="true" param="@popSizes"/>
             </distribution>
             <distribution id='likelihood' idref="treeLikelihood"/>
         </distribution>
 
-        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
-        <operator id='frequenciesDelta' spec='DeltaExchangeOperator' delta="0.01" weight="0.1"
-                  parameter="@hky.frequencies"/>
-        <operator id='popSizesScaler' spec='ScaleOperator' scaleFactor="0.75" weight="15" parameter="@popSizes"/>
-        <operator id='groupSizesDelta' spec='DeltaExchangeOperator' delta="1" weight="3" integer="true"
-                  intparameter="@groupSizes"/>
-        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree"/>
+        <operator id="kappaScaler" spec="beast.base.spec.inference.operator.ScaleOperator"
+                  scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
+        <operator id="frequenciesDelta" spec="beast.base.spec.inference.operator.DeltaExchangeOperator"
+                  delta="0.01" weight="0.1" rvparameter="@hky.frequencies"/>
+        <operator id="popSizesScaler" spec="beast.base.spec.inference.operator.ScaleOperator"
+                  scaleFactor="0.75" weight="15" parameter="@popSizes"/>
+        <operator id="groupSizesDelta" spec="beast.base.spec.inference.operator.DeltaExchangeOperator"
+                  delta="1" weight="3" ivparameter="@groupSizes"/>
+        <operator id="treeScaler" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"
+                  scaleFactor="0.75" weight="3" tree="@tree"/>
+
         <operator spec='Uniform' weight="30" tree="@tree"/>
         <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree"/>
         <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree"/>
         <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree"/>
         <operator spec='WilsonBalding' weight="1" tree="@tree"/>
-        <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
+        <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
             <model idref='posterior'/>
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testBirthDeathAsYule.xml b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testBirthDeathAsYule.xml
index 329c847d..974f8597 100644
--- a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testBirthDeathAsYule.xml
+++ b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testBirthDeathAsYule.xml
@@ -1,7 +1,12 @@
 <?xml version="1.0" standalone="yes"?>
 <!-- test Yule birth model and Birth Death model per Gernhard 2008-->
 <beast version='2.0'
-       namespace='beast.base.evolution.speciation:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
+       beast.evolution.nuc:beast.base.evolution.alignment:
+       beast.base.evolution.operator:beast.base.spec.inference.operator:
+       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
+       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
+       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
 
     <data id="alignment" dataType="nucleotide">
         <sequence taxon="tip1">A</sequence>
@@ -112,16 +117,16 @@
 
     <!-- A prior on the distribution node heights defined given                  -->
     <!-- a Yule speciation process (a pure birth process).                       -->
-    <input spec='BirthDeathGernhard08Model' id="birthDeath">
+    <input spec='beast.base.spec.evolution.speciation.BirthDeathGernhard08Model' id="birthDeath">
         <birthDiffRate idref="birthRate"/>
         <relativeDeathRate idref='relativeDeathRate'/>
         <sampleProbability idref="sampleProbability"/>
         <tree idref='tree'/>
     </input>
 
-    <parameter id="birthRate" value="1.0" lower="0.0" upper="1000000.0"/>
-    <parameter id='relativeDeathRate' value='0.0' lower="0.0" upper="1.0"/>
-    <parameter id="sampleProbability" value="1.0"/>
+    <parameter id="birthRate" value="1.0" spec="RealScalarParam" domain="PositiveReal"/>
+    <parameter id="relativeDeathRate" value="0.0" spec="RealScalarParam" domain="NonNegativeReal"/>
+    <parameter id="sampleProbability" value="1.0" spec="RealScalarParam" domain="UnitInterval"/>
 
     <run spec='MCMC' chainLength="1000000">
         <state>
@@ -131,12 +136,11 @@
 
         <distribution spec="CompoundDistribution" id="posterior">
             <distribution id="birthDeath.prior" idref='birthDeath'/>
-            <distribution id="birthRate.prior" spec="beast.base.inference.distribution.Prior" x="@birthRate">
-                <distr id="OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX"/>
-            </distribution>
+            <distribution id="birthRate.prior" spec="beast.base.spec.beast2vs1.OneOnX" param="@birthRate"/>
         </distribution>
 
-        <operator id='birthScaler' spec='ScaleOperator' scaleFactor="0.75" weight="1" parameter="@birthRate"/>
+        <operator id='birthScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
+                  scaleFactor="0.75" weight="1" parameter="@birthRate"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
             <model idref='posterior'/>
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testBirthDeathModel_10taxa.xml b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testBirthDeathModel_10taxa.xml
index 0d1376f3..65ae16e3 100644
--- a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testBirthDeathModel_10taxa.xml
+++ b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testBirthDeathModel_10taxa.xml
@@ -1,7 +1,12 @@
 <?xml version="1.0" standalone="yes"?>
 <!-- test Yule birth model and Birth Death model per Gernhard 2008-->
 <beast version='2.0'
-       namespace='beast.base.evolution.speciation:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
+       beast.evolution.nuc:beast.base.evolution.alignment:
+       beast.base.evolution.operator:beast.base.spec.inference.operator:
+       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
+       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
+       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
 
     <data id="alignment" dataType="nucleotide">
         <sequence taxon="A">A</sequence>
@@ -16,20 +21,20 @@
         <sequence taxon="J">A</sequence>
     </data>
 
-    <input spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+    <input spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
         <taxa idref='alignment'/>
     </input>
 
     <!-- A prior on the distribution node heights defined given                  -->
     <!-- a Yule speciation process (a pure birth process).                       -->
-    <input spec='BirthDeathGernhard08Model' id="birthDeath">
+    <input spec='beast.base.spec.evolution.speciation.BirthDeathGernhard08Model' id="birthDeath">
         <birthDiffRate idref="birthRate"/>
         <relativeDeathRate idref='relativeDeathRate'/>
         <tree idref='tree'/>
     </input>
 
-    <parameter id="birthRate" value="2.0" lower="0.0" upper="1000000.0"/>
-    <parameter id='relativeDeathRate' value='0.5' lower="0.0" upper="100.0"/>
+    <parameter id="birthRate" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
+    <parameter id="relativeDeathRate" value="0.5" spec="RealScalarParam" domain="PositiveReal"/>
 
     <run spec='MCMC' chainLength="2000000">
         <state>
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testCalibration.xml b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testCalibration.xml
index f1505d82..ad037d6c 100644
--- a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testCalibration.xml
+++ b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testCalibration.xml
@@ -1,8 +1,12 @@
 <beast version='2.0'
-       namespace='beast.base.evolution.alignment:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
+       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
+       beast.base.evolution.operator:beast.base.spec.inference.operator:
+       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
+       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
+       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
 
-
-    <!-- The sequence alignment                                                  -->
+<!-- The sequence alignment                                                  -->
     <!-- ntax=6 nchar=768                                                        -->
     <!-- npatterns=69                                                            -->
     <data id="alignment" dataType="nucleotide">
@@ -26,45 +30,56 @@
         </sequence>
     </data>
 
+    <parameter id="hky.kappa" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
+    <parameter dimension="4" id="hky.frequencies" spec="SimplexParam" value="0.25"/>
+    <parameter id="popSize" value="17" spec="RealScalarParam" domain="PositiveReal"/>
 
     <run spec="MCMC" id="mcmc" chainLength="10000000"> <!--autoOptimize="true"-->
-        <init spec='beast.base.evolution.tree.coalescent.RandomTree' id='randomTree' initial='@tree' taxa='@alignment'>
-            <populationModel spec='ConstantPopulation' popSize='@popSize'/>
+        <init spec='beast.base.spec.evolution.tree.coalescent.RandomTree' id='randomTree' initial='@tree' taxa='@alignment'>
+            <populationModel spec='beast.base.spec.evolution.tree.coalescent.ConstantPopulation' popSize='@popSize'/>
         </init>
 
         <state>
-            <stateNode spec='parameter.RealParameter' id="hky.kappa" value="2.0" lower="0.0"/>
-            <stateNode spec='parameter.RealParameter' id="hky.frequencies" value="0.25" dimension="4" lower='0.0'/>
-            <stateNode spec='parameter.RealParameter' id="popSize" value="17" lower="0.0"/>
+            <stateNode idref='hky.kappa'/>
+            <stateNode idref='hky.frequencies'/>
+            <stateNode idref='popSize'/>
             <stateNode spec='beast.base.evolution.tree.Tree' id='tree'/>
         </state>
 
         <distribution spec='CompoundDistribution' id='posterior'>
             <distribution spec='CompoundDistribution' id='prior'>
-                <distribution id="hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@hky.kappa">
-                    <distr id="LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false"
-                                  spec="beast.base.inference.distribution.LogNormalDistributionModel"/>
-                </distribution>
-                <distribution id="hky.frequencies.prior" spec="beast.base.inference.distribution.Prior" x="@hky.frequencies">
-                    <distr id="Uniform" lower="0.0" upper="1.0" spec="beast.base.inference.distribution.Uniform"/>
+                <distribution id="hky.kappa.prior" spec='LogNormal' param='@hky.kappa' >
+                    <!-- M="1" S="1.25" />-->
+                    <M spec="RealScalarParam" domain="Real" value="1.0"/>
+                    <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>
                 </distribution>
-                <distribution id="popSize.prior" spec="beast.base.inference.distribution.Prior" x="@popSize">
-                    <distr id="OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX"/>
+                <distribution id="hky.frequencies.prior" spec="beast.base.spec.inference.distribution.IID"
+                              param="@hky.frequencies">
+                    <distr id="Uniform" spec="beast.base.spec.inference.distribution.Uniform">
+                        <lower id="freqs.lower" spec="RealScalarParam" domain="Real" value="0.0"/>
+                        <upper id="freqs.upper" spec="RealScalarParam" domain="Real" value="1.0"/>
+                    </distr>
                 </distribution>
+                <!-- OneOnX is deprecated, test only -->
+                <distribution id="popSize.prior" spec='beast.base.spec.beast2vs1.OneOnX'
+                              param='@popSize' />
 
-                <distribution spec='beast.base.evolution.tree.MRCAPrior' tree='@tree' id='HumanChimpMRCA'>
+                <distribution spec='beast.base.spec.evolution.tree.MRCAPrior' tree='@tree' id='HumanChimpMRCA'>
                     <taxonset spec='TaxonSet' id='human,chimp'>
                         <taxon spec='Taxon' id='human'/>
                         <taxon spec='Taxon' id='chimp'/>
                     </taxonset>
-                    <distr spec='beast.base.inference.distribution.Normal' mean='6.0' sigma='0.5'/>
+                    <distr spec='beast.base.spec.inference.distribution.Normal'>
+                        <mean spec="RealScalarParam" domain="Real" value="6.0"/>
+                        <sigma spec="RealScalarParam" domain="PositiveReal" value="0.5"/>
+                    </distr>
                 </distribution>
 
                 <distribution id="coalescent" spec="Coalescent">
                     <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
                         <tree idref="tree"/>
                     </treeIntervals>
-                    <populationModel spec="ConstantPopulation" id='ConstantPopulation'>
+                    <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation" id='ConstantPopulation'>
                         <parameter name="popSize" idref="popSize"/>
                     </populationModel>
                 </distribution>
@@ -80,17 +95,20 @@
             </distribution>
         </distribution>
 
-        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
-        <operator id='frequenciesDelta' spec='DeltaExchangeOperator' delta="0.01" weight="0.1"
-                  parameter="@hky.frequencies"/>
-        <operator id='popSizeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize"/>
-        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree"/>
+        <operator id='kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
+                  scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
+        <operator id='frequenciesDelta' spec='beast.base.spec.inference.operator.DeltaExchangeOperator'
+                  delta="0.01" weight="0.1" rvparameter="@hky.frequencies"/>
+        <operator id='popSizeScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
+                  scaleFactor="0.75" weight="3" parameter="@popSize"/>
+        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator'
+                  scaleFactor="0.75" weight="3" tree="@tree"/>
         <operator spec='Uniform' weight="30" tree="@tree"/>
         <operator spec='SubtreeSlide' weight="15" gaussian="true" size="1.7" tree="@tree"/>
         <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree"/>
         <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree"/>
         <operator spec='WilsonBalding' weight="1" tree="@tree"/>
-        <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
+        <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
             <model idref='posterior'/>
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testCalibrationMono.xml b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testCalibrationMono.xml
index 62ecbc91..a33fc581 100644
--- a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testCalibrationMono.xml
+++ b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testCalibrationMono.xml
@@ -1,6 +1,10 @@
 <beast version='2.0'
-       namespace='beast.base.evolution.alignment:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
-
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
+       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
+       beast.base.evolution.operator:beast.base.spec.inference.operator:
+       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
+       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
+       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
 
     <!-- The sequence alignment                                                  -->
     <!-- ntax=6 nchar=768                                                        -->
@@ -26,36 +30,45 @@
         </sequence>
     </data>
 
+    <parameter id="hky.kappa" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
+    <parameter dimension="4" id="hky.frequencies" spec="SimplexParam" value="0.25"/>
+    <parameter id="popSize" value="17" spec="RealScalarParam" domain="PositiveReal"/>
 
     <run spec="MCMC" id="mcmc" chainLength="10000000"> <!--autoOptimize="true"-->
-        <init spec='beast.base.evolution.tree.coalescent.RandomTree' id='randomTree' initial='@tree' taxa='@alignment'>
-            <populationModel spec='ConstantPopulation' popSize='@popSize'/>
+        <init spec='beast.base.spec.evolution.tree.coalescent.RandomTree' id='randomTree' initial='@tree' taxa='@alignment'>
+            <populationModel spec='beast.base.spec.evolution.tree.coalescent.ConstantPopulation' popSize='@popSize'/>
         </init>
 
         <state>
-            <stateNode spec='parameter.RealParameter' id="hky.kappa" value="2.0" lower="0.0"/>
-            <stateNode spec='parameter.RealParameter' id="hky.frequencies" value="0.25" dimension="4" lower='0.0'/>
-            <stateNode spec='parameter.RealParameter' id="popSize" value="17" lower="0.0"/>
+            <stateNode idref='hky.kappa'/>
+            <stateNode idref='hky.frequencies'/>
+            <stateNode idref='popSize'/>
             <stateNode spec='beast.base.evolution.tree.Tree' id='tree'/>
         </state>
 
         <distribution spec='CompoundDistribution' id='posterior'>
             <distribution spec='CompoundDistribution' id='prior'>
-                <distribution id="hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@hky.kappa">
-                    <distr id="LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false"
-                                  spec="beast.base.inference.distribution.LogNormalDistributionModel"/>
-                </distribution>
-                <distribution id="hky.frequencies.prior" spec="beast.base.inference.distribution.Prior" x="@hky.frequencies">
-                    <distr id="Uniform" lower="0.0" upper="1.0" spec="beast.base.inference.distribution.Uniform"/>
+                <distribution id="hky.kappa.prior" spec='LogNormal' param='@hky.kappa' >
+                    <!-- M="1" S="1.25" />-->
+                    <M spec="RealScalarParam" domain="Real" value="1.0"/>
+                    <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>
                 </distribution>
-                <distribution id="popSize.prior" spec="beast.base.inference.distribution.Prior" x="@popSize">
-                    <distr id="OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX"/>
+                <distribution id="hky.frequencies.prior" spec="beast.base.spec.inference.distribution.IID"
+                              param="@hky.frequencies">
+                    <distr id="Uniform" spec="beast.base.spec.inference.distribution.Uniform">
+                        <lower id="freqs.lower" spec="RealScalarParam" domain="Real" value="0.0"/>
+                        <upper id="freqs.upper" spec="RealScalarParam" domain="Real" value="1.0"/>
+                    </distr>
                 </distribution>
+                <!-- OneOnX is deprecated, test only -->
+                <distribution id="popSize.prior" spec='beast.base.spec.beast2vs1.OneOnX'
+                              param='@popSize' />
 
-                <distribution spec='beast.base.evolution.tree.MRCAPrior' tree='@tree' id='mrcaPrior2' taxonset='@human,chimp' monophyletic='true'>
-                    <distr spec='beast.base.inference.distribution.Normal'>
-                        <parameter name='mean' value='6.0'/>
-                        <parameter name='sigma' value='0.5'/>
+                <distribution spec='beast.base.spec.evolution.tree.MRCAPrior' tree='@tree' id='mrcaPrior2'
+                              taxonset='@human,chimp' monophyletic='true'>
+                    <distr spec='beast.base.spec.inference.distribution.Normal'>
+                        <mean spec="RealScalarParam" domain="Real" value="6.0"/>
+                        <sigma spec="RealScalarParam" domain="PositiveReal" value="0.5"/>
                     </distr>
                 </distribution>
 
@@ -63,7 +76,7 @@
                     <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
                         <tree idref="tree"/>
                     </treeIntervals>
-                    <populationModel spec="ConstantPopulation" id='ConstantPopulation'>
+                    <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation" id='ConstantPopulation'>
                         <parameter name="popSize" idref="popSize"/>
                     </populationModel>
                 </distribution>
@@ -79,24 +92,27 @@
             </distribution>
         </distribution>
 
-        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
-        <operator id='frequenciesDelta' spec='DeltaExchangeOperator' delta="0.01" weight="0.1"
-                  parameter="@hky.frequencies"/>
-        <operator id='popSizeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize"/>
-        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree"/>
+        <operator id='kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
+                  scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
+        <operator id='frequenciesDelta' spec='beast.base.spec.inference.operator.DeltaExchangeOperator'
+                  delta="0.01" weight="0.1" rvparameter="@hky.frequencies"/>
+        <operator id='popSizeScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
+                  scaleFactor="0.75" weight="3" parameter="@popSize"/>
+        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator'
+                  scaleFactor="0.75" weight="3" tree="@tree"/>
         <operator spec='Uniform' weight="30" tree="@tree"/>
         <operator spec='SubtreeSlide' weight="15" gaussian="true" size="1.7" tree="@tree"/>
         <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree"/>
         <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree"/>
         <operator spec='WilsonBalding' weight="1" tree="@tree"/>
-        <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
+        <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
             <model idref='posterior'/>
             <log idref="posterior"/>
             <log idref="prior"/>
             <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree'/>
-            <log spec='beast.base.evolution.tree.MRCAPrior' tree='@tree' id='HumanChimpMRCA'>
+            <log spec='beast.base.spec.evolution.tree.MRCAPrior' tree='@tree' id='HumanChimpMRCA'>
                 <taxonset spec='TaxonSet' id='human,chimp'>
                     <taxon spec='Taxon' id='human'/>
                     <taxon spec='Taxon' id='chimp'/>
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testCoalescentNoClock.xml b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testCoalescentNoClock.xml
index 66ecccf3..39465000 100644
--- a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testCoalescentNoClock.xml
+++ b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testCoalescentNoClock.xml
@@ -1,5 +1,10 @@
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
+       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
+       beast.base.evolution.operator:beast.base.spec.inference.operator:
+       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
+       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
+       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
     <!-- equivalent to testCoalescentNoClock.xml in BEAST 1          -->
 
     <!-- The sequence alignment (each sequence refers to a taxon above).         -->
@@ -28,8 +33,8 @@
 
     <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
     <input spec='HKY' id="hky">
-        <parameter name='kappa' idref='hky.kappa'/>
-        <input id='freqs' name='frequencies' spec='Frequencies' frequencies='@hky.frequencies'/>
+        <kappa idref='hky.kappa'/>
+        <frequencies id='freqs' spec='Frequencies' frequencies='@hky.frequencies'/>
     </input>
 
     <!-- site model                                                              -->
@@ -44,14 +49,14 @@
         <siteModel idref="siteModel"/>
     </input>
 
-   <input spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+   <input spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
         <!--trait idref='rateCategories'/-->
         <taxa idref='alignment'/>
     </input>
 
-    <parameter id="hky.kappa" value="2.0" lower="0.0"/>
-    <parameter id="hky.frequencies" value="0.25" dimension="4"/>
-    <parameter id="popSize" value="0.077" lower="0.0"/>
+    <parameter id="hky.kappa" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
+    <parameter dimension="4" id="hky.frequencies" spec="SimplexParam" value="0.25"/>
+    <parameter id="popSize" value="0.077" spec="RealScalarParam" domain="PositiveReal"/>
 
     <run spec="MCMC" id="mcmc" chainLength="10000000"> <!--autoOptimize="true"-->
         <state>
@@ -63,40 +68,50 @@
 
         <distribution spec="CompoundDistribution" id="posterior">
             <distribution spec="CompoundDistribution" id="prior">
-                <distribution id="hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@hky.kappa">
-                    <distr id="LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false"
-                                  spec="beast.base.inference.distribution.LogNormalDistributionModel"/>
+                <distribution id="hky.kappa.prior" spec='LogNormal' param='@hky.kappa' >
+                    <!-- M="1" S="1.25" />-->
+                    <M spec="RealScalarParam" domain="Real" value="1.0"/>
+                    <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>
                 </distribution>
-                <distribution id="hky.frequencies.prior" spec="beast.base.inference.distribution.Prior" x="@hky.frequencies">
-                    <distr id="Uniform" lower="0.0" upper="1.0" spec="beast.base.inference.distribution.Uniform"/>
-                </distribution>
-                <distribution id="popSize.prior" spec="beast.base.inference.distribution.Prior" x="@popSize">
-                    <distr id="OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX"/>
+
+                <distribution id="hky.frequencies.prior" spec="beast.base.spec.inference.distribution.IID"
+                              param="@hky.frequencies">
+                    <distr id="Uniform" spec="beast.base.spec.inference.distribution.Uniform">
+                        <lower id="freqs.lower" spec="RealScalarParam" domain="Real" value="0.0"/>
+                        <upper id="freqs.upper" spec="RealScalarParam" domain="Real" value="1.0"/>
+                    </distr>
                 </distribution>
 
+                <!-- OneOnX is deprecated, test only -->
+                <distribution id="popSize.prior" spec='beast.base.spec.beast2vs1.OneOnX'
+                              param='@popSize' />
+
                 <distribution id="coalescent" spec="Coalescent">
                     <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
                         <tree idref="tree"/>
                     </treeIntervals>
-                    <populationModel spec="ConstantPopulation" id='ConstantPopulation'>
-                        <parameter name="popSize" idref="popSize"/>
+                    <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation" id='ConstantPopulation'>
+                        <popSize idref="popSize"/>
                     </populationModel>
                 </distribution>
             </distribution>
             <distribution id='likelihood' idref="treeLikelihood"/>
         </distribution>
 
-        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
-        <operator id='frequenciesDelta' spec='DeltaExchangeOperator' delta="0.01" weight="0.1"
-                  parameter="@hky.frequencies"/>
-        <operator id='popSizeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize"/>
-        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree"/>
+        <operator id='kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
+                  scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
+        <operator id='frequenciesDelta' spec='beast.base.spec.inference.operator.DeltaExchangeOperator'
+                  delta="0.01" weight="0.1" rvparameter="@hky.frequencies"/>
+        <operator id='popSizeScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
+                  scaleFactor="0.75" weight="3" parameter="@popSize"/>
+        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator'
+                  scaleFactor="0.75" weight="3" tree="@tree"/>
         <operator spec='Uniform' weight="30" tree="@tree"/>
         <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree"/>
         <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree"/>
         <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree"/>
         <operator spec='WilsonBalding' weight="1" tree="@tree"/>
-        <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
+        <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
             <model idref='posterior'/>
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testCoalescentNoClock1.xml b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testCoalescentNoClock1.xml
index 48954761..5974a9b9 100644
--- a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testCoalescentNoClock1.xml
+++ b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testCoalescentNoClock1.xml
@@ -1,6 +1,11 @@
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
-    <!-- equivalent to testCoalescentNoClock1.xml in BEAST 1          -->
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
+       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
+       beast.base.evolution.operator:beast.base.spec.inference.operator:
+       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
+       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
+       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
+    <!-- equivalent to testCoalescentNoClock1.xml in BEAST 1 -->
 
     <!-- The sequence alignment (each sequence refers to a taxon above).         -->
     <!-- ntax=6 nchar=768                                                        -->
@@ -52,10 +57,10 @@
           taxa='@alignment'/>
 
 
-    <parameter id="hky.kappa" value="2.0" lower="0.0"/>
-    <parameter id="hky.frequencies" value="0.25" dimension="4"/>
-    <parameter id="popSize" value="0.077" lower="0.0"/>
-
+    <!-- Parameters -->
+    <parameter id="hky.kappa" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
+    <parameter id="hky.frequencies" dimension="4" value="0.25" spec="SimplexParam"/>
+    <parameter id="popSize" value="0.077" spec="RealScalarParam" domain="PositiveReal"/>
 
     <run spec="MCMC" id="mcmc" chainLength="20000000"> <!--autoOptimize="true"-->
         <state>
@@ -70,25 +75,28 @@
                 <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
                     <tree idref="tree"/>
                 </treeIntervals>
-                <populationModel spec="ConstantPopulation" id='ConstantPopulation'>
+                <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation" id='ConstantPopulation'>
                     <popSize idref="popSize"/>
                 </populationModel>
             </distribution>
             <distribution id='likelihood' idref="treeLikelihood"/>
         </distribution>
 
-        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
-        <operator id='frequenciesDelta' spec='DeltaExchangeOperator' delta="0.01" weight="0.1"
-                  parameter="@hky.frequencies"/>
-        <operator id='popSizeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize"/>
-        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree"/>
+        <operator id='kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
+                  scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
+        <operator id='frequenciesDelta' spec='beast.base.spec.inference.operator.DeltaExchangeOperator'
+                  delta="0.01" weight="0.1" rvparameter="@hky.frequencies"/>
+        <operator id='popSizeScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
+                  scaleFactor="0.75" weight="3" parameter="@popSize"/>
+        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator'
+                  scaleFactor="0.75" weight="3" tree="@tree"/>
+
         <operator spec='Uniform' weight="30" tree="@tree"/>
         <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree"/>
         <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree"/>
         <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree"/>
         <operator spec='WilsonBalding' weight="1" tree="@tree"/>
 
-
         <logger logEvery="1000" fileName="test.$(seed).log">
             <model idref='posterior'/>
             <log idref="posterior"/>
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testCoalescentTipDates.xml b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testCoalescentTipDates.xml
index d4a01f57..08f4e4b9 100644
--- a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testCoalescentTipDates.xml
+++ b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testCoalescentTipDates.xml
@@ -1,5 +1,10 @@
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
+       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
+       beast.base.evolution.operator:beast.base.spec.inference.operator:
+       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
+       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
+       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
 
     <data id="alignment" dataType="nucleotide">
         <sequence taxon="A">
@@ -16,7 +21,7 @@
         </sequence>
     </data>
 
-   <tree spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+   <tree spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
         <trait spec='beast.base.evolution.tree.TraitSet' traitname='date-forward' units='day'
                value='
 		A  = 5000,
@@ -28,7 +33,7 @@
         <taxa idref='alignment'/>
     </tree>
 
-    <parameter id="popSize" value="10000" lower="0.0"/>
+    <parameter id="popSize" value="10000" spec="RealScalarParam" domain="PositiveReal"/>
 
     <run spec="MCMC" id="mcmc" chainLength="1000000"> <!--autoOptimize="true"-->
         <state>
@@ -40,7 +45,7 @@
                 <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
                      <tree idref="tree"/>
                 </treeIntervals>
-                <populationModel spec="ConstantPopulation" id='ConstantPopulation'>
+                <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation" id='ConstantPopulation'>
                     <popSize idref="popSize"/>
                 </populationModel>
             </distribution>
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testCoalescentTipDates1.xml b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testCoalescentTipDates1.xml
index 437d0dc2..71a7b7c6 100644
--- a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testCoalescentTipDates1.xml
+++ b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testCoalescentTipDates1.xml
@@ -1,5 +1,10 @@
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
+       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
+       beast.base.evolution.operator:beast.base.spec.inference.operator:
+       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
+       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
+       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
 
     <data id="alignment" dataType="nucleotide">
         <sequence taxon="A">
@@ -16,7 +21,7 @@
         </sequence>
     </data>
 
-   <tree spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+   <tree spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
         <trait spec='beast.base.evolution.tree.TraitSet' traitname='date-forward' units='day'
                value='
 		A  = 0,
@@ -28,7 +33,7 @@
 		<taxa idref='alignment'/>
     </tree>
 
-    <parameter id="popSize" value="10000" lower="0.0"/>
+    <parameter id="popSize" value="10000" spec="RealScalarParam" domain="PositiveReal"/>
 
     <run spec="MCMC" id="mcmc" chainLength="1000000"> <!--autoOptimize="true"-->
         <state>
@@ -40,7 +45,7 @@
                 <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
                      <tree idref="tree"/>
                 </treeIntervals>
-                <populationModel spec="ConstantPopulation" id='ConstantPopulation'>
+                <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation" id='ConstantPopulation'>
                     <popSize idref="popSize"/>
                 </populationModel>
             </distribution>
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testCoalescentTipDatesSampling.xml b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testCoalescentTipDatesSampling.xml
index eb346874..ca707c76 100644
--- a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testCoalescentTipDatesSampling.xml
+++ b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testCoalescentTipDatesSampling.xml
@@ -1,5 +1,10 @@
 <beast version='2.0'
-       namespace='beast.base.math:beast.base.evolution.alignment:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
+       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
+       beast.base.evolution.operator:beast.base.spec.inference.operator:
+       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
+       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
+       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
 
     <data id="alignment" dataType="nucleotide">
         <sequence taxon="A">
@@ -16,19 +21,19 @@
         </sequence>
     </data>
 
-   <tree spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+   <tree spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
         <trait spec='beast.base.evolution.tree.TraitSet' traitname='date-backward' units='day'
                value='
 		A  = 5000,
 		B  = 5000,
 		C  = 5000,
-		D  = 5000'>
+		D  = 19999'>
 			<taxa spec='beast.base.evolution.alignment.TaxonSet' alignment='@alignment'/>
         </trait>
 		<taxa idref='alignment'/>
     </tree>
 
-    <parameter id="popSize" value="1000000" lower="0.0"/>
+    <parameter id="popSize" value="10000" spec="RealScalarParam" domain="PositiveReal"/>
 
     <run spec="MCMC" id="mcmc" chainLength="10000000"> <!--autoOptimize="true"-->
         <state>
@@ -40,28 +45,37 @@
                 <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
                      <tree idref="tree"/>
                 </treeIntervals>
-                <populationModel spec="ConstantPopulation" id='ConstantPopulation'>
+                <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation" id='ConstantPopulation'>
                     <popSize idref="popSize"/>
                 </populationModel>
             </distribution>
 
-            <distribution id="tipDateA" monophyletic="false" spec="beast.base.evolution.tree.MRCAPrior" tipsonly="true" tree="@tree">
+            <distribution id="tipDateA" monophyletic="false" spec="beast.base.spec.evolution.tree.MRCAPrior" tipsonly="true" tree="@tree">
                 <taxonset id="TaxonSetA" spec="TaxonSet">
                     <taxon id="A" spec="Taxon"/>
                 </taxonset>
-                <distr id="Uniform0" lower="4999" offset="0.0" spec="distribution.Uniform" upper="5001"/>
+                <distr id="Uniform0" spec="beast.base.spec.inference.distribution.Uniform">
+                    <lower id="Uniform0.lower" spec="RealScalarParam" domain="Real" value="4999"/>
+                    <upper id="Uniform0.upper" spec="RealScalarParam" domain="Real" value="5001"/>
+                </distr>
             </distribution>
 
-            <distribution id="tipDateB" monophyletic="false" spec="beast.base.evolution.tree.MRCAPrior" tipsonly="true" tree="@tree">
+            <distribution id="tipDateB" monophyletic="false" spec="beast.base.spec.evolution.tree.MRCAPrior" tipsonly="true" tree="@tree">
                 <taxonset id="TaxonSetB" spec="TaxonSet">
                     <taxon id="B" spec="Taxon"/>
                 </taxonset>
-                <distr id="Noraml0" offset="0.0" spec="distribution.Normal" mean="5000" sigma="1"/>
+                <distr id="Normal0" spec="beast.base.spec.inference.distribution.Normal">
+                    <mean id="Normal0.mean" spec="RealScalarParam" domain="Real" value="5000"/>
+                    <sigma id="Normal0.sigma" spec="RealScalarParam" domain="PositiveReal" value="1"/>
+                </distr>
             </distribution>
 
-            <distribution id="rootHeight" monophyletic="false" spec="beast.base.evolution.tree.MRCAPrior" tipsonly="false" tree="@tree">
+            <distribution id="rootHeight" monophyletic="false" spec="beast.base.spec.evolution.tree.MRCAPrior" tipsonly="false" tree="@tree">
                 <taxonset id="TaxonSetAll" spec="TaxonSet" alignment="@alignment"/>
-                <distr id="Noraml1" offset="0.0" spec="distribution.Normal" mean="20000" sigma="1"/>
+                <distr id="Normal1" spec="beast.base.spec.inference.distribution.Normal">
+                    <mean id="Normal1.mean" spec="RealScalarParam" domain="Real" value="20000"/>
+                    <sigma id="Normal1.sigma" spec="RealScalarParam" domain="PositiveReal" value="1"/>
+                </distr>
             </distribution>
 
             <!--<distribution id="tipDateD" monophyletic="false" spec="beast.base.evolution.tree.MRCAPrior" tipsonly="true" tree="@tree">-->
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testEBSP.xml b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testEBSP.xml
index c9174c98..878208ba 100644
--- a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testEBSP.xml
+++ b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testEBSP.xml
@@ -1,7 +1,11 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<beast namespace="beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood:beast.base.inference.parameter:beast.base.inference.distribution"
-       version="2.0">
-
+<beast version='2.0'
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
+       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
+       beast.base.evolution.operator:beast.base.spec.inference.operator:
+       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
+       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
+       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
 
     <data dataType="nucleotide" id="alignment.26" name="taxa">
         <sequence id="seq_Orthogeomys_heterodus" taxon="Orthogeomys_heterodus" totalcount="4"
@@ -175,20 +179,20 @@
         <!-- site model                                                              -->
         <input spec='SiteModel' id="siteModel$(n)" substModel='@hky$(n)'/>
 
-        <tree spec='beast.base.evolution.tree.ClusterTree' id='tree$(n)' clusterType='upgma' taxa='@alignment$(n)'/>
+        <tree spec='beast.base.spec.evolution.tree.ClusterTree' id='tree$(n)' clusterType='upgma' taxa='@alignment$(n)'/>
 
         <input spec='TreeLikelihood' id="treeLikelihood$(n)"
                data="@alignment$(n)"
                tree="@tree$(n)"
                siteModel="@siteModel$(n)"/>
 
-        <parameter id="hky.kappa$(n)" value="2.0" lower="0.0"/>
-        <parameter id="hky.frequencies$(n)" value="0.25" dimension="4"/>
+        <parameter id="hky.kappa$(n)" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
+        <parameter id="hky.frequencies$(n)" value="0.25" dimension="4" spec="SimplexParam"/>
     </plate>
 
-    <parameter id="popSizes" value="0.017" lower="0.0"/>
-    <input name="indicators" spec='BooleanParameter' id='indicators' value="false"/>
-    <parameter id="populationMean" value="0.017" lower="0.0"/>
+    <parameter id="popSizes" dimension="3" value="0.017" spec="RealVectorParam" domain="PositiveReal"/>
+    <parameter id='indicators' dimension="3" spec='BoolVectorParam' value="false"/>
+    <parameter id="populationMean" value="0.017" spec="RealScalarParam" domain="PositiveReal"/>
 
     <run spec="MCMC" id="mcmc" chainLength="10000000"> <!--autoOptimize="true"-->
         <state>
@@ -204,30 +208,36 @@
 
         <distribution id="posterior" spec="CompoundDistribution">
             <distribution id="prior" spec="CompoundDistribution">
-                <distribution spec="Prior" x="@populationMean">
-                    <distr offset="0.0" spec="OneOnX"/>
+                <!-- OneOnX is deprecated, test only -->
+                <distribution id="populationMean.prior" spec='beast.base.spec.beast2vs1.OneOnX'
+                              param='@populationMean' />
+                <!-- Prior on sum(indicators) -->
+                <distribution spec="beast.base.spec.inference.distribution.Poisson">
+                    <lambda estimate="true" spec="RealScalarParam" domain="PositiveReal" value="0.6931471805599453"/>
+                    <param id="indsSun" spec="beast.base.spec.inference.util.AsIntScalar" domain="NonNegativeInt" >
+                         <arg spec="beast.base.spec.evolution.IntSum" arg="@indicators" />
+                    </param>
                 </distribution>
-                <distribution spec="Prior">
-                    <x arg="@indicators" id="indsSun" spec="beast.base.evolution.Sum"/>
-                    <distr offset="0.0" spec="Poisson">
-                        <parameter dimension="1" estimate="true" lower="0.0" name="lambda" upper="0.0" value="0.6931471805599453"/>
+
+                <!-- Prior on popSizes -->
+                <distribution id="popPriorDist" spec="beast.base.spec.inference.distribution.IID"
+                              param="@popSizes">
+                    <distr id="popSizesExponential" spec="beast.base.spec.inference.distribution.Exponential">
+                        <mean idref="populationMean"/>
                     </distr>
                 </distribution>
-                <distribution id="populationMeanPrior" spec="Prior" x="@popSizes">
-                    <distr id="popPriorDist" mean="@populationMean" offset="0.0" spec="Exponential"/>
-                </distribution>
 
                 <distribution id="coalescent" spec="CompoundDistribution">
                     <distribution id="Coal.26" spec="Coalescent" treeIntervals="@TreeIntervals.26">
-                        <populationModel id="scaledDemo4" spec="beast.base.evolution.tree.coalescent.ScaledPopulationFunction">
+                        <populationModel id="scaledDemo4" spec="beast.base.spec.evolution.tree.coalescent.ScaledPopulationFunction">
                             <population id="demographic" populationIndicators="@indicators" populationSizes="@popSizes"
-                                        spec="beast.base.evolution.tree.coalescent.CompoundPopulationFunction" type="linear"
+                                        spec="beast.base.spec.evolution.tree.coalescent.CompoundPopulationFunction" type="linear"
                                         useIntervalsMiddle="false">
                                 <plate spec='Plate' var='n' range='.26,.29,.47'>
                                     <itree id="TreeIntervals$(n)" spec="beast.base.evolution.tree.TreeIntervals" tree="@tree$(n)"/>
                                 </plate>
                             </population>
-                            <parameter dimension="1" estimate="true" lower="0.0" name="factor" upper="0.0" value="3"/>
+                            <factor value="3" spec="RealScalarParam" domain="PositiveReal"/>
                         </populationModel>
                     </distribution>
 
@@ -236,11 +246,16 @@
                 </distribution>
 
                 <plate spec='Plate' var='n' range='.26,.29,.47'>
-                    <distribution spec="Prior" x="@hky.kappa$(n)">
-                        <distr M="1.0" S="1.25" meanInRealSpace="false" spec="LogNormalDistributionModel"/>
+                    <distribution spec="LogNormal" param="@hky.kappa$(n)">
+                        <M spec="RealScalarParam" domain="Real" value="1.0"/>
+                        <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>
                     </distribution>
-                    <distribution spec="Prior" x="@hky.frequencies$(n)">
-                        <distr lower="0.0" upper="1.0" spec="beast.base.inference.distribution.Uniform"/>
+                    <distribution spec="beast.base.spec.inference.distribution.IID"
+                                  param="@hky.frequencies$(n)">
+                        <distr spec="beast.base.spec.inference.distribution.Uniform">
+                            <lower spec="RealScalarParam" domain="Real" value="0.0"/>
+                            <upper spec="RealScalarParam" domain="Real" value="1.0"/>
+                        </distr>
                     </distribution>
                 </plate>
             </distribution>
@@ -252,14 +267,17 @@
             </distribution>
         </distribution>
 
+<!-- TODO check SampleOffValues -->
+        <operator spec="beast.base.spec.inference.operator.SampleOffValues"
+                  dist="@popSizesExponential" indicators="@indicators" values="@popSizes" weight="15.0"/>
 
-        <operator id="bitflip" parameter="@indicators" spec="BitFlipOperator" uniform="true" weight="30.0"/>
-        <operator dist="@popPriorDist" indicators="@indicators" spec="beast.base.evolution.tree.coalescent.SampleOffValues"
-                  values="@popSizes" weight="15.0"/>
+        <operator id="bitflip" parameter="@indicators" spec="beast.base.spec.inference.operator.BitFlipOperator"
+                  uniform="true" weight="30.0"/>
         <operator degreesOfFreedom="1" indicator="@indicators" parameter="@popSizes" scaleAll="false"
-                  scaleAllIndependently="false" scaleFactor="0.5" spec="ScaleOperator" weight="6.0"/>
-        <operator spec='ScaleOperator' scaleFactor="0.9" weight="3" parameter="@populationMean"/>
-        <operator scaleFactor="0.7" spec="UpDownOperator" weight="30.0">
+                  scaleAllIndependently="false" scaleFactor="0.5" spec="beast.base.spec.inference.operator.ScaleOperator" weight="6.0"/>
+        <operator spec='beast.base.spec.inference.operator.ScaleOperator'
+                  scaleFactor="0.9" weight="3" parameter="@populationMean"/>
+        <operator scaleFactor="0.7" spec="beast.base.spec.evolution.operator.UpDownOperator" weight="30.0">
             <down idref="popSizes"/>
             <down idref="populationMean"/>
             <plate spec='Plate' var='n' range='.26,.29,.47'>
@@ -268,15 +286,15 @@
         </operator>
 
         <plate spec='Plate' var='n' range='.26,.29,.47'>
-            <operator spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa$(n)"/>
-            <operator spec='DeltaExchangeOperator' delta="0.01" weight="0.1" parameter="@hky.frequencies$(n)"/>
-            <operator spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree$(n)"/>
+            <operator spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa$(n)"/>
+            <operator spec='beast.base.spec.inference.operator.DeltaExchangeOperator' delta="0.01" weight="0.1" parameter="@hky.frequencies$(n)"/>
+            <operator spec='beast.base.spec.evolution.operator.ScaleTreeOperator' scaleFactor="0.75" weight="3" tree="@tree$(n)"/>
             <operator spec='Uniform' weight="30" tree="@tree$(n)"/>
             <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree$(n)"/>
             <operator spec='Exchange' isNarrow='true' weight="15" tree="@tree$(n)"/>
             <operator spec='Exchange' isNarrow='false' weight="3" tree="@tree$(n)"/>
             <operator spec='WilsonBalding' weight="1" tree="@tree$(n)"/>
-            <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" down="@tree$(n)"/>
+            <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" down="@tree$(n)"/>
         </plate>
 
         <logger logEvery="100000" mode="autodetect">
@@ -284,7 +302,7 @@
             <log idref="prior"/>
             <log idref="likelihood"/>
             <log idref="populationMean"/>
-            <log spec="beast.base.evolution.Sum" arg="@indicators"/>
+            <log spec="beast.base.spec.evolution.Sum" arg="@indicators"/>
             <log idref="indicators"/>
             <plate spec='Plate' var='n' range='.26,.29,.47'>
                 <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree$(n)'/>
@@ -301,7 +319,7 @@
             <log idref="prior"/>
             <log idref="likelihood"/>
             <log idref="populationMean"/>
-            <log spec="beast.base.evolution.Sum" arg="@indicators"/>
+            <log spec="beast.base.spec.evolution.Sum" arg="@indicators"/>
             <log idref="indicators"/>
             <plate spec='Plate' var='n' range='.26,.29,.47'>
                 <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree$(n)'/>
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testExponentialGrowth.xml b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testExponentialGrowth.xml
index ff659be5..66136c9e 100644
--- a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testExponentialGrowth.xml
+++ b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testExponentialGrowth.xml
@@ -1,8 +1,12 @@
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
-
-
-    <!-- The sequence alignment (each sequence refers to a taxon above).         -->
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
+       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
+       beast.base.evolution.operator:beast.base.spec.inference.operator:
+       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
+       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
+       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
+
+<!-- The sequence alignment (each sequence refers to a taxon above).         -->
     <!-- ntax=6 nchar=768                                                        -->
     <!-- npatterns=69                                                            -->
     <data id="alignment" dataType="nucleotide">
@@ -45,15 +49,15 @@
     </input>
 
 
-    <input spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+    <input spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
         <taxa idref='alignment'/>
     </input>
 
-    <parameter id="hky.kappa" value="2.0" lower="0.0"/>
-    <parameter id="hky.frequencies" value="0.25" dimension="4" lower='0.0'/>
-    <parameter id="popSize" value="0.077" lower="0.0"/>
-    <parameter id="growthRate" value="7.7E-5"/>
-
+    <!-- Parameters -->
+    <parameter id="hky.kappa" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
+    <parameter id="hky.frequencies" dimension="4" value="0.25" spec="SimplexParam"/>
+    <parameter id="popSize" value="0.077" spec="RealScalarParam" domain="PositiveReal"/>
+    <parameter id="growthRate" value="7.7E-5" spec="RealScalarParam" domain="Real"/>
 
     <run spec="MCMC" id="mcmc" chainLength="10000000"> <!--autoOptimize="true"-->
         <state>
@@ -72,48 +76,63 @@
 
         <distribution spec="CompoundDistribution" id="posterior">
             <distribution spec="CompoundDistribution" id="prior">
-                <distribution id="hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@hky.kappa">
-                    <distr id="LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false"
-                                  spec="beast.base.inference.distribution.LogNormalDistributionModel"/>
+                <!-- kappa prior -->
+                <distribution id="hky.kappa.prior" spec="LogNormal" param="@hky.kappa">
+                    <M spec="RealScalarParam" domain="Real" value="1.0"/>
+                    <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>
                 </distribution>
-                <distribution id="hky.frequencies.prior" spec="beast.base.inference.distribution.Prior" x="@hky.frequencies">
-                    <distr id="Uniform" lower="0.0" upper="1.0" spec="beast.base.inference.distribution.Uniform"/>
-                </distribution>
-                <distribution id="popSize.prior" spec="beast.base.inference.distribution.Prior" x="@popSize">
-                    <distr id="OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX"/>
+
+                <!-- frequencies prior -->
+                <distribution id="hky.frequencies.prior" spec="beast.base.spec.inference.distribution.IID" param="@hky.frequencies">
+                    <distr spec="beast.base.spec.inference.distribution.Uniform">
+                        <lower spec="RealScalarParam" domain="Real" value="0.0"/>
+                        <upper spec="RealScalarParam" domain="Real" value="1.0"/>
+                    </distr>
                 </distribution>
 
-                <distribution id="growthRate.prior" spec="beast.base.inference.distribution.Prior" x="@growthRate">
-                    <distr id="LaplaceDistribution" mu="0.001" scale="119.61481002566472"
-                                  spec="beast.base.inference.distribution.LaplaceDistribution"/>
+                <!-- popSize prior -->
+                <distribution id="popSize.prior" spec="beast.base.spec.beast2vs1.OneOnX" param="@popSize"/>
+
+                <!-- growthRate prior -->
+                <distribution id="growthRate.prior" spec="beast.base.spec.inference.distribution.Laplace"
+                              param="@growthRate">
+                    <mu spec="RealScalarParam" domain="Real" value="0.001"/>
+                    <scale spec="RealScalarParam" domain="PositiveReal" value="119.61481002566472"/>
                 </distribution>
 
+                <!-- Coalescent -->
                 <distribution id="coalescent" spec="Coalescent">
-                    <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
+                    <treeIntervals spec="beast.base.evolution.tree.TreeIntervals">
                         <tree idref="tree"/>
                     </treeIntervals>
-                    <populationModel spec="ExponentialGrowth">
-                        <parameter name="popSize" idref="popSize"/>
-                        <parameter name="growthRate" idref="growthRate"/>
+                    <populationModel spec="beast.base.spec.evolution.tree.coalescent.ExponentialGrowth">
+                        <popSize idref="popSize"/>
+                        <growthRate idref="growthRate"/>
                     </populationModel>
                 </distribution>
+
             </distribution>
+
             <distribution id='likelihood' idref="treeLikelihood"/>
         </distribution>
 
-        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
-        <operator id='frequenciesDelta' spec='DeltaExchangeOperator' delta="0.01" weight="0.1"
-                  parameter="@hky.frequencies"/>
-        <operator id='popSizeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize"/>
-        <operator id='growthRateRandomWalk' spec='RealRandomWalkOperator' windowSize="1.0" weight="3"
-                  parameter="@growthRate"/>
-        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree"/>
+        <operator id='kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
+                  scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
+        <operator id='frequenciesDelta' spec='beast.base.spec.inference.operator.DeltaExchangeOperator'
+                  delta="0.01" weight="0.1" rvparameter="@hky.frequencies"/>
+        <operator id='popSizeScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
+                  scaleFactor="0.75" weight="3" parameter="@popSize"/>
+        <operator id='growthRateRandomWalk' spec='beast.base.spec.inference.operator.RealRandomWalkOperator'
+                  windowSize="1.0" weight="3" scalar="@growthRate"/>
+        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator'
+                  scaleFactor="0.75" weight="3" tree="@tree"/>
+
         <operator spec='Uniform' weight="30" tree="@tree"/>
         <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree"/>
         <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree"/>
         <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree"/>
         <operator spec='WilsonBalding' weight="1" tree="@tree"/>
-        <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
+        <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
             <model idref='posterior'/>
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testHKY.xml b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testHKY.xml
index 0461eabe..f3219c5e 100644
--- a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testHKY.xml
+++ b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testHKY.xml
@@ -1,5 +1,10 @@
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
+       beast.base.evolution.tree.coalescent:beast.evolution.nuc:
+       beast.base.evolution.operator:beast.base.spec.inference.operator:
+       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
+       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
+       beast.base.spec.evolution.likelihood'>
 
     <!-- same as testMCMC.xml in BEAST 1                                         -->
     <!-- The sequence alignment                                                  -->
@@ -26,6 +31,11 @@
         </sequence>
     </data>
 
+    <input id="hky.kappa" spec="RealScalarParam" domain="PositiveReal" value="1.0"/>
+<!--    <parameter id="hky.kappa" value="1.0" lower="0.0"/>-->
+
+<!--    <input id="freqs" spec="SimplexParam" dimension="4" value="0.25 0.25 0.25 0.25"/>-->
+
     <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
     <input spec='HKY' id='hky'>
         <kappa idref='hky.kappa'/>
@@ -45,9 +55,8 @@
         <siteModel idref="siteModel"/>
     </input>
 
-    <parameter id="hky.kappa" value="1.0" lower="0.0"/>
 
-    <tree spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+    <tree spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
         <taxa idref='alignment'/>
     </tree>
 
@@ -60,8 +69,8 @@
 
         <distribution id='likelihood' idref="treeLikelihood"/>
 
-        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" parameter="@hky.kappa"/>
-        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" tree="@tree"/>
+        <operator id='kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.5" weight="1" parameter="@hky.kappa"/>
+        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator' scaleFactor="0.5" weight="1" tree="@tree"/>
         <operator spec='Uniform' weight="10" tree="@tree"/>
         <operator spec='SubtreeSlide' weight="5" gaussian="true" size="1.0" tree="@tree"/>
         <operator id='narrow' spec='Exchange' isNarrow='true' weight="1" tree="@tree"/>
@@ -77,12 +86,12 @@
 <!--         <logger logEvery="1000" fileName="test.$(seed).trees">
             <log idref="tree"/>
         </logger>       -->
-        <logger logEvery="10000">
+        <logger logEvery="100000">
 	        <model idref='likelihood'/>
             <log idref="likelihood"/>
-    	    <ESS spec='ESS' name='log' arg="@likelihood"/>
+    	    <ESS spec='beast.base.spec.inference.util.ESS' name='log' arg="@likelihood"/>
             <log idref='hky.kappa'/>
-    	    <ESS spec='ESS' name='log' arg="@hky.kappa"/>
+    	    <ESS spec='beast.base.spec.inference.util.ESS' name='log' arg="@hky.kappa"/>
         </logger>
     </run>
 
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testMultiSubstModel.xml b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testMultiSubstModel.xml
index 12457576..71b3f9b7 100644
--- a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testMultiSubstModel.xml
+++ b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testMultiSubstModel.xml
@@ -1,4 +1,11 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?><beast namespace="beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.alignment:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood" version="2.0">
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<beast version='2.0'
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
+       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
+       beast.base.evolution.operator:beast.base.spec.inference.operator:
+       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
+       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
+       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
 
 
     <data dataType="nucleotide" filter="1-449" id="firsthalf" name="alignment" spec="FilteredAlignment" strip="false">
@@ -24,39 +31,42 @@
     <distribution id="posterior" spec="CompoundDistribution" useThreads="false">
         <distribution id="prior" spec="CompoundDistribution" useThreads="false">
             <distribution id="CoalescentConstant.firsthalf" spec="Coalescent">
-                <populationModel id="ConstantPopulation.firsthalf" spec="ConstantPopulation">
-                    <parameter dimension="1" estimate="true" id="popSize.firsthalf" name="popSize" value="1"/>
+                <populationModel id="ConstantPopulation.firsthalf" spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
+                    <popSize id="popSize.firsthalf" spec="RealScalarParam" domain="PositiveReal" value="1.0" estimate="true"/>
                 </populationModel>
                 <treeIntervals id="TreeIntervals.firsthalf" spec="beast.base.evolution.tree.TreeIntervals" tree="@Tree.firsthalf"/>
             </distribution>
-            <distribution id="KappaPrior.firsthalf" spec="beast.base.inference.distribution.Prior" x="@kappa.firsthalf">
-                    <distr id="LogNormalDistributionModel.firsthalf" M="1.0" S="1.25" meanInRealSpace="false" spec="beast.base.inference.distribution.LogNormalDistributionModel"/>
-                </distribution>
-            <distribution id="KappaPrior.secondhalf" spec="beast.base.inference.distribution.Prior" x="@kappa.secondhalf">
-                    <distr id="LogNormalDistributionModel.secondhalf" M="1.0" S="1.25" meanInRealSpace="false" spec="beast.base.inference.distribution.LogNormalDistributionModel"/>
-                </distribution>
-            <distribution id="popSize.prior" spec="beast.base.inference.distribution.Prior" x="@popSize.firsthalf">
-                    <distr id="OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX"/>
-                </distribution>
+            <distribution id="KappaPrior.firsthalf" spec='LogNormal' param='@kappa.firsthalf' >
+                <!-- M="1" S="1.25" />-->
+                <M spec="RealScalarParam" domain="Real" value="1.0"/>
+                <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>
+            </distribution>
+            <distribution id="KappaPrior.secondhalf" spec='LogNormal' param='@kappa.secondhalf' >
+                <M spec="RealScalarParam" domain="Real" value="1.0"/>
+                <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>
+            </distribution>
+<!-- OneOnX is deprecated, test only -->
+            <distribution id="popSize.prior" spec='beast.base.spec.beast2vs1.OneOnX'
+                          param='@popSize.firsthalf' />
         </distribution>
         <distribution id="likelihood" spec="CompoundDistribution" useThreads="false">
             <distribution data="@firsthalf" id="treeLikelihood.firsthalf" spec="TreeLikelihood" tree="@Tree.firsthalf" useAmbiguities="false">
                 <siteModel gammaCategoryCount="0" id="SiteModel.firsthalf" spec="SiteModel">
-                    <parameter dimension="1" estimate="false" id="mutationRate.firsthalf" name="mutationRate" value="1.0"/>
-                    <parameter dimension="1" estimate="false" id="gammaShape.firsthalf" name="shape" value="1.0"/>
-                    <parameter dimension="1" estimate="false" id="proportionInvariant.firsthalf" name="proportionInvariant" value="0.0"/>
+                    <parameter estimate="false" id="mutationRate.firsthalf" name="mutationRate" spec="RealScalarParam" domain="PositiveReal" value="1.0"/>
+                    <parameter estimate="false" id="gammaShape.firsthalf" name="shape" spec="RealScalarParam" domain="PositiveReal" value="1.0"/>
+                    <parameter estimate="false" id="proportionInvariant.firsthalf" name="proportionInvariant" spec="RealScalarParam" domain="UnitInterval" value="0.0"/>
                     <substModel id="hky.firsthalf" kappa="@kappa.firsthalf" spec="HKY">
                         <frequencies estimate="true" frequencies="@freqParameter.firsthalf" id="estimatedFreqs.firsthalf" spec="Frequencies"/>
                     </substModel>
                 </siteModel>
-                <branchRateModel clock.rate="@clockRate.firsthalf" id="StrictClock.firsthalf" spec="beast.base.evolution.branchratemodel.StrictClockModel"/>
+                <branchRateModel clock.rate="@clockRate.firsthalf" id="StrictClock.firsthalf" spec="beast.base.spec.evolution.branchratemodel.StrictClockModel"/>
             </distribution>
             <distribution branchRateModel="@StrictClock.firsthalf" id="treeLikelihood.secondhalf" spec="TreeLikelihood" tree="@Tree.firsthalf" useAmbiguities="false">
                 <data idref="secondhalf"/>
                 <siteModel gammaCategoryCount="0" id="SiteModel.secondhalf" spec="SiteModel">
-                    <parameter dimension="1" estimate="false" id="mutationRate.secondhalf" name="mutationRate" value="1.0"/>
-                    <parameter dimension="1" estimate="false" id="gammaShape.secondhalf" name="shape" value="1.0"/>
-                    <parameter dimension="1" estimate="false" id="proportionInvariant.secondhalf" name="proportionInvariant" value="0.0"/>
+                    <parameter estimate="false" id="mutationRate.secondhalf" name="mutationRate" spec="RealScalarParam" domain="PositiveReal" value="1.0"/>
+                    <parameter estimate="false" id="gammaShape.secondhalf" name="shape" spec="RealScalarParam" domain="PositiveReal" value="1.0"/>
+                    <parameter estimate="false" id="proportionInvariant.secondhalf" name="proportionInvariant" spec="RealScalarParam" domain="UnitInterval" value="0.0"/>
                     <substModel id="hky.secondhalf" kappa="@kappa.secondhalf" spec="HKY">
                         <frequencies estimate="true" frequencies="@freqParameter.secondhalf" id="estimatedFreqs.secondhalf" spec="Frequencies"/>
                     </substModel>
@@ -65,7 +75,7 @@
         </distribution>
     </distribution>
 
-<parameter dimension="1" id="clockRate.firsthalf" value="1.0"/>
+<parameter id="clockRate.firsthalf" spec="RealScalarParam" domain="PositiveReal" value="1.0"/>
     
 <run chainLength="10000000" id="mcmc" preBurnin="0" sampleFromPrior="false" spec="MCMC" storeEvery="-1">
     <state id="state" storeEvery="100000">
@@ -75,15 +85,17 @@
             </taxonset>
         </tree>
         <stateNode idref='popSize.firsthalf'/>
-        <parameter dimension="1" estimate="true" id="kappa.firsthalf" lower="0.0" name="stateNode" value="1.0"/>
-        <parameter dimension="4" estimate="true" id="freqParameter.firsthalf" lower="0.0" name="stateNode" upper="1.0" value="0.25"/>
-        <parameter dimension="1" estimate="true" id="kappa.secondhalf" lower="0.0" name="stateNode" value="1.0"/>
-        <parameter dimension="4" estimate="true" id="freqParameter.secondhalf" lower="0.0" name="stateNode" upper="1.0" value="0.25"/>
+        <parameter estimate="true" id="kappa.firsthalf" spec="RealScalarParam" domain="PositiveReal" name="stateNode" value="1.0"/>
+        <parameter dimension="4" estimate="true" id="freqParameter.firsthalf" spec="SimplexParam" name="stateNode" value="0.25"/>
+        <parameter estimate="true" id="kappa.secondhalf" spec="RealScalarParam" domain="PositiveReal" name="stateNode" value="1.0"/>
+        <parameter dimension="4" estimate="true" id="freqParameter.secondhalf" spec="SimplexParam" name="stateNode" value="0.25"/>
     </state>
 
     <distribution idref="posterior"/>
 
-    <operator degreesOfFreedom="1" id="treeScaler.firsthalf" optimise="true" rootOnly="false" scaleAll="false" scaleAllIndependently="false" scaleFactor="0.75" spec="ScaleOperator" tree="@Tree.firsthalf" weight="3.0"/>
+    <operator degreesOfFreedom="1" id="treeScaler.firsthalf" optimise="true" rootOnly="false"
+              scaleAll="false" scaleAllIndependently="false" scaleFactor="0.75"
+              spec="ScaleOperator" tree="@Tree.firsthalf" weight="3.0"/>
 
     <operator id="UniformOperator.firsthalf" spec="Uniform" tree="@Tree.firsthalf" weight="30.0"/>
 
@@ -95,21 +107,25 @@
 
     <operator id="WilsonBalding.firsthalf" spec="WilsonBalding" tree="@Tree.firsthalf" weight="3.0"/>
 
-    <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" down="@Tree.firsthalf"/>
+    <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" down="@Tree.firsthalf"/>
 
-    <operator degreesOfFreedom="1" id="KappaScaler.firsthalf" optimise="true" parameter="@kappa.firsthalf" rootOnly="false" scaleAll="false" scaleAllIndependently="false" scaleFactor="0.75" spec="ScaleOperator" weight="1.0"/>
+    <operator id="KappaScaler.firsthalf" parameter="@kappa.firsthalf" scaleFactor="0.75"
+              spec="beast.base.spec.inference.operator.ScaleOperator" weight="1.0"/>
 
-    <operator autoOptimize="true" delta="0.01" id="FrequenciesExchanger.firsthalf" integer="false" spec="DeltaExchangeOperator" weight="0.1">
+    <operator autoOptimize="true" delta="0.01" id="FrequenciesExchanger.firsthalf"
+              integer="false" spec="beast.base.spec.inference.operator.DeltaExchangeOperator" weight="0.1">
         <parameter idref="freqParameter.firsthalf"/>
     </operator>
 
-    <operator degreesOfFreedom="1" id="KappaScaler.secondhalf" optimise="true" parameter="@kappa.secondhalf" rootOnly="false" scaleAll="false" scaleAllIndependently="false" scaleFactor="0.75" spec="ScaleOperator" weight="1.0"/>
+    <operator id="KappaScaler.secondhalf" parameter="@kappa.secondhalf" scaleFactor="0.75"
+              spec="beast.base.spec.inference.operator.ScaleOperator" weight="1.0"/>
 
-    <operator autoOptimize="true" delta="0.01" id="FrequenciesExchanger.secondhalf" integer="false" spec="DeltaExchangeOperator" weight="0.1">
+    <operator autoOptimize="true" delta="0.01" id="FrequenciesExchanger.secondhalf"
+              integer="false" spec="beast.base.spec.inference.operator.DeltaExchangeOperator" weight="0.1">
         <parameter idref="freqParameter.secondhalf"/>
     </operator>
 
-    <operator id='popSizeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize.firsthalf"/>
+    <operator id='popSizeScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize.firsthalf"/>
 
     <logger fileName="test.$(seed).log" id="tracelog" logEvery="1000" mode="autodetect" model="@posterior">
         <distribution idref="posterior" name="log"/>
@@ -127,14 +143,14 @@
         <parameter idref="popSize.firsthalf" name="log"/>
     </logger>
 
-    <logger id="screenlog" logEvery="10000" mode="autodetect">
+    <logger id="screenlog" logEvery="100000" mode="autodetect">
         <distribution idref="posterior" name="log"/>
-        <log arg="@posterior" id="ESS.0" spec="util.ESS"/>
+        <log arg="@posterior" id="ESS.0" spec="beast.base.spec.inference.util.ESS"/>
         <distribution idref="likelihood" name="log"/>
         <distribution idref="prior" name="log"/>
     </logger>
 
-    <tree estimate="false" id="RandomTree.firsthalf" initial="@Tree.firsthalf" name="init" populationModel="@ConstantPopulation.firsthalf" spec="beast.base.evolution.tree.coalescent.RandomTree" taxa="@firsthalf"/>
+    <tree estimate="false" id="RandomTree.firsthalf" initial="@Tree.firsthalf" name="init" populationModel="@ConstantPopulation.firsthalf" spec="beast.base.spec.evolution.tree.coalescent.RandomTree" taxa="@firsthalf"/>
 
 </run>
 
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testRandomLocalClock.xml b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testRandomLocalClock.xml
index c084eff7..d455bde3 100644
--- a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testRandomLocalClock.xml
+++ b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testRandomLocalClock.xml
@@ -1,8 +1,12 @@
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
+       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
+       beast.base.evolution.operator:beast.base.spec.inference.operator:
+       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
+       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
+       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
 
-
-    <!-- The sequence alignment (each sequence refers to a taxon above).         -->
+<!-- The sequence alignment (each sequence refers to a taxon above).         -->
     <!-- ntax=6 nchar=768                                                        -->
     <!-- npatterns=69                                                            -->
     <data id="alignment" dataType="nucleotide">
@@ -28,7 +32,7 @@
 
     <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
     <input spec='HKY' id="hky">
-        <parameter name='kappa' idref='hky.kappa'/>
+        <kappa idref='hky.kappa'/>
         <input id='freqs' name='frequencies' spec='Frequencies' frequencies='@hky.frequencies'/>
     </input>
 
@@ -38,14 +42,14 @@
         <substModel idref='hky'/>
     </input>
 
-    <input spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+    <input spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
         <taxa idref='alignment'/>
     </input>
 
-    <input spec='RandomLocalClockModel' id="branchRates" ratesAreMultipliers="false">
+    <input spec='beast.base.spec.evolution.branchratemodel.RandomLocalClockModel' id="branchRates" ratesAreMultipliers="false">
         <!--<parameter name='mutationRate'>1.0</parameter>-->
-        <parameter name='rates' id='rates' value="1.0" lower='0.0'/>
-        <input name="indicators" spec='BooleanParameter' id='indicators' value="false"/>
+        <rates idref='rates'/>
+        <indicators idref='indicators'/>
         <tree idref="tree"/>
     </input>
 
@@ -56,9 +60,11 @@
         <branchRateModel idref="branchRates"/>
     </input>
 
-    <parameter id="hky.kappa" value="2.0" lower="0.0"/>
-    <parameter id="hky.frequencies" value="0.25" dimension="4" lower='0.0'/>
-    <parameter id="popSize" value="0.077" lower="0.0"/>
+    <parameter id="hky.kappa" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
+    <parameter dimension="4" id="hky.frequencies" spec="SimplexParam" value="0.25"/>
+    <parameter id="popSize" value="0.077" spec="RealScalarParam" domain="PositiveReal"/>
+    <parameter id="rates" value="1.0" spec="RealVectorParam" domain="PositiveReal"/>
+    <parameter id='indicators' spec='BoolVectorParam' value="false"/>
 
     <run spec="MCMC" id="mcmc" chainLength="10000000"> <!--autoOptimize="true"-->
         <state>
@@ -72,19 +78,31 @@
 
         <distribution spec="CompoundDistribution" id="posterior">
             <distribution spec="CompoundDistribution" id="prior">
-                <distribution id="hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@hky.kappa">
-                    <distr id="LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false"
-                                  spec="beast.base.inference.distribution.LogNormalDistributionModel"/>
-                </distribution>
-                <distribution id="hky.frequencies.prior" spec="beast.base.inference.distribution.Prior" x="@hky.frequencies">
-                    <distr id="Uniform" lower="0.0" upper="1.0" spec="beast.base.inference.distribution.Uniform"/>
+                <distribution id="hky.kappa.prior" spec='LogNormal' param='@hky.kappa' >
+                    <!-- M="1" S="1.25" />-->
+                    <M spec="RealScalarParam" domain="Real" value="1.0"/>
+                    <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>
                 </distribution>
-                <distribution id="popSize.prior" spec="beast.base.inference.distribution.Prior" x="@popSize">
-                    <distr id="OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX"/>
+                <distribution id="hky.frequencies.prior" spec="beast.base.spec.inference.distribution.IID"
+                              param="@hky.frequencies">
+                    <distr id="Uniform" spec="beast.base.spec.inference.distribution.Uniform">
+                        <lower id="freqs.lower" spec="RealScalarParam" domain="Real" value="0.0"/>
+                        <upper id="freqs.upper" spec="RealScalarParam" domain="Real" value="1.0"/>
+                    </distr>
                 </distribution>
-                <distribution id="rates.prior" spec="beast.base.inference.distribution.Prior" x="@rates">
-                    <distr id="Gamma" alpha="0.5" beta="2.0" spec="beast.base.inference.distribution.Gamma"/>
+                <!-- OneOnX is deprecated, test only -->
+                <distribution id="popSize.prior" spec='beast.base.spec.beast2vs1.OneOnX'
+                              param='@popSize' />
+
+                <distribution id="rates.prior" spec="beast.base.spec.inference.distribution.IID"
+                              param="@rates">
+                    <distr id="Gamma" spec="beast.base.spec.inference.distribution.Gamma">
+                        <alpha id="Gamma.alpha" spec="RealScalarParam" domain="PositiveReal" value="0.5"/>
+                        <!-- Shape–Scale -->
+                        <theta id="Gamma.theta" spec="RealScalarParam" domain="PositiveReal" value="2.0"/>
+                    </distr>
                 </distribution>
+
                 <!--<distribution id="indicators.prior" spec="beast.base.inference.distribution.Prior" x="@indicators">
                     <distribution id="Poisson" lambda="0.6931471805599453" spec="beast.base.inference.distribution.Poisson"/>
                 </distribution>-->
@@ -93,7 +111,7 @@
                     <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
                         <tree idref="tree"/>
                     </treeIntervals>
-                    <populationModel spec="ConstantPopulation" id='ConstantPopulation'>
+                    <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation" id='ConstantPopulation'>
                         <popSize idref="popSize"/>
                     </populationModel>
                 </distribution>
@@ -101,20 +119,25 @@
             <distribution id='likelihood' idref="treeLikelihood"/>
         </distribution>
 
-        <operator id="indicatorsBitFlip" spec="BitFlipOperator" weight="15" parameter="@indicators"/>
-        <operator id='rateScaler' spec='ScaleOperator' scaleFactor="0.75" weight="15" parameter="@rates"/>
+        <operator id="indicatorsBitFlip" spec="beast.base.spec.inference.operator.BitFlipOperator"
+                  weight="15" parameter="@indicators"/>
+        <operator id='rateScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
+                  scaleFactor="0.75" weight="15" parameter="@rates"/>
 
-        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
-        <operator id='frequenciesDelta' spec='DeltaExchangeOperator' delta="0.01" weight="0.1"
-                  parameter="@hky.frequencies"/>
-        <operator id='popSizeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize"/>
-        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree"/>
+        <operator id='kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
+                  scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
+        <operator id='frequenciesDelta' spec='beast.base.spec.inference.operator.DeltaExchangeOperator'
+                  delta="0.01" weight="0.1" rvparameter="@hky.frequencies"/>
+        <operator id='popSizeScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
+                  scaleFactor="0.75" weight="3" parameter="@popSize"/>
+        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator'
+                  scaleFactor="0.75" weight="3" tree="@tree"/>
         <operator spec='Uniform' weight="30" tree="@tree"/>
         <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree"/>
         <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree"/>
         <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree"/>
         <operator spec='WilsonBalding' weight="1" tree="@tree"/>
-        <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
+        <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
             <model idref='posterior'/>
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testSRD06CP12_3.xml b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testSRD06CP12_3.xml
index f0f7c97c..6d340685 100644
--- a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testSRD06CP12_3.xml
+++ b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testSRD06CP12_3.xml
@@ -1,171 +1,193 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<beast namespace="beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood:beast.base.evolution.branchratemodel"
-       version="2.0">
-    <!-- SRD06 model: split sequences in first together with seconds and thirds of all sites -->
-    <data id="alignment" dataType="nucleotide">
-        <sequence taxon="human">
-            AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCCTTATTTCTACTAGGACTATGAGAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTG-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCGGAGCTTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGGCCTCCATGACTTTTTCAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAATTATAGGCT-AAATCCTATATATCTTA-CACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACACCTCTTTACAGTGA
-        </sequence>
-        <sequence taxon="chimp">
-            AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTCAAATCCCCTTATTTCTACTAGGACTATAAGAATCGAACTCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTAAGCACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCTCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AACCCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCGACACCTCTTTACAGTGA
-        </sequence>
-        <sequence taxon="bonobo">
-            AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTTAAATCCCCTTATTTCTACTAGGACTATGAGAGTCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCTCTCAGTAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAGC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTTGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCCCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCAACACCTCTTTACAGTGA
-        </sequence>
-        <sequence taxon="gorilla">
-            AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGAGGTTTAAACCCCCTTATTTCTACTAGGACTATGAGAATTGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTGTCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTCACATCCTTCCCGTACTAAGAAATTTAGGTTAAACATAGACCAAGAGCCTTCAAAGCCCTTAGTAAGTTA-CAACACTTAATTTCTGTAAGGACTGCAAAACCCTACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCAATGGGACTCAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAT-TCACCTCGGAGCTTGGTAAAAAGAGGCCCAGCCTCTGTCTTTAGATTTACAGTCCAATGCCTTA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGACCTTCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAGGTTAAATTACGGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCGTTAACCTTTTAAGTTAAAGATTAAGAGTATCGGCACCTCTTTGCAGTGA
-        </sequence>
-        <sequence taxon="orangutan">
-            AGAAATATGTCTGACAAAAGAGTTACTTTGATAGAGTAAAAAATAGAGGTCTAAATCCCCTTATTTCTACTAGGACTATGGGAATTGAACCCACCCCTGAGAATCCAAAATTCTCCGTGCCACCCATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTA--CACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTCA-CAGCACTTAATTTCTGTAAGGACTGCAAAACCCCACTTTGCATCAACTGAGCGCAAATCAGCCACTTTAATTAAGCTAAGCCCTCCTAGACCGATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAT-TGGCTTCAGTCCAAAGCCCCGGCAGGCCTTAAAGCTGCTCCTTCGAATTTGCAATTCAACATGACAA-TCACCTCAGGGCTTGGTAAAAAGAGGTCTGACCCCTGTTCTTAGATTTACAGCCTAATGCCTTAACTCGGCCATTTTACCGCAAAAAAGGAAGGAATCGAACCTCCTAAAGCTGGTTTCAAGCCAACCCCATAACCCCCATGACTTTTTCAAAAGGTACTAGAAAAACCATTTCGTAACTTTGTCAAAGTTAAATTACAGGTC-AGACCCTGTGTATCTTA-CATTGCAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACCAGCCTCTCTTTGCAATGA
-        </sequence>
-        <sequence taxon="siamang">
-            AGAAATACGTCTGACGAAAGAGTTACTTTGATAGAGTAAATAACAGGGGTTTAAATCCCCTTATTTCTACTAGAACCATAGGAGTCGAACCCATCCTTGAGAATCCAAAACTCTCCGTGCCACCCGTCGCACCCTGTTCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCATACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTAACAAAACTTAATTTCTGCAAGGGCTGCAAAACCCTACTTTGCATCAACCGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCGATGGGACTTAAACCCATAAAAATTTAGTTAACAGCTAAACACCCTAAACAACCTGGCTTCAATCTAAAGCCCCGGCAGA-GTTGAAGCTGCTTCTTTGAACTTGCAATTCAACGTGAAAAATCACTTCGGAGCTTGGCAAAAAGAGGTTTCACCTCTGTCCTTAGATTTACAGTCTAATGCTTTA-CTCAGCCACTTTACCACAAAAAAGGAAGGAATCGAACCCTCTAAAACCGGTTTCAAGCCAGCCCCATAACCTTTATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATCACAGGTCCAAACCCCGTATATCTTATCACTGTAGAGCTAGACCAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACTACCGCCTCTTTACAGTGA
-        </sequence>
-    </data>
-
-    <data data="@alignment" dataType="nucleotide" filter="1::3,2::3" id="CP12" name="taxa"
-          spec="beast.base.evolution.alignment.FilteredAlignment"/>
-    <data data="@alignment" dataType="nucleotide" filter="3::3" id="CP3" name="taxa"
-          spec="beast.base.evolution.alignment.FilteredAlignment"/>
-
-    <siteModel gammaCategoryCount="4" id="CP12.siteModel" spec="SiteModel">
-        <parameter dimension="1" id="CP12.mutationRate" name="mutationRate" value="1.0" lower="0.0"/>
-        <parameter dimension="1" id="CP12.gammaShape" name="shape" value="0.5" lower="0.0" upper="1000.0"/>
-        <substModel id="CP12.hky" kappa="@CP12.hky.kappa" spec="HKY">
-            <frequencies frequencies="@CP12.frequencies" id="CP12.freqs" spec="Frequencies"/>
-        </substModel>
-    </siteModel>
-
-    <siteModel gammaCategoryCount="4" id="CP3.siteModel" spec="SiteModel">
-        <parameter dimension="1" id="CP3.mutationRate" name="mutationRate" value="1.0" lower="0.0"/>
-        <parameter dimension="1" id="CP3.gammaShape" name="shape" value="0.5" lower="0.0" upper="1000.0"/>
-        <substModel id="CP3.hky" kappa="@CP3.hky.kappa" spec="HKY">
-            <frequencies frequencies="@CP3.frequencies" id="CP3.freqs" spec="Frequencies"/>
-        </substModel>
-    </siteModel>
-
-    <input spec='StrictClockModel' id="branchRates">
-        <parameter name='clock.rate' id='clockRate' value="1.0"/>
-    </input>
-
-    <input spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
-        <!--trait idref='rateCategories'/-->
-        <taxa idref='alignment'/>
-    </input>
-
-    <input spec='TreeLikelihood' id="CP12.treeLikelihood">
-        <data idref="CP12"/>
-        <tree idref="tree"/>
-        <siteModel idref="CP12.siteModel"/>
-        <branchRateModel idref="branchRates"/>
-    </input>
-
-    <input spec='TreeLikelihood' id="CP3.treeLikelihood">
-        <data idref="CP3"/>
-        <tree idref="tree"/>
-        <siteModel idref="CP3.siteModel"/>
-        <branchRateModel idref="branchRates"/>
-    </input>
-
-    <parameter id="CP12.hky.kappa" value="2.0" lower="0.0"/>
-    <parameter id="CP3.hky.kappa" value="2.0" lower="0.0"/>
-    <parameter id="CP12.frequencies" value="0.25" dimension="4" lower="0.0" upper="1.0"/>
-    <parameter id="CP3.frequencies" value="0.25" dimension="4" lower="0.0" upper="1.0"/>
-    <parameter id="popSize" value="0.077" lower="0.0"/>
-
-    <run spec="MCMC" id="mcmc" chainLength="10000000"> <!--autoOptimize="true"-->
-
-        <distribution spec="CompoundDistribution" id="posterior">
-            <distribution spec="CompoundDistribution" id="prior">
-                <distribution id="CP12.hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@CP12.hky.kappa">
-                    <distr id="CP12.LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false"
-                           spec="beast.base.inference.distribution.LogNormalDistributionModel"/>
-                </distribution>
-                <distribution id="CP12.gammaShape.prior" spec="beast.base.inference.distribution.Prior" x="@CP12.gammaShape">
-                    <distr id="CP12.gammaShape.OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX"/>
-                </distribution>
-                <distribution id="CP3.hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@CP3.hky.kappa">
-                    <distr id="CP3.LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false"
-                           spec="beast.base.inference.distribution.LogNormalDistributionModel"/>
-                </distribution>
-                <distribution id="CP3.gammaShape.prior" spec="beast.base.inference.distribution.Prior" x="@CP3.gammaShape">
-                    <distr id="CP3.gammaShape.OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX"/>
-                </distribution>
-                <distribution id="popSize.prior" spec="beast.base.inference.distribution.Prior" x="@popSize">
-                    <distr id="OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX"/>
-                </distribution>
-
-                <distribution id="coalescent" spec="Coalescent">
-                    <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
-                        <tree idref="tree"/>
-                    </treeIntervals>
-                    <populationModel spec="ConstantPopulation">
-                        <popSize idref="popSize"/>
-                    </populationModel>
-                </distribution>
-            </distribution>
-            <distribution spec="CompoundDistribution" id='likelihood'>
-                <distribution idref="CP12.treeLikelihood"/>
-                <distribution idref="CP3.treeLikelihood"/>
-            </distribution>
-        </distribution>
-
-        <operator id='compMuDelta' spec='DeltaExchangeOperator' delta="0.75" weightvector="512 256" weight="2">
-            <parameter idref="CP12.mutationRate"/>
-            <parameter idref="CP3.mutationRate"/>
-        </operator>
-
-        <operator id='CP12kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1"
-                  parameter="@CP12.hky.kappa"/>
-        <operator id='CP12frequenciesDelta' spec='DeltaExchangeOperator' delta="0.01" weight="0.1"
-                  parameter="@CP12.frequencies"/>
-        <operator id='CP3kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@CP3.hky.kappa"/>
-        <operator id='CP3frequenciesDelta' spec='DeltaExchangeOperator' delta="0.01" weight="0.1"
-                  parameter="@CP3.frequencies"/>
-        <operator id='CP12alphaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1"
-                  parameter="@CP12.gammaShape"/>
-        <operator id='CP3alphaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@CP3.gammaShape"/>
-        <operator id='popSizeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize"/>
-        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree"/>
-        <operator spec='Uniform' weight="30" tree="@tree"/>
-        <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree"/>
-        <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree"/>
-        <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree"/>
-        <operator spec='WilsonBalding' weight="1" tree="@tree"/>
-        <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
-
-        <logger logEvery="1000" fileName="test.$(seed).log">
-            <model idref='posterior'/>
-            <log idref="posterior"/>
-            <log idref="prior"/>
-            <log idref="likelihood"/>
-            <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree'/>
-            <log idref="popSize"/>
-            <log idref="CP12.hky.kappa"/>
-            <log idref="CP3.hky.kappa"/>
-            <log idref="CP12.frequencies"/>
-            <log idref="CP3.frequencies"/>
-            <log idref="CP12.gammaShape"/>
-            <log idref="CP3.gammaShape"/>
-            <log idref="CP12.mutationRate"/>
-            <log idref="CP3.mutationRate"/>
-            <log idref="clockRate"/>
-            <log idref="CP12.treeLikelihood"/>
-            <log idref="CP3.treeLikelihood"/>
-            <log idref="coalescent"/>
-        </logger>
-        <!--         <logger logEvery="1000" fileName="test.$(seed).trees">
-    <log idref="tree"/>
-</logger>        -->
-        <logger logEvery="100000">
-            <model idref='posterior'/>
-            <log idref="posterior"/>
-            <log idref="prior"/>
-            <log idref="likelihood"/>
-            <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree'/>
-            <log idref="popSize"/>
-            <log idref="coalescent"/>
-        </logger>
-    </run>
-
-</beast>
+<!--<?xml version="1.0" encoding="UTF-8" standalone="no"?>-->
+<!--<beast version='2.0'-->
+<!--       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:-->
+<!--       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:-->
+<!--       beast.base.evolution.operator:beast.base.spec.inference.operator:-->
+<!--       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:-->
+<!--       beast.base.spec.evolution.branchratemodel:beast.base.spec.inference.parameter:-->
+<!--       beast.base.spec.inference.distribution:beast.base.spec.inference.util:-->
+<!--       beast.base.spec.evolution.tree:beast.base.spec.evolution.likelihood'>-->
+
+<!--    &lt;!&ndash; SRD06 model: split sequences in first together with seconds and thirds of all sites &ndash;&gt;-->
+<!--    <data id="alignment" dataType="nucleotide">-->
+<!--        <sequence taxon="human">-->
+<!--            AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCCTTATTTCTACTAGGACTATGAGAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTG-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCGGAGCTTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGGCCTCCATGACTTTTTCAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAATTATAGGCT-AAATCCTATATATCTTA-CACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACACCTCTTTACAGTGA-->
+<!--        </sequence>-->
+<!--        <sequence taxon="chimp">-->
+<!--            AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTCAAATCCCCTTATTTCTACTAGGACTATAAGAATCGAACTCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTAAGCACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCTCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AACCCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCGACACCTCTTTACAGTGA-->
+<!--        </sequence>-->
+<!--        <sequence taxon="bonobo">-->
+<!--            AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTTAAATCCCCTTATTTCTACTAGGACTATGAGAGTCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCTCTCAGTAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAGC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTTGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCCCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCAACACCTCTTTACAGTGA-->
+<!--        </sequence>-->
+<!--        <sequence taxon="gorilla">-->
+<!--            AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGAGGTTTAAACCCCCTTATTTCTACTAGGACTATGAGAATTGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTGTCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTCACATCCTTCCCGTACTAAGAAATTTAGGTTAAACATAGACCAAGAGCCTTCAAAGCCCTTAGTAAGTTA-CAACACTTAATTTCTGTAAGGACTGCAAAACCCTACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCAATGGGACTCAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAT-TCACCTCGGAGCTTGGTAAAAAGAGGCCCAGCCTCTGTCTTTAGATTTACAGTCCAATGCCTTA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGACCTTCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAGGTTAAATTACGGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCGTTAACCTTTTAAGTTAAAGATTAAGAGTATCGGCACCTCTTTGCAGTGA-->
+<!--        </sequence>-->
+<!--        <sequence taxon="orangutan">-->
+<!--            AGAAATATGTCTGACAAAAGAGTTACTTTGATAGAGTAAAAAATAGAGGTCTAAATCCCCTTATTTCTACTAGGACTATGGGAATTGAACCCACCCCTGAGAATCCAAAATTCTCCGTGCCACCCATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTA&#45;&#45;CACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTCA-CAGCACTTAATTTCTGTAAGGACTGCAAAACCCCACTTTGCATCAACTGAGCGCAAATCAGCCACTTTAATTAAGCTAAGCCCTCCTAGACCGATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAT-TGGCTTCAGTCCAAAGCCCCGGCAGGCCTTAAAGCTGCTCCTTCGAATTTGCAATTCAACATGACAA-TCACCTCAGGGCTTGGTAAAAAGAGGTCTGACCCCTGTTCTTAGATTTACAGCCTAATGCCTTAACTCGGCCATTTTACCGCAAAAAAGGAAGGAATCGAACCTCCTAAAGCTGGTTTCAAGCCAACCCCATAACCCCCATGACTTTTTCAAAAGGTACTAGAAAAACCATTTCGTAACTTTGTCAAAGTTAAATTACAGGTC-AGACCCTGTGTATCTTA-CATTGCAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACCAGCCTCTCTTTGCAATGA-->
+<!--        </sequence>-->
+<!--        <sequence taxon="siamang">-->
+<!--            AGAAATACGTCTGACGAAAGAGTTACTTTGATAGAGTAAATAACAGGGGTTTAAATCCCCTTATTTCTACTAGAACCATAGGAGTCGAACCCATCCTTGAGAATCCAAAACTCTCCGTGCCACCCGTCGCACCCTGTTCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCATACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTAACAAAACTTAATTTCTGCAAGGGCTGCAAAACCCTACTTTGCATCAACCGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCGATGGGACTTAAACCCATAAAAATTTAGTTAACAGCTAAACACCCTAAACAACCTGGCTTCAATCTAAAGCCCCGGCAGA-GTTGAAGCTGCTTCTTTGAACTTGCAATTCAACGTGAAAAATCACTTCGGAGCTTGGCAAAAAGAGGTTTCACCTCTGTCCTTAGATTTACAGTCTAATGCTTTA-CTCAGCCACTTTACCACAAAAAAGGAAGGAATCGAACCCTCTAAAACCGGTTTCAAGCCAGCCCCATAACCTTTATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATCACAGGTCCAAACCCCGTATATCTTATCACTGTAGAGCTAGACCAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACTACCGCCTCTTTACAGTGA-->
+<!--        </sequence>-->
+<!--    </data>-->
+
+<!--    <data data="@alignment" dataType="nucleotide" filter="1::3,2::3" id="CP12" name="taxa"-->
+<!--          spec="beast.base.spec.evolution.alignment.FilteredAlignment"/>-->
+<!--    <data data="@alignment" dataType="nucleotide" filter="3::3" id="CP3" name="taxa"-->
+<!--          spec="beast.base.spec.evolution.alignment.FilteredAlignment"/>-->
+
+<!--    <siteModel gammaCategoryCount="4" id="CP12.siteModel" spec="beast.base.spec.evolution.sitemodel.SiteModel">-->
+<!--        <parameter id="CP12.mutationRate" name="mutationRate" spec="RealScalarParam" domain="PositiveReal" value="1.0"/>-->
+<!--        <parameter id="CP12.gammaShape" name="shape" spec="RealScalarParam" domain="PositiveReal" value="0.5"/>-->
+<!--        <substModel id="CP12.hky" kappa="@CP12.hky.kappa" spec="HKY">-->
+<!--            <frequencies frequencies="@CP12.frequencies" id="CP12.freqs" spec="Frequencies"/>-->
+<!--        </substModel>-->
+<!--    </siteModel>-->
+
+<!--    <siteModel gammaCategoryCount="4" id="CP3.siteModel" spec="beast.base.spec.evolution.sitemodel.SiteModel">-->
+<!--        <parameter id="CP3.mutationRate" name="mutationRate" spec="RealScalarParam" domain="PositiveReal" value="1.0"/>-->
+<!--        <parameter id="CP3.gammaShape" name="shape" spec="RealScalarParam" domain="PositiveReal" value="0.5"/>-->
+<!--        <substModel id="CP3.hky" kappa="@CP3.hky.kappa" spec="HKY">-->
+<!--            <frequencies frequencies="@CP3.frequencies" id="CP3.freqs" spec="Frequencies"/>-->
+<!--        </substModel>-->
+<!--    </siteModel>-->
+
+<!--    <input spec='beast.base.spec.evolution.branchratemodel.StrictClockModel' id="branchRates">-->
+<!--        <clock.rate id="clockRate" spec="RealScalarParam" domain="PositiveReal" value="1.0"/>-->
+<!--    </input>-->
+
+<!--    <input spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>-->
+<!--        &lt;!&ndash;trait idref='rateCategories'/&ndash;&gt;-->
+<!--        <taxa idref='alignment'/>-->
+<!--    </input>-->
+
+<!--    <input spec='TreeLikelihood' id="CP12.treeLikelihood">-->
+<!--        <data idref="CP12"/>-->
+<!--        <tree idref="tree"/>-->
+<!--        <siteModel idref="CP12.siteModel"/>-->
+<!--        <branchRateModel idref="branchRates"/>-->
+<!--    </input>-->
+
+<!--    <input spec='TreeLikelihood' id="CP3.treeLikelihood">-->
+<!--        <data idref="CP3"/>-->
+<!--        <tree idref="tree"/>-->
+<!--        <siteModel idref="CP3.siteModel"/>-->
+<!--        <branchRateModel idref="branchRates"/>-->
+<!--    </input>-->
+
+<!--    <parameter id="CP12.hky.kappa" spec="RealScalarParam" domain="PositiveReal" value="2.0"/>-->
+<!--    <parameter id="CP3.hky.kappa" spec="RealScalarParam" domain="PositiveReal" value="2.0"/>-->
+<!--    <parameter dimension="4" id="CP12.frequencies" spec="SimplexParam" value="0.25"/>-->
+<!--    <parameter dimension="4" id="CP3.frequencies" spec="SimplexParam" value="0.25"/>-->
+<!--    <parameter id="popSize" spec="RealScalarParam" domain="PositiveReal" value="0.077"/>-->
+
+<!--    <run spec="MCMC" id="mcmc" chainLength="10000000"> &lt;!&ndash;autoOptimize="true"&ndash;&gt;-->
+
+<!--        <distribution spec="CompoundDistribution" id="posterior">-->
+<!--            <distribution spec="CompoundDistribution" id="prior">-->
+<!--                <distribution id="CP12.hky.kappa.prior" spec='LogNormal' param='@CP12.hky.kappa' >-->
+<!--                    &lt;!&ndash; M="1" S="1.25" />&ndash;&gt;-->
+<!--                    <M spec="RealScalarParam" domain="Real" value="1.0"/>-->
+<!--                    <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>-->
+<!--                </distribution>-->
+<!--                <distribution id="CP3.hky.kappa.prior" spec='LogNormal' param='@CP3.hky.kappa' >-->
+<!--                    <M spec="RealScalarParam" domain="Real" value="1.0"/>-->
+<!--                    <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>-->
+<!--                </distribution>-->
+
+<!--                &lt;!&ndash; cannot use TruncatedReal to OneOnX &ndash;&gt;-->
+<!--&lt;!&ndash;                <distribution id='CP12.gammaShape.prior' spec='beast.base.spec.inference.distribution.TruncatedReal'&ndash;&gt;-->
+<!--&lt;!&ndash;                              param='@CP12.gammaShape' >&ndash;&gt;-->
+<!--&lt;!&ndash;                    <lower spec="RealScalarParam" domain="Real" value="0.1" estimate="false"/>&ndash;&gt;-->
+<!--&lt;!&ndash;                    <upper spec="RealScalarParam" domain="Real" value="1000.0" estimate="false"/>&ndash;&gt;-->
+<!--&lt;!&ndash;                    <distribution spec='beast.base.spec.beast2vs1.OneOnX' />&ndash;&gt;-->
+<!--&lt;!&ndash;                </distribution>&ndash;&gt;-->
+<!--&lt;!&ndash;                <distribution id='CP3.gammaShape.prior' spec='beast.base.spec.inference.distribution.TruncatedReal'&ndash;&gt;-->
+<!--&lt;!&ndash;                              param='@CP3.gammaShape' >&ndash;&gt;-->
+<!--&lt;!&ndash;                    <lower spec="RealScalarParam" domain="Real" value="0.1" estimate="false"/>&ndash;&gt;-->
+<!--&lt;!&ndash;                    <upper spec="RealScalarParam" domain="Real" value="1000.0" estimate="false"/>&ndash;&gt;-->
+<!--&lt;!&ndash;                    <distribution spec='beast.base.spec.beast2vs1.OneOnX' />&ndash;&gt;-->
+<!--&lt;!&ndash;                </distribution>&ndash;&gt;-->
+
+<!--                <distribution id="popSize.prior" spec='beast.base.spec.beast2vs1.OneOnX'-->
+<!--                              param='@popSize' />-->
+
+<!--                <distribution id="coalescent" spec="Coalescent">-->
+<!--                    <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>-->
+<!--                        <tree idref="tree"/>-->
+<!--                    </treeIntervals>-->
+<!--                    <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">-->
+<!--                        <popSize idref="popSize"/>-->
+<!--                    </populationModel>-->
+<!--                </distribution>-->
+<!--            </distribution>-->
+<!--            <distribution spec="CompoundDistribution" id='likelihood'>-->
+<!--                <distribution idref="CP12.treeLikelihood"/>-->
+<!--                <distribution idref="CP3.treeLikelihood"/>-->
+<!--            </distribution>-->
+<!--        </distribution>-->
+
+<!--        <operator id='compMuDelta' spec='beast.base.spec.inference.operator.DeltaExchangeOperator'-->
+<!--                  delta="0.75" weight="2">-->
+<!--            <weightvector  spec='beast.base.spec.inference.parameter.IntVectorParam'-->
+<!--                       domain="PositiveInt" value="512 256"/>-->
+<!--            <parameter idref="CP12.mutationRate"/>-->
+<!--            <parameter idref="CP3.mutationRate"/>-->
+<!--        </operator>-->
+
+<!--        <operator id='CP12kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.75" weight="0.1"-->
+<!--                  parameter="@CP12.hky.kappa"/>-->
+<!--        <operator id='CP12frequenciesDelta' spec='beast.base.spec.inference.operator.DeltaExchangeOperator' delta="0.01" weight="0.1"-->
+<!--                  rvparameter="@CP12.frequencies"/>-->
+<!--        <operator id='CP3kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.75" weight="0.1"-->
+<!--                  parameter="@CP3.hky.kappa"/>-->
+<!--        <operator id='CP3frequenciesDelta' spec='DeltaExchangeOperator' delta="0.01" weight="0.1"-->
+<!--                  rvparameter="@CP3.frequencies"/>-->
+<!--        <operator id='CP12alphaScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.75" weight="0.1"-->
+<!--                  parameter="@CP12.gammaShape"/>-->
+<!--        <operator id='CP3alphaScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.75" weight="0.1"-->
+<!--                  parameter="@CP3.gammaShape"/>-->
+<!--        <operator id='popSizeScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.75" weight="3"-->
+<!--                  parameter="@popSize"/>-->
+<!--        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator' scaleFactor="0.75" weight="3" tree="@tree"/>-->
+<!--        <operator spec='Uniform' weight="30" tree="@tree"/>-->
+<!--        <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree"/>-->
+<!--        <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree"/>-->
+<!--        <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree"/>-->
+<!--        <operator spec='WilsonBalding' weight="1" tree="@tree"/>-->
+<!--        <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>-->
+
+<!--        <logger logEvery="1000" fileName="test.$(seed).log">-->
+<!--            <model idref='posterior'/>-->
+<!--            <log idref="posterior"/>-->
+<!--            <log idref="prior"/>-->
+<!--            <log idref="likelihood"/>-->
+<!--            <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree'/>-->
+<!--            <log idref="popSize"/>-->
+<!--            <log idref="CP12.hky.kappa"/>-->
+<!--            <log idref="CP3.hky.kappa"/>-->
+<!--            <log idref="CP12.frequencies"/>-->
+<!--            <log idref="CP3.frequencies"/>-->
+<!--            <log idref="CP12.gammaShape"/>-->
+<!--            <log idref="CP3.gammaShape"/>-->
+<!--            <log idref="CP12.mutationRate"/>-->
+<!--            <log idref="CP3.mutationRate"/>-->
+<!--            <log idref="clockRate"/>-->
+<!--            <log idref="CP12.treeLikelihood"/>-->
+<!--            <log idref="CP3.treeLikelihood"/>-->
+<!--            <log idref="coalescent"/>-->
+<!--        </logger>-->
+<!--        &lt;!&ndash;         <logger logEvery="1000" fileName="test.$(seed).trees">-->
+<!--    <log idref="tree"/>-->
+<!--</logger>        &ndash;&gt;-->
+<!--        <logger logEvery="100000">-->
+<!--            <model idref='posterior'/>-->
+<!--            <log idref="posterior"/>-->
+<!--            <log idref="prior"/>-->
+<!--            <log idref="likelihood"/>-->
+<!--            <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree'/>-->
+<!--            <log idref="popSize"/>-->
+<!--            <log idref="coalescent"/>-->
+<!--        </logger>-->
+<!--    </run>-->
+
+<!--</beast>-->
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testSiteModelAlpha.xml b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testSiteModelAlpha.xml
index 94ae74e2..911190a5 100644
--- a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testSiteModelAlpha.xml
+++ b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testSiteModelAlpha.xml
@@ -1,6 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood:beast.base.evolution.branchratemodel'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
+       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
+       beast.base.evolution.operator:beast.base.spec.inference.operator:
+       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
+       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
+       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
 
     <!-- 17 taxa, 1485 sites, 138 patterns -->
     <data dataType="nucleotide" id="alignment">
@@ -70,7 +75,7 @@
 
     </data>
 
-    <tree spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+    <tree spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
         <trait spec='beast.base.evolution.tree.TraitSet' traitname='date-forward' units='year'
                value='
 		TREESPARROW_HENAN_1_2004=2004.0,
@@ -94,22 +99,22 @@
 		PEREGRINEFALCON_HK_D0028_2004=2004.0,
 		TREESPARROW_HENAN_2_2004=2004.0,
 		HONGKONG_538_1997=1997.0'>
-		<taxa spec='beast.base.evolution.alignment.TaxonSet' alignment='@alignment'/>
+            <taxa spec='beast.base.evolution.alignment.TaxonSet' alignment='@alignment'/>
         </trait>
         <taxa idref='alignment'/>
     </tree>
 
     <siteModel spec='SiteModel' id="siteModel" gammaCategoryCount="4">
-        <parameter id='siteModel.alpha' name='shape' value="0.05" lower="0.0" upper="100.0"/>
+        <parameter id='siteModel.alpha' name='shape' spec="RealScalarParam" domain="PositiveReal" value="0.05"/>
 
         <substModel spec='HKY' id="hky">
-            <parameter name='kappa' id="hky.kappa" value="2.0" lower="0.0" upper="100.0"/>
+            <kappa id="hky.kappa" spec="RealScalarParam" domain="PositiveReal" value="2.0"/>
             <frequencies id='freqs' spec='Frequencies' data="@alignment"/>
         </substModel>
     </siteModel>
 
-    <input spec='StrictClockModel' id="branchRates">
-        <parameter name='clock.rate' id='clockRate' value="4.0E-4"/>
+    <input spec='beast.base.spec.evolution.branchratemodel.StrictClockModel' id="branchRates">
+        <parameter id="clockRate" name='clock.rate' spec="RealScalarParam" domain="PositiveReal" value="4.0E-4"/>
     </input>
 
     <input spec='TreeLikelihood' id="treeLikelihood">
@@ -119,7 +124,7 @@
         <branchRateModel idref="branchRates"/>
     </input>
 
-    <parameter id="popSize" value="380.0" lower="0.0" upper="38000.0"/>
+    <parameter id="popSize" spec="RealScalarParam" domain="PositiveReal" value="380.0"/>
 
     <run spec="MCMC" id="mcmc" chainLength="5000000"> <!--autoOptimize="true"-->
         <state>
@@ -131,40 +136,43 @@
         </state>
 
         <distribution spec="CompoundDistribution" id="posterior">
-            <!--<distribution spec="CompoundDistribution" id="prior">-->
-                <!--<distribution id="hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@hky.kappa">-->
-                <!--<distr id="LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false" spec="beast.base.inference.distribution.LogNormalDistributionModel"/>-->
-                <!--</distribution>-->
-                <!--<distribution id="hky.frequencies.prior" spec="beast.base.inference.distribution.Prior" x="@hky.frequencies">-->
-                <!--<distr id="Uniform" lower="0.0" upper="1.0" spec="beast.base.inference.distribution.Uniform"/>-->
-                <!--</distribution>-->
-                <!--<distribution id="popSize.prior" spec="beast.base.inference.distribution.Prior" x="@popSize">-->
-                <!--<distr id="OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX"/>-->
-                <!--</distribution>-->
+<!--use Uniform or TruncatedDistribution to replace bounds -->
+<!--            <distribution id="shape.prior" spec="beast.base.spec.inference.distribution.Uniform" param="@siteModel.alpha">-->
+<!--                <lower id="shape.lower" spec="RealScalarParam" domain="Real" value="0.001"/>-->
+<!--                <upper id="shape.upper" spec="RealScalarParam" domain="Real" value="100.0"/>-->
+<!--            </distribution>-->
+<!--            <distribution id="kappa.prior" spec="beast.base.spec.inference.distribution.Uniform" param="@hky.kappa">-->
+<!--                <lower id="kappa.lower" spec="RealScalarParam" domain="Real" value="0.001"/>-->
+<!--                <upper id="kappa.upper" spec="RealScalarParam" domain="Real" value="100.0"/>-->
+<!--            </distribution>-->
+<!--            <distribution id="popSize.prior" spec="beast.base.spec.inference.distribution.Uniform" param="@popSize">-->
+<!--                <lower id="popSize.lower" spec="RealScalarParam" domain="Real" value="0.001"/>-->
+<!--                <upper id="popSize.upper" spec="RealScalarParam" domain="Real" value="38000.0"/>-->
+<!--            </distribution>-->
 
-                <distribution id="coalescent" spec="Coalescent">
-                    <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
-                        <tree idref="tree"/>
-                    </treeIntervals>
-                    <populationModel spec="ConstantPopulation">
-                        <popSize idref="popSize"/>
-                    </populationModel>
-                </distribution>
+            <distribution id="coalescent" spec="Coalescent">
+                <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
+                    <tree idref="tree"/>
+                </treeIntervals>
+                <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
+                    <popSize idref="popSize"/>
+                </populationModel>
+            </distribution>
             <!--</distribution>-->
             <distribution id='likelihood' idref="treeLikelihood"/>
         </distribution>
 
-        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="1" parameter="@hky.kappa"/>
-        <operator id='shapeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="1" parameter="@siteModel.alpha"/>
-        <operator id='clockRateScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" parameter="@clockRate"/>
-        <operator id='popSizeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize"/>
-        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree"/>
+        <operator id='kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.75" weight="1" parameter="@hky.kappa"/>
+        <operator id='shapeScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.75" weight="1" parameter="@siteModel.alpha"/>
+        <operator id='clockRateScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.5" weight="1" parameter="@clockRate"/>
+        <operator id='popSizeScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize"/>
+        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator' scaleFactor="0.75" weight="3" tree="@tree"/>
         <operator spec='Uniform' weight="30" tree="@tree"/>
         <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree"/>
         <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree"/>
         <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree"/>
         <operator spec='WilsonBalding' weight="1" tree="@tree"/>
-        <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" up="@clockRate" down="@tree"/>
+        <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" up="@clockRate" down="@tree"/>
 
         <logger logEvery="500" fileName="test.$(seed).log">
             <model idref='posterior'/>
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testStrictClock.xml b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testStrictClock.xml
index 15d3e93a..774e2fd5 100644
--- a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testStrictClock.xml
+++ b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testStrictClock.xml
@@ -1,7 +1,12 @@
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
+       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
+       beast.base.evolution.operator:beast.base.spec.inference.operator:
+       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
+       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
+       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
 
-    <!-- same as testStrictClockNoDate.xml in BEAST 1                            -->
+<!-- same as testStrictClockNoDate.xml in BEAST 1                            -->
     <!-- The sequence alignment (each sequence refers to a taxon above).         -->
     <!-- ntax=6 nchar=768                                                        -->
     <!-- npatterns=69                                                            -->
@@ -28,7 +33,7 @@
 
     <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
     <input spec='HKY' id="hky">
-        <parameter name='kappa' idref='hky.kappa'/>
+        <kappa idref='hky.kappa'/>
         <input id='freqs' name='frequencies' spec='Frequencies' frequencies='@hky.frequencies'/>
     </input>
 
@@ -38,9 +43,8 @@
         <substModel idref='hky'/>
     </input>
 
-
-    <input spec='StrictClockModel' id="branchRates">
-        <parameter name='clock.rate' id='clockRate' value="1.0"/>
+    <input spec='beast.base.spec.evolution.branchratemodel.StrictClockModel' id="branchRates">
+        <clock.rate id='clockRate' value="1.0" spec="RealScalarParam" domain="PositiveReal"/>
     </input>
 
     <input spec='TreeLikelihood' id="treeLikelihood">
@@ -50,14 +54,14 @@
         <branchRateModel idref="branchRates"/>
     </input>
 
-    <input spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+    <input spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
         <!--trait idref='rateCategories'/-->
         <taxa idref='alignment'/>
     </input>
 
-    <parameter id="hky.kappa" value="2.0" lower="0.0"/>
-    <parameter id="hky.frequencies" value="0.25" dimension="4"/>
-    <parameter id="popSize" value="0.077" lower="0.0"/>
+    <parameter id="hky.kappa" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
+    <parameter dimension="4" id="hky.frequencies" spec="SimplexParam" value="0.25"/>
+    <parameter id="popSize" value="0.077" spec="RealScalarParam" domain="PositiveReal"/>
 
     <run spec="MCMC" id="mcmc" chainLength="10000000"> <!--autoOptimize="true"-->
         <state>
@@ -69,21 +73,29 @@
 
         <distribution spec="CompoundDistribution" id="posterior">
             <distribution spec="CompoundDistribution" id="prior">
-                <distribution id="hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@hky.kappa">
-                    <distr id="LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false" spec="beast.base.inference.distribution.LogNormalDistributionModel"/>
-                </distribution>
-                <distribution id="hky.frequencies.prior" spec="beast.base.inference.distribution.Prior" x="@hky.frequencies">
-                    <distr id="Uniform" lower="0.0" upper="1.0" spec="beast.base.inference.distribution.Uniform"/>
+                <distribution id="hky.kappa.prior" spec='LogNormal' param='@hky.kappa' >
+                    <!-- M="1" S="1.25" />-->
+                    <M spec="RealScalarParam" domain="Real" value="1.0"/>
+                    <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>
                 </distribution>
-                <distribution id="popSize.prior" spec="beast.base.inference.distribution.Prior" x="@popSize">
-                    <distr id="OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX"/>
+
+                <distribution id="hky.frequencies.prior" spec="beast.base.spec.inference.distribution.IID"
+                              param="@hky.frequencies">
+                    <distr id="Uniform" spec="beast.base.spec.inference.distribution.Uniform">
+                        <lower id="freqs.lower" spec="RealScalarParam" domain="Real" value="0.0"/>
+                        <upper id="freqs.upper" spec="RealScalarParam" domain="Real" value="1.0"/>
+                    </distr>
                 </distribution>
 
+                <!-- OneOnX is deprecated, test only -->
+                <distribution id="popSize.prior" spec='beast.base.spec.beast2vs1.OneOnX'
+                              param='@popSize' />
+
                 <distribution id="coalescent" spec="Coalescent">
                     <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
                         <tree idref="tree"/>
                     </treeIntervals>
-                    <populationModel spec="ConstantPopulation">
+                    <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation" id='ConstantPopulation'>
                         <popSize idref="popSize"/>
                     </populationModel>
                 </distribution>
@@ -91,17 +103,20 @@
             <distribution id='likelihood' idref="treeLikelihood"/>
         </distribution>
 
-        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
-        <operator id='frequenciesDelta' spec='DeltaExchangeOperator' delta="0.01" weight="0.1"
-                  parameter="@hky.frequencies"/>
-        <operator id='popSizeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize"/>
-        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree"/>
+        <operator id='kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
+                  scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
+        <operator id='frequenciesDelta' spec='beast.base.spec.inference.operator.DeltaExchangeOperator'
+                  delta="0.01" weight="0.1" rvparameter="@hky.frequencies"/>
+        <operator id='popSizeScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
+                  scaleFactor="0.75" weight="3" parameter="@popSize"/>
+        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator'
+                  scaleFactor="0.75" weight="3" tree="@tree"/>
         <operator spec='Uniform' weight="30" tree="@tree"/>
         <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree"/>
         <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree"/>
         <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree"/>
         <operator spec='WilsonBalding' weight="1" tree="@tree"/>
-        <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
+        <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
             <model idref='posterior'/>
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testStrictClock2.xml b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testStrictClock2.xml
index e8507116..470e124b 100644
--- a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testStrictClock2.xml
+++ b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testStrictClock2.xml
@@ -1,7 +1,12 @@
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
+       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
+       beast.base.evolution.operator:beast.base.spec.inference.operator:
+       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
+       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
+       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
 
-    <!-- same as testStrictClockNoDate2.xml in BEAST 1                            -->
+<!-- same as testStrictClockNoDate2.xml in BEAST 1                            -->
     <!-- The sequence alignment (each sequence refers to a taxon above).         -->
     <!-- ntax=6 nchar=768                                                        -->
     <!-- npatterns=69                                                            -->
@@ -28,7 +33,7 @@
 
     <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
     <input spec='HKY' id="hky">
-        <parameter name='kappa' idref='hky.kappa'/>
+        <kappa idref='hky.kappa'/>
         <frequencies id='freqs' spec='Frequencies'>
             <data idref='alignment'/>
         </frequencies>
@@ -41,8 +46,8 @@
     </input>
 
 
-    <input spec='StrictClockModel' id="branchRates">
-        <parameter name='clock.rate' id='clockRate' value="1.0"/>
+    <input spec='beast.base.spec.evolution.branchratemodel.StrictClockModel' id="branchRates">
+        <clock.rate id='clockRate' value="1.0" spec="RealScalarParam" domain="PositiveReal"/>
     </input>
 
     <input spec='TreeLikelihood' id="treeLikelihood">
@@ -52,13 +57,13 @@
         <branchRateModel idref="branchRates"/>
     </input>
 
-    <input spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+    <input spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
         <!--trait idref='rateCategories'/-->
         <taxa idref='alignment'/>
     </input>
 
-    <parameter id="hky.kappa" value="2.0" lower="0.0"/>
-    <parameter id="popSize" value="0.077" lower="0.0"/>
+    <parameter id="hky.kappa" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
+    <parameter id="popSize" value="0.077" spec="RealScalarParam" domain="PositiveReal"/>
 
     <run spec="MCMC" id="mcmc" chainLength="10000000"> <!--autoOptimize="true"-->
         <state>
@@ -69,19 +74,21 @@
 
         <distribution spec="CompoundDistribution" id="posterior">
             <distribution spec="CompoundDistribution" id="prior">
-                <distribution id="hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@hky.kappa">
-                    <distr id="LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false"
-                                  spec="beast.base.inference.distribution.LogNormalDistributionModel"/>
-                </distribution>
-                <distribution id="popSize.prior" spec="beast.base.inference.distribution.Prior" x="@popSize">
-                    <distr id="OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX"/>
+                <distribution id="hky.kappa.prior" spec='LogNormal' param='@hky.kappa' >
+                    <!-- M="1" S="1.25" />-->
+                    <M spec="RealScalarParam" domain="Real" value="1.0"/>
+                    <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>
                 </distribution>
 
+                <!-- OneOnX is deprecated, test only -->
+                <distribution id="popSize.prior" spec='beast.base.spec.beast2vs1.OneOnX'
+                              param='@popSize' />
+
                 <distribution id="coalescent" spec="Coalescent">
                     <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
                         <tree idref="tree"/>
                     </treeIntervals>
-                    <populationModel spec="ConstantPopulation">
+                    <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation" id='ConstantPopulation'>
                         <popSize idref="popSize"/>
                     </populationModel>
                 </distribution>
@@ -89,15 +96,18 @@
             <distribution id='likelihood' idref="treeLikelihood"/>
         </distribution>
 
-        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
-        <operator id='popSizeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize"/>
-        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree"/>
+        <operator id='kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
+                  scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
+        <operator id='popSizeScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
+                  scaleFactor="0.75" weight="3" parameter="@popSize"/>
+        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator'
+                  scaleFactor="0.75" weight="3" tree="@tree"/>
         <operator spec='Uniform' weight="30" tree="@tree"/>
         <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree"/>
         <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree"/>
         <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree"/>
         <operator spec='WilsonBalding' weight="1" tree="@tree"/>
-        <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
+        <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
             <model idref='posterior'/>
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testStrictClockTipDatesSampling.xml b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testStrictClockTipDatesSampling.xml
index c0de665a..1198b0ac 100644
--- a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testStrictClockTipDatesSampling.xml
+++ b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testStrictClockTipDatesSampling.xml
@@ -1,7 +1,12 @@
 <beast version='2.0'
-       namespace='beast.base.math:beast.base.evolution.alignment:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter'>
-
-    <!-- 17 taxa, 1485 sites, 138 patterns -->
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
+       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
+       beast.base.evolution.operator:beast.base.spec.inference.operator:
+       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
+       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
+       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
+
+<!-- 17 taxa, 1485 sites, 138 patterns -->
     <data dataType="nucleotide" id="alignment">
         <sequence taxon="TREESPARROW_HENAN_1_2004">
             ATGGAGAAAATAGTGCTTCTTCGTGCAATGATCAATCTTGTTAAAAGTGATCAGATTGGCGTTGGTTACCATGCAGACTACTCGACAGAGCAGGGTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATATTGGAAAAGACACACAACGGGAAGCTCTGCGACCTAGATGGAGTGAAGCCTCTAATTTTGAAAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTGACGAATTCATCAATGTGCCGGAGTGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAAAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCGATCATGAAGCCTCATCAGGGGTGAGCTCAGCATGTCCATACCTGGGGAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTACATACCCAACAATAAAGAGGGGCTACAATAATACCAACCCAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGGAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCAAAGTAAATGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGACGCTATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACCAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACAGGGCTCAGAAATAGCCCTCAAAGAGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAAGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAAAATTTAAACAAGAAGATGGAGGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGAAAAGGTCCGACTACAACTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT
@@ -69,7 +74,7 @@
 
     </data>
 
-    <tree spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+    <tree spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
         <trait spec='beast.base.evolution.tree.TraitSet' traitname='date-forward' units='year'
                value='
 		TREESPARROW_HENAN_1_2004=2004.0,
@@ -110,7 +115,7 @@
         <substModel idref='hky'/>
     </input>
 
-    <input spec='StrictClockModel' id="branchRates">
+    <input spec='beast.base.spec.evolution.branchratemodel.StrictClockModel' id="branchRates">
         <clock.rate idref='clockRate'/>
     </input>
 
@@ -121,12 +126,13 @@
         <branchRateModel idref="branchRates"/>
     </input>
 
-    <parameter id="hky.kappa" value="2.0" lower="0.0"/>
-    <parameter id="hky.frequencies" value="0.25" dimension="4"/>
-    <parameter id="popSize" value="380.0" lower="0.0" upper="38000.0"/>
-    <parameter id='clockRate' value="2.3E-5" lower="0.0" upper="100.0"/>
+    <parameter id='clockRate' value="2.3E-5" spec="RealScalarParam" domain="PositiveReal" />
+    <parameter id="hky.kappa" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
+    <parameter dimension="4" id="hky.frequencies" spec="SimplexParam" value="0.25"/>
+    <parameter id="popSize" value="380.0" spec="RealScalarParam" domain="PositiveReal"/>
 
-    <distribution id="tipDateB" monophyletic="false" spec="beast.base.evolution.tree.MRCAPrior" tipsonly="true" tree="@tree">
+    <distribution id="tipDateB" monophyletic="false" spec="beast.base.spec.evolution.tree.MRCAPrior"
+                  tipsonly="true" tree="@tree">
         <taxonset id="age(CHICKEN_HONGKONG_915_1997)" spec="TaxonSet">
             <taxon id="CHICKEN_HONGKONG_915_1997" spec="Taxon"/>
         </taxonset>
@@ -143,33 +149,43 @@
 
         <distribution spec="CompoundDistribution" id="posterior">
             <distribution spec="CompoundDistribution" id="prior">
-                <distribution id="hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@hky.kappa">
-                    <distr id="LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false"
-                           spec="beast.base.inference.distribution.LogNormalDistributionModel"/>
+                <distribution id="hky.kappa.prior" spec='LogNormal' param='@hky.kappa' >
+                    <!-- M="1" S="1.25" />-->
+                    <M spec="RealScalarParam" domain="Real" value="1.0"/>
+                    <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>
                 </distribution>
-                <distribution id="hky.frequencies.prior" spec="beast.base.inference.distribution.Prior" x="@hky.frequencies">
-                    <distr id="Uniform" lower="0.0" upper="1.0" spec="beast.base.inference.distribution.Uniform"/>
+                <distribution id="hky.frequencies.prior" spec="beast.base.spec.inference.distribution.IID"
+                              param="@hky.frequencies">
+                    <distr id="Uniform" spec="beast.base.spec.inference.distribution.Uniform">
+                        <lower id="freqs.lower" spec="RealScalarParam" domain="Real" value="0.0"/>
+                        <upper id="freqs.upper" spec="RealScalarParam" domain="Real" value="1.0"/>
+                    </distr>
                 </distribution>
-                <distribution id="popSize.prior" spec="beast.base.inference.distribution.Prior" x="@popSize">
-                    <distr id="OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX"/>
+                <!-- OneOnX is deprecated, test only -->
+                <distribution id="popSize.prior" spec='beast.base.spec.beast2vs1.OneOnX'
+                              param='@popSize' />
+                <distribution id="clockRate.prior" spec="beast.base.spec.inference.distribution.Uniform"
+                              param="@clockRate">
+                    <lower id="clockRate.lower" spec="RealScalarParam" domain="Real" value="0.0"/>
+                    <upper id="clockRate.upper" spec="RealScalarParam" domain="Real" value="100.0"/>
                 </distribution>
-                <!--<distribution id="clockRate.prior" spec="beast.base.inference.distribution.Prior" x="@clockRate">-->
-                <!--<distr id="Uniform2" lower="0.0" upper="100.0" spec="beast.base.inference.distribution.Uniform"/>-->
-                <!--</distribution>-->
 
-                <distribution id="tipDateA" monophyletic="false" spec="beast.base.evolution.tree.MRCAPrior" tipsonly="true"
+                <distribution id="tipDateA" monophyletic="false" spec="beast.base.spec.evolution.tree.MRCAPrior" tipsonly="true"
                               tree="@tree">
                     <taxonset id="age(TREESPARROW_HENAN_1_2004)" spec="TaxonSet">
                         <taxon id="TREESPARROW_HENAN_1_2004" spec="Taxon"/>
                     </taxonset>
-                    <distr id="Uniform0" offset="0.0" spec="distribution.Uniform" upper="2005"/>
+                    <distr id="Uniform0" spec="beast.base.spec.inference.distribution.Uniform">
+<!--                        <lower id="Uniform0.lower" spec="RealScalarParam" domain="Real" value="0.0"/>-->
+                        <upper id="Uniform0.upper" spec="RealScalarParam" domain="Real" value="2500.0"/>
+                    </distr>
                 </distribution>
 
                 <distribution id="coalescent" spec="Coalescent">
                     <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
                         <tree idref="tree"/>
                     </treeIntervals>
-                    <populationModel spec="ConstantPopulation">
+                    <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
                         <popSize idref="popSize"/>
                     </populationModel>
                 </distribution>
@@ -182,18 +198,22 @@
         <operator id="TipDatesRandomWalkerB" windowSize="1" spec="TipDatesRandomWalker"
                   taxonset="@age(CHICKEN_HONGKONG_915_1997)" tree="@tree" weight="1.0"/>
 
-        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
-        <operator id='frequenciesDelta' spec='DeltaExchangeOperator' delta="0.01" weight="0.1"
-                  parameter="@hky.frequencies"/>
-        <operator id='popSizeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize"/>
-        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree"/>
+        <operator id='kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
+                  scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
+        <operator id='frequenciesDelta' spec='beast.base.spec.inference.operator.DeltaExchangeOperator'
+                  delta="0.01" weight="0.1" rvparameter="@hky.frequencies"/>
+        <operator id='popSizeScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
+                  scaleFactor="0.75" weight="3" parameter="@popSize"/>
+        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator'
+                  scaleFactor="0.75" weight="3" tree="@tree"/>
         <operator spec='Uniform' weight="30" tree="@tree"/>
         <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree"/>
         <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree"/>
         <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree"/>
         <operator spec='WilsonBalding' weight="3" tree="@tree"/>
-        <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" up="@clockRate" down="@tree"/>
-        <operator id='clockRateScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@clockRate"/>
+        <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" up="@clockRate" down="@tree"/>
+        <operator id='clockRateScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
+                  scaleFactor="0.75" weight="3" parameter="@clockRate" />
 
         <logger logEvery="1000" fileName="test.$(seed).log">
             <model idref='posterior'/>
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testStrictClockTipTime.xml b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testStrictClockTipTime.xml
index db32ae41..891ceb16 100644
--- a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testStrictClockTipTime.xml
+++ b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testStrictClockTipTime.xml
@@ -1,5 +1,10 @@
 <beast version='2.0'
-	namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
+       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
+       beast.base.evolution.operator:beast.base.spec.inference.operator:
+       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
+       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
+       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
 
 	<data dataType="nucleotide" id="alignment">
 		<sequence taxon="D4Brazi82">
@@ -67,7 +72,7 @@
 		<substModel idref='hky' />
 	</input>
 	
-	<input spec='StrictClockModel' id="branchRates">
+	<input spec='beast.base.spec.evolution.branchratemodel.StrictClockModel' id="branchRates">
 		<clock.rate idref='clockRate' />
 	</input>
 
@@ -78,7 +83,7 @@
 		<branchRateModel idref="branchRates" />
 	</input>
 
-	<input spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+	<input spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
 		<trait spec='beast.base.evolution.tree.TraitSet' traitname='date-forward' units='year'
 			value='
         D4Brazi82  = 1982, D4ElSal83  = 1983, D4ElSal94  = 1994, D4Indon76  = 1976, D4Indon77  = 1977,
@@ -90,10 +95,11 @@
 		<taxa idref='alignment' />
 	</input>
 
-	<parameter id="hky.kappa" value="2.0" lower="0.0" />
-	<parameter id="hky.frequencies" value="0.25" dimension="4" />
-	<parameter id="popSize" value="380.0" lower="0.0" upper="38000.0" />
-	<parameter id='clockRate' value="2.3E-5" lower="0.0" upper="100.0" />
+
+	<parameter id='clockRate' value="2.3E-5" spec="RealScalarParam" domain="PositiveReal" />
+    <parameter id="hky.kappa" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
+    <parameter dimension="4" id="hky.frequencies" spec="SimplexParam" value="0.25"/>
+    <parameter id="popSize" value="380.0" spec="RealScalarParam" domain="PositiveReal"/>
 
 	<run spec="MCMC" id="mcmc" chainLength="10000000"> <!--autoOptimize="true" -->
 		<state>
@@ -106,25 +112,33 @@
 
 		<distribution spec="CompoundDistribution" id="posterior">
 			<distribution spec="CompoundDistribution" id="prior">
-				<distribution id="hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@hky.kappa">
-					<distr id="LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false"
-						spec="beast.base.inference.distribution.LogNormalDistributionModel" />
-				</distribution>
-				<distribution id="hky.frequencies.prior" spec="beast.base.inference.distribution.Prior" x="@hky.frequencies">
-					<distr id="Uniform" lower="0.0" upper="1.0" spec="beast.base.inference.distribution.Uniform" />
-				</distribution>
-				<distribution id="popSize.prior" spec="beast.base.inference.distribution.Prior" x="@popSize">
-					<distr id="OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX" />
-				</distribution>
-				<distribution id="clockRate.prior" spec="beast.base.inference.distribution.Prior" x="@clockRate">
-					<distr id="Uniform2" lower="0.0" upper="100.0" spec="beast.base.inference.distribution.Uniform" />
+                <distribution id="hky.kappa.prior" spec='LogNormal' param='@hky.kappa' >
+                    <!-- M="1" S="1.25" />-->
+                    <M spec="RealScalarParam" domain="Real" value="1.0"/>
+                    <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>
+                </distribution>
+                <distribution id="hky.frequencies.prior" spec="beast.base.spec.inference.distribution.IID"
+                              param="@hky.frequencies">
+                    <distr id="Uniform" spec="beast.base.spec.inference.distribution.Uniform">
+                        <lower id="freqs.lower" spec="RealScalarParam" domain="Real" value="0.0"/>
+                        <upper id="freqs.upper" spec="RealScalarParam" domain="Real" value="1.0"/>
+                    </distr>
+                </distribution>
+                <!-- OneOnX is deprecated, test only -->
+                <distribution id="popSize.prior" spec='beast.base.spec.beast2vs1.OneOnX'
+                              param='@popSize' />
+
+				<distribution id="clockRate.prior" spec="beast.base.spec.inference.distribution.Uniform"
+                              param="@clockRate">
+                    <lower id="clockRate.lower" spec="RealScalarParam" domain="Real" value="0.0"/>
+                    <upper id="clockRate.upper" spec="RealScalarParam" domain="Real" value="100.0"/>
 				</distribution>
 
 				<distribution id="coalescent" spec="Coalescent">
 					<treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
 						<tree idref="tree" />
 					</treeIntervals>
-					<populationModel spec="ConstantPopulation">
+					<populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
 						<popSize idref="popSize" />
 					</populationModel>
 				</distribution>
@@ -132,17 +146,22 @@
 			<distribution id='likelihood' idref="treeLikelihood" />
 		</distribution>
 
-		<operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa" />
-		<operator id='frequenciesDelta' spec='DeltaExchangeOperator' delta="0.01" weight="0.1" parameter="@hky.frequencies" />
-		<operator id='popSizeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize" />
-		<operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree" />
-		<operator spec='Uniform' weight="30" tree="@tree" />
-		<operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree" />
+        <operator id='kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
+                  scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
+        <operator id='frequenciesDelta' spec='beast.base.spec.inference.operator.DeltaExchangeOperator'
+                  delta="0.01" weight="0.1" rvparameter="@hky.frequencies"/>
+        <operator id='popSizeScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
+                  scaleFactor="0.75" weight="3" parameter="@popSize"/>
+        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator'
+                  scaleFactor="0.75" weight="3" tree="@tree"/>
+        <operator spec='Uniform' weight="30" tree="@tree"/>
+        <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree" />
 		<operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree" />
 		<operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree" />
 		<operator spec='WilsonBalding' weight="3" tree="@tree" />
-		<operator spec='UpDownOperator' scaleFactor="0.75" weight="3" up="@clockRate" down="@tree" />
-		<operator id='clockRateScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@clockRate" />
+		<operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" up="@clockRate" down="@tree" />
+		<operator id='clockRateScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
+                  scaleFactor="0.75" weight="3" parameter="@clockRate" />
 
 		<logger logEvery="1000" fileName="test.$(seed).log">
 			<model idref='posterior' />
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testUCRelaxedClockLogNormal.xml b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testUCRelaxedClockLogNormal.xml
index 25472084..0e881147 100644
--- a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testUCRelaxedClockLogNormal.xml
+++ b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testUCRelaxedClockLogNormal.xml
@@ -1,8 +1,12 @@
 <beast version='2.0'
-    namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter'>
-
-
-    <!-- The sequence alignment (each sequence refers to a taxon above). -->
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
+       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
+       beast.base.evolution.operator:beast.base.spec.inference.operator:
+       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
+       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
+       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
+
+<!-- The sequence alignment (each sequence refers to a taxon above). -->
     <!-- ntax=6 nchar=768 -->
     <!-- npatterns=69 -->
     <data id="alignment" dataType="nucleotide">
@@ -28,7 +32,7 @@
 
     <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985) -->
     <input spec='HKY' id="hky">
-        <parameter name='kappa' idref='hky.kappa' />
+        <kappa idref='hky.kappa'/>
         <input id='freqs' name='frequencies' spec='Frequencies' frequencies='@hky.frequencies' />
     </input>
 
@@ -39,13 +43,13 @@
     </input>
 
 
-    <input spec='UCRelaxedClockModel' id="branchRates">
+    <input spec='beast.base.spec.evolution.branchratemodel.UCRelaxedClockModel' id="branchRates">
         <!-- <parameter name='mutationRate'>1.0</parameter> -->
-        <distr id='lognormal' spec="beast.base.inference.distribution.LogNormalDistributionModel" meanInRealSpace="true">
-            <parameter name='M' id='M' value="1" lower="0.0" />
-            <parameter name='S' id='S' value="0.3333333333333333" lower="0" />
+        <distr id='lognormal' spec="beast.base.spec.inference.distribution.LogNormal" meanInRealSpace="true">
+            <M id='M' spec="RealScalarParam" domain="Real" value="1.0"/>
+            <S id='S' spec="RealScalarParam" domain="PositiveReal" value="0.3333333333333333"/>
         </distr>
-        <parameter spec='IntegerParameter' name='rateCategories' id='rateCategories' dimension="11" value="1" />
+        <rateCategories spec='IntVectorParam' domain="NonNegativeInt" id='rateCategories' dimension="11" value="1" />
         <tree idref="tree" />
     </input> 
 
@@ -62,57 +66,69 @@
         :0.009871782435416254);'
           taxa='@alignment'/>
 
-    <parameter id="hky.kappa" value="2.0" lower="0.0" />
-    <parameter id="hky.frequencies" value="0.25" dimension="4" />
-    <parameter id="popSize" value="0.077" lower="0.0" />
+    <parameter id="hky.kappa" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
+    <parameter dimension="4" id="hky.frequencies" spec="SimplexParam" value="0.25"/>
+    <parameter id="popSize" value="0.077" spec="RealScalarParam" domain="PositiveReal"/>
 
     <run spec="MCMC" id="mcmc" chainLength="10000000"> <!--autoOptimize="true" -->
 
         <distribution spec="CompoundDistribution" id="posterior">
             <distribution spec="CompoundDistribution" id="prior">
-                <distribution id="hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@hky.kappa">
-                    <distr id="LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false"
-                        spec="beast.base.inference.distribution.LogNormalDistributionModel" />
+                <distribution id="hky.kappa.prior" spec='LogNormal' param='@hky.kappa' >
+                    <!-- M="1" S="1.25" />-->
+                    <M spec="RealScalarParam" domain="Real" value="1.0"/>
+                    <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>
                 </distribution>
-                <distribution id="hky.frequencies.prior" spec="beast.base.inference.distribution.Prior" x="@hky.frequencies">
-                    <distr id="Uniform" lower="0.0" upper="1.0" spec="beast.base.inference.distribution.Uniform" />
+                <distribution id="hky.frequencies.prior" spec="beast.base.spec.inference.distribution.IID"
+                              param="@hky.frequencies">
+                    <distr id="Uniform" spec="beast.base.spec.inference.distribution.Uniform">
+                        <lower id="freqs.lower" spec="RealScalarParam" domain="Real" value="0.0"/>
+                        <upper id="freqs.upper" spec="RealScalarParam" domain="Real" value="1.0"/>
+                    </distr>
                 </distribution>
-                <distribution id="popSize.prior" spec="beast.base.inference.distribution.Prior" x="@popSize">
-                    <distr id="OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX" />
-                </distribution>
-                <distribution id="S.prior" spec="beast.base.inference.distribution.Prior" x="@S">
-                    <distr id="Exponential" mean="0.3333333333333333" spec="beast.base.inference.distribution.Exponential" />
+                <!-- OneOnX is deprecated, test only -->
+                <distribution id="popSize.prior" spec='beast.base.spec.beast2vs1.OneOnX'
+                              param='@popSize' />
+                <distribution id="S.prior" spec="beast.base.spec.inference.distribution.Exponential"
+                              param="@S">
+                    <mean spec="RealScalarParam" domain="PositiveReal" value="0.3333333333333333"/>
                 </distribution>   
 
                 <distribution id="coalescent" spec="Coalescent">
                     <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
                         <tree idref="tree" />
                     </treeIntervals>
-                    <populationModel spec="ConstantPopulation">
-                        <popSize idref="popSize" />
+                    <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation" id='ConstantPopulation'>
+                        <popSize idref="popSize"/>
                     </populationModel>
                 </distribution>
             </distribution>
             <distribution id='likelihood' idref="treeLikelihood" />
         </distribution>
 
-        <operator id='SScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3">
-            <parameter idref="S" />
-        </operator>  
-        <operator id="CategoriesRandomWalk" spec="IntRandomWalkOperator" windowSize='1' weight="10" parameter="@rateCategories" />
-        <operator id='CategoriesSwapOperator' spec='SwapOperator' howMany="1" weight="10" intparameter='@rateCategories' />
-        <operator id='CategoriesUniform' spec='UniformOperator' weight="10" parameter='@rateCategories' /> 
-
-        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa" />
-        <operator id='frequenciesDelta' spec='DeltaExchangeOperator' delta="0.01" weight="0.1" parameter="@hky.frequencies" />
-        <operator id='popSizeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize" />
-        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree" />
+        <operator id='SScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
+                  parameter="@S" scaleFactor="0.75" weight="3"/>
+        <operator id="CategoriesRandomWalk" spec="beast.base.spec.inference.operator.IntRandomWalkOperator"
+                  parameter="@rateCategories" windowSize='1' weight="10" />
+        <operator id='CategoriesSwapOperator' spec='beast.base.spec.inference.operator.SwapOperator'
+                  intparameter='@rateCategories' howMany="1" weight="10" />
+        <operator id='CategoriesUniform' spec='beast.base.spec.inference.operator.uniform.IntUniformOperator'
+                  parameter='@rateCategories' weight="10"/>
+
+        <operator id='kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
+                  scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
+        <operator id='frequenciesDelta' spec='beast.base.spec.inference.operator.DeltaExchangeOperator'
+                  delta="0.01" weight="0.1" rvparameter="@hky.frequencies"/>
+        <operator id='popSizeScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
+                  scaleFactor="0.75" weight="3" parameter="@popSize"/>
+        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator'
+                  scaleFactor="0.75" weight="3" tree="@tree"/>
         <operator spec='Uniform' weight="30" tree="@tree" />
         <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree" />
         <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree" />
         <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree" />
         <operator spec='WilsonBalding' weight="1" tree="@tree" />
-        <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" down="@tree" /> 
+        <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" down="@tree" />
 
         <logger logEvery="10000" fileName="test.$(seed).log">
             <model idref='posterior' />
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testYuleModel_10taxa.xml b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testYuleModel_10taxa.xml
index b4053489..989bfa01 100644
--- a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testYuleModel_10taxa.xml
+++ b/beast-base/src/test/resources/beast.base/examples/beast2vs1/testYuleModel_10taxa.xml
@@ -1,7 +1,12 @@
 <?xml version="1.0" standalone="yes"?>
 <!-- test Yule birth model and Birth Death model per Gernhard 2008-->
 <beast version='2.0'
-       namespace='beast.base.evolution.speciation:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
+       beast.evolution.nuc:beast.base.evolution.alignment:
+       beast.base.evolution.operator:beast.base.spec.inference.operator:
+       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
+       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
+       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
 
     <data id="alignment" dataType="nucleotide">
         <sequence taxon="A">A</sequence>
@@ -16,18 +21,18 @@
         <sequence taxon="J">A</sequence>
     </data>
 
-    <input spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+    <input spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma' allowSampledAncestors='false' isUltrametric='true'>
         <taxa idref='alignment'/>
     </input>
 
     <!-- A prior on the distribution node heights defined given                  -->
     <!-- a Yule speciation process (a pure birth process).                       -->
-    <input spec='YuleModel' id="yule">
+    <input spec='beast.base.spec.evolution.speciation.YuleModel' id="yule">
         <birthDiffRate idref="birthRate"/>
         <tree idref='tree'/>
     </input>
 
-    <parameter id="birthRate" value="2.0" lower="0.0" upper="100.0"/>
+    <parameter id="birthRate" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
 
     <run spec='MCMC' chainLength="2000000">
         <state>
diff --git a/beast-base/src/test/resources/beast.base/examples/bitflip.xml b/beast-base/src/test/resources/beast.base/examples/bitflip.xml
index 5991c100..383b77fb 100644
--- a/beast-base/src/test/resources/beast.base/examples/bitflip.xml
+++ b/beast-base/src/test/resources/beast.base/examples/bitflip.xml
@@ -1,16 +1,17 @@
-<beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter'>
+<?xml version='1.0' encoding='UTF-8'?>
+<beast version="2.8"
+       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt">
 
-    <parameter spec='BooleanParameter' name='indicators' id='indicators' dimension="5" value="false"/>
+    <parameter name="indicators" id="indicators" dimension="5" value="false" spec="beast.base.spec.inference.parameter.BoolVectorParam"/>
 
     <run spec="MCMC" id="mcmc" chainLength="100000"> <!--autoOptimize="true"-->
         <state>
-            <input name='stateNode' idref='indicators'/>
+            <input name="stateNode" idref="indicators"/>
         </state>
 	
 	<distribution spec="CompoundDistribution" id="posterior"/>
 
-        <operator id="bitflip" spec="BitFlipOperator" weight="1">
+        <operator id="bitflip" spec="beast.base.spec.inference.operator.BitFlipOperator" weight="1">
             <input name="parameter" idref="indicators"/>
         </operator>
 
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testBSP1.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testBSP1.xml
similarity index 74%
rename from beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testBSP1.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testBSP1.xml
index 07067317..ccaaf232 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testBSP1.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testBSP1.xml
@@ -1,11 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
-       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
-       beast.base.evolution.operator:beast.base.spec.inference.operator:
-       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
-       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
-       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
 
     <!-- 17 taxa, 1485 sites, 138 patterns -->
     <data dataType="nucleotide" id="alignment">
@@ -79,7 +74,7 @@
         </sequence>
     </data>
 
-    <tree spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+    <tree spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
         <trait spec='beast.base.evolution.tree.TraitSet' traitname='date-forward' units='year'
                value='
 		D4Brazi82  = 1982,
@@ -106,43 +101,50 @@
 
     <distribution spec="CompoundDistribution" id="posterior">
         <distribution spec="CompoundDistribution" id="prior">
+<!--	
+            <distribution id="hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@hky.kappa">
+                <distr id="LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false"
+                              spec="beast.base.inference.distribution.LogNormalDistributionModel"/>
+            </distribution>
+            <distribution id="hky.frequencies.prior" spec="beast.base.inference.distribution.Prior" x="@hky.frequencies">
+                <distr id="Uniform" lower="0.0" upper="1.0" spec="beast.base.inference.distribution.Uniform"/>
+            </distribution>
+-->
 
-            <distribution spec="beast.base.spec.evolution.tree.coalescent.BayesianSkyline" id='skyline'>
+            <distribution spec="BayesianSkyline" id='skyline'>
                 <popSizes idref="skyline.popSize"/>
                 <groupSizes idref='skyline.groupSize'/>
                 <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
                     <tree idref="tree"/>
                 </treeIntervals>
             </distribution>
-
-            <distribution id='eml1' spec="beast.base.spec.inference.distribution.MarkovChainDistribution"
-				jeffreys="true" param="@skyline.popSize"/>
+            
+            <distribution id='eml1' spec="beast.base.inference.distribution.MarkovChainDistribution"
+				jeffreys="true"
+				parameter="@skyline.popSize"/>
         </distribution>
 
 		<distribution spec='TreeLikelihood' id="likelihood">
 		    <data idref="alignment"/>
 		    <tree idref="tree"/>
 			<siteModel spec='SiteModel' id="siteModel" gammaCategoryCount="4">
-                <parameter id='siteModel.alpha' name='shape' spec="RealScalarParam" domain="PositiveReal" value="5.40372E-2"/>
+				<parameter id='siteModel.alpha' name='shape' value="5.40372E-2" lower="0.0" upper="100.0"/>
 
-                <substModel spec='HKY' id="hky">
-                    <kappa id="hky.kappa" spec="RealScalarParam" domain="PositiveReal" value="21.5056"/>
-                    <frequencies id='freqs' spec='Frequencies' data="@alignment"/>
-                </substModel>
+				<substModel spec='HKY' id="hky">
+					<parameter name='kappa' id="hky.kappa" value="21.5056" lower="0.0" upper="100.0"/>
+					<frequencies id='freqs' spec='Frequencies' data="@alignment"/>
+				</substModel>
 			</siteModel>
-			<branchRateModel spec='beast.base.spec.evolution.branchratemodel.StrictClockModel' id="branchRates">
-				<parameter id="clock.rate" name='clock.rate' spec="RealScalarParam" domain="PositiveReal" value="8.8579E-4"/>
+			<branchRateModel spec='beast.base.evolution.branchratemodel.StrictClockModel' id="branchRates">
+				<parameter name='clock.rate' id='clock.rate' value="8.8579E-4" lower="0.0" upper="100.0"/>
 			</branchRateModel>
 		</distribution>
     </distribution>
 
     <run spec="MCMC" id="mcmc" chainLength="5000000">
         <state>
-            <stateNode id="skyline.popSize" spec='beast.base.spec.inference.parameter.RealVectorParam'
-                       domain="PositiveReal" dimension="5" value="380.0"/>
-            <!--  Note: for group size of BSP, need to set domain="PositiveInt" -->
-            <stateNode id='skyline.groupSize' spec='beast.base.spec.inference.parameter.IntSimplexParam'
-                       domain="PositiveInt" dimension="5" value="1"/>
+			<parameter name='stateNode' id="skyline.popSize" dimension="5" value="380.0" lower="0.0" upper="38000.0"/>
+			<stateNode spec='parameter.IntegerParameter' id='skyline.groupSize' dimension="5" value="0"/>
             <stateNode idref="hky.kappa"/>
             <stateNode idref="tree"/>
             <stateNode idref="clock.rate"/>
@@ -150,24 +152,20 @@
         </state>
 
         <distribution idref="posterior"/>
-        <operator id='kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.75" weight="1" parameter="@hky.kappa"/>
-        <operator id='clockRateScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.75" weight="3" parameter="@clock.rate"/>
-        <operator id='shapeScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.75" weight="1" parameter="@siteModel.alpha"/>
-
-<!--        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree"/>-->
-        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator'
-                  scaleFactor="0.75" weight="3" tree="@tree"/>
-        <operator spec='beast.base.evolution.operator.Uniform' weight="30" tree="@tree"/>
+        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="1" parameter="@hky.kappa"/>
+        <operator id='clockRateScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@clock.rate"/>
+        <operator id='shapeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="1" parameter="@siteModel.alpha"/>
+        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree"/>
+        <operator spec='Uniform' weight="30" tree="@tree"/>
         <operator spec='SubtreeSlide' weight="15" gaussian="true" tree="@tree"/>
         <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree"/>
         <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree"/>
         <operator spec='WilsonBalding' weight="3" tree="@tree"/>
-        <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3"
-                  up="@clock.rate" down="@tree"/>
+        <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" up="@clock.rate" down="@tree"/>
 
-        <operator id='popSizesScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.75" weight="15" parameter="@skyline.popSize"/>
-        <operator id='groupSizesDelta' spec='beast.base.spec.inference.operator.DeltaExchangeOperator'
-                  delta="1" weight="6" ivparameter="@skyline.groupSize"/>
+        <operator id='popSizesScaler' spec='ScaleOperator' scaleFactor="0.75" weight="15" parameter="@skyline.popSize"/>
+        <operator id='groupSizesDelta' spec='DeltaExchangeOperator' delta="1" weight="6" integer="true"
+                  intparameter="@skyline.groupSize"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
             <log idref="posterior"/>
@@ -197,62 +195,3 @@
     </run>
 </beast>
 
-<!--        posterior : -3865.9542466284047 +- 0.0961389601876614, ESS = 3492.604498800299, expectation is -3865.3635 +- 0.082236-->
-<!--        prior : -92.83210229903075 +- 0.08003083882360096, ESS = 3526.0536725304587, expectation is -92.178 +- 0.075174-->
-<!--        siteModel.alpha : 0.05497788953106609 +- 5.299331110248909E-4, ESS = 4359.688517553307, expectation is 0.054354 +- 5.2519E-4-->
-<!--        clock.rate : 9.458175044728434E-4 +- 2.0321064507817452E-6, ESS = 3931.1423167686116, expectation is 9.4858E-4 +- 1.9706E-6-->
-<!--        skyline.popSize.1 : 173.76402579265374 +- 29.860420930332154, ESS = 3790.3791104367774, expectation is 67.8827 +- 2.2639-->
-<!--        skyline.popSize.2 : 72.87159412926472 +- 30.305852200599514, ESS = 4293.640695139613, expectation is 25.4281 +- 0.3165-->
-<!--        skyline.popSize.3 : 39.87848820895047 +- 3.462081443420053, ESS = 4260.583420175925, expectation is 31.9271 +- 0.3819-->
-<!--        skyline.popSize.4 : 37.32718252996777 +- 0.4472310626854941, ESS = 4097.472800164088, expectation is 41.6596 +- 0.3976-->
-<!--        skyline.popSize.5 : 33.55786864929906 +- 0.550735781840017, ESS = 4057.284272072856, expectation is 33.5967 +- 0.3554-->
-<!--        skyline.groupSize.1 : 2.7127305043323706 +- 0.06306608837776836, ESS = 2398.929431240526, expectation is 2.4686 +- 0.040465-->
-<!--        skyline.groupSize.2 : 3.3061541879582315 +- 0.05994709875781661, ESS = 2772.55083764436, expectation is 3.3671 +- 0.039454-->
-<!--        skyline.groupSize.3 : 3.5143301488558096 +- 0.05338807957250786, ESS = 3592.6273024874827, expectation is 3.181 +- 0.033807-->
-<!--        skyline.groupSize.4 : 3.4534547878249278 +- 0.06293620983239555, ESS = 2705.219849449633, expectation is 3.723 +- 0.050187-->
-<!--        skyline.groupSize.5 : 3.01333037102866 +- 0.06597484934953088, ESS = 2423.979975652484, expectation is 3.2603 +- 0.059824-->
-<!--        hky.kappa : 21.61103060838405 +- 0.06324776408653743, ESS = 4501.000000000001, expectation is 21.6911 +- 0.052142-->
-<!--        likelihood : -3773.1221443293744 +- 0.05486169919391575, ESS = 3815.825171853874, expectation is -3773.1854 +- 0.039474-->
-<!--        skyline : -70.2720392679962 +- 0.055065315407511715, ESS = 3360.9793129247732, expectation is -69.725 +- 0.05435-->
-<!--        eml1 : -22.560063031034492 +- 0.052431171754551725, ESS = 2963.8139809178087, expectation is -22.453 +- 0.031115-->
-
-
-<!-- Uniform prior-->
-<!--        posterior : -3918.723673298291 +- 0.09293307120140108, ESS = 3737.03597399822, expectation is -3865.3635 +- 0.082236-->
-<!--        prior : -145.592239548388 +- 0.08139134407857418, ESS = 3330.253918111081, expectation is -92.178 +- 0.075174-->
-<!--        siteModel.alpha : 0.05575303704611519 +- 5.944657534632992E-4, ESS = 3362.732291389403, expectation is 0.054354 +- 5.2519E-4-->
-<!--        clock.rate : 9.47976581828431E-4 +- 2.1266182866295015E-6, ESS = 3444.6362179749535, expectation is 9.4858E-4 +- 1.9706E-6-->
-<!--        skyline.popSize.1 : 163.1044085425222 +- 22.593891532033254, ESS = 2321.735979191498, expectation is 67.8827 +- 2.2639-->
-<!--        skyline.popSize.2 : 50.939151229419615 +- 9.07633634051999, ESS = 1467.111240235273, expectation is 25.4281 +- 0.3165-->
-<!--        skyline.popSize.3 : 41.0104252266342 +- 4.718937661308659, ESS = 3855.6620005064383, expectation is 31.9271 +- 0.3819-->
-<!--        skyline.popSize.4 : 37.135462041283105 +- 0.4462350613992348, ESS = 3731.988309847787, expectation is 41.6596 +- 0.3976-->
-<!--        skyline.popSize.5 : 34.17745448837122 +- 0.5473854560669065, ESS = 4016.578695468486, expectation is 33.5967 +- 0.3554-->
-<!--        skyline.groupSize.1 : 2.4890024439013554 +- 0.0564806436428423, ESS = 2657.0167213248005, expectation is 2.4686 +- 0.040465-->
-<!--        skyline.groupSize.2 : 3.282159520106643 +- 0.05647092935103854, ESS = 3070.85720372171, expectation is 3.3671 +- 0.039454-->
-<!--        skyline.groupSize.3 : 3.4034658964674516 +- 0.05133295951550351, ESS = 3614.4717293796266, expectation is 3.181 +- 0.033807-->
-<!--        skyline.groupSize.4 : 3.597200622083981 +- 0.0636065492027155, ESS = 2714.9046234601724, expectation is 3.723 +- 0.050187-->
-<!--        skyline.groupSize.5 : 3.2281715174405687 +- 0.07138178790261579, ESS = 2225.0890477043995, expectation is 3.2603 +- 0.059824-->
-<!--        hky.kappa : 21.706993859867826 +- 0.06519983739530205, ESS = 4421.030218272883, expectation is 21.6911 +- 0.052142-->
-<!--        likelihood : -3773.131433749916 +- 0.05689918245086899, ESS = 3710.0809574936966, expectation is -3773.1854 +- 0.039474-->
-<!--        skyline : -70.1887676852798 +- 0.052847791629031235, ESS = 3547.545071612453, expectation is -69.725 +- 0.05435-->
-<!--        eml1 : -22.676764801144497 +- 0.05522848188228343, ESS = 2636.96968956787, expectation is -22.453 +- 0.031115-->
-
-
-<!--        posterior : -3917.9498143004666 +- 0.08565826258812939, ESS = 3915.6596753020604, expectation is -3865.3635 +- 0.082236-->
-<!--        prior : -144.92219722155576 +- 0.0716846034994167, ESS = 3702.4421228085616, expectation is -92.178 +- 0.075174-->
-<!--        siteModel.alpha : 0.05409879470678472 +- 5.083947725398481E-4, ESS = 4404.751737929933, expectation is 0.054354 +- 5.2519E-4-->
-<!--        clock.rate : 9.490971564476442E-4 +- 2.2088548142697736E-6, ESS = 3176.895074955792, expectation is 9.4858E-4 +- 1.9706E-6-->
-<!--        skyline.popSize.1 : 63.81156608863796 +- 1.6921469269889846, ESS = 4236.376838314304, expectation is 67.8827 +- 2.2639-->
-<!--        skyline.popSize.2 : 25.434787606102066 +- 0.3636549889452317, ESS = 3545.580404779142, expectation is 25.4281 +- 0.3165-->
-<!--        skyline.popSize.3 : 32.40195192030104 +- 0.3965431307420086, ESS = 3730.674552441753, expectation is 31.9271 +- 0.3819-->
-<!--        skyline.popSize.4 : 40.870729251940446 +- 0.406585858420294, ESS = 3810.877649501971, expectation is 41.6596 +- 0.3976-->
-<!--        skyline.popSize.5 : 33.87653529388686 +- 0.44469436767918263, ESS = 3962.1583904865975, expectation is 33.5967 +- 0.3554-->
-<!--        skyline.groupSize.1 : 2.512108420351033 +- 0.039466698140399714, ESS = 2797.7482686302988, expectation is 2.4686 +- 0.040465-->
-<!--        skyline.groupSize.2 : 3.374805598755832 +- 0.036870783125188336, ESS = 3467.728566706139, expectation is 3.3671 +- 0.039454-->
-<!--        skyline.groupSize.3 : 3.2448344812263943 +- 0.03324235155534377, ESS = 3958.7444794721573, expectation is 3.181 +- 0.033807-->
-<!--        skyline.groupSize.4 : 3.6665185514330147 +- 0.04135488020523446, ESS = 3399.502449281693, expectation is 3.723 +- 0.050187-->
-<!--        skyline.groupSize.5 : 3.201732948233726 +- 0.04660359139697981, ESS = 2798.2478556787314, expectation is 3.2603 +- 0.059824-->
-<!--        hky.kappa : 21.589261203122547 +- 0.06314340352206708, ESS = 4488.708350190953, expectation is 21.6911 +- 0.052142-->
-<!--        likelihood : -3773.0276170789084 +- 0.056627001899388164, ESS = 3782.5079405522606, expectation is -3773.1854 +- 0.039474-->
-<!--        skyline : -69.77661896471284 +- 0.052313445818236035, ESS = 3885.3498389520378, expectation is -69.725 +- 0.05435-->
-<!--        eml1 : -22.41887119487888 +- 0.032732487520717904, ESS = 3976.6606751683016, expectation is -22.453 +- 0.031115-->
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testBSPNoClock.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testBSPNoClock.xml
similarity index 73%
rename from beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testBSPNoClock.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testBSPNoClock.xml
index cb337366..94691f06 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testBSPNoClock.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testBSPNoClock.xml
@@ -1,10 +1,6 @@
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
-       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
-       beast.base.evolution.operator:beast.base.spec.inference.operator:
-       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
-       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
-       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter'>
+
 
     <!-- The sequence alignment (each sequence refers to a taxon above).         -->
     <!-- ntax=6 nchar=768                                                        -->
@@ -48,16 +44,14 @@
         <siteModel idref="siteModel"/>
     </input>
 
-    <input spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+    <input spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
         <taxa idref='alignment'/>
     </input>
 
-    <parameter id="hky.kappa" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
-    <parameter id="hky.frequencies" dimension="4" value="0.25" spec="SimplexParam"/>
-    <parameter id="popSizes" dimension="3" value="380.0" spec="RealVectorParam" domain="PositiveReal"/>
-<!--  groupSizes 0 ?  -->
-    <parameter id="groupSizes" dimension="3" value="1"
-               spec='beast.base.spec.inference.parameter.IntSimplexParam' domain="PositiveInt"/>
+    <parameter id="hky.kappa" value="2.0" lower="0.0"/>
+    <parameter id="hky.frequencies" value="0.25" dimension="4" lower='0.0'/>
+    <parameter id="popSizes" dimension="3" value="380.0" lower="0.0" upper="38000.0"/>
+    <input name="groupSizes" spec='IntegerParameter' id='groupSizes' dimension="3" value="0" lower='0'/>
 
     <run spec="MCMC" id="mcmc" chainLength="10000000"> <!--autoOptimize="true"-->
         <state>
@@ -70,52 +64,42 @@
 
         <distribution spec="CompoundDistribution" id="posterior">
             <distribution spec="CompoundDistribution" id="prior">
-                <distribution id="hky.kappa.prior" spec="LogNormal" param="@hky.kappa">
-                    <M spec="RealScalarParam" domain="Real" value="1.0"/>
-                    <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>
+                <distribution id="hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@hky.kappa">
+                    <distr id="LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false"
+                           spec="beast.base.inference.distribution.LogNormalDistributionModel"/>
                 </distribution>
-
-                <!-- frequencies prior -->
-                <distribution id="hky.frequencies.prior" spec="beast.base.spec.inference.distribution.IID"
-                              param="@hky.frequencies">
-                    <distr spec="beast.base.spec.inference.distribution.Uniform">
-                        <lower spec="RealScalarParam" domain="Real" value="0.0"/>
-                        <upper spec="RealScalarParam" domain="Real" value="1.0"/>
-                    </distr>
+                <distribution id="hky.frequencies.prior" spec="beast.base.inference.distribution.Prior" x="@hky.frequencies">
+                    <distr id="Uniform" lower="0.0" upper="1.0" spec="beast.base.inference.distribution.Uniform"/>
                 </distribution>
 
-                <!-- Bayesian Skyline -->
-                <distribution id="skyline" spec="beast.base.spec.evolution.tree.coalescent.BayesianSkyline">
+                <distribution spec="BayesianSkyline" id='skyline'>
                     <popSizes idref="popSizes"/>
-                    <groupSizes idref="groupSizes"/>
-                    <treeIntervals spec="beast.base.evolution.tree.TreeIntervals">
+                    <groupSizes idref='groupSizes'/>
+                    <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
                         <tree idref="tree"/>
                     </treeIntervals>
                 </distribution>
-                <!-- Jeffrey’s prior on popSizes -->
-                <distribution id="eml1" spec="beast.base.spec.inference.distribution.MarkovChainDistribution"
-                              jeffreys="true" param="@popSizes"/>
+
+                <distribution id='eml1' spec="beast.base.inference.distribution.MarkovChainDistribution"
+				jeffreys="true"
+				parameter="@popSizes"/>
             </distribution>
             <distribution id='likelihood' idref="treeLikelihood"/>
         </distribution>
 
-        <operator id="kappaScaler" spec="beast.base.spec.inference.operator.ScaleOperator"
-                  scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
-        <operator id="frequenciesDelta" spec="beast.base.spec.inference.operator.DeltaExchangeOperator"
-                  delta="0.01" weight="0.1" rvparameter="@hky.frequencies"/>
-        <operator id="popSizesScaler" spec="beast.base.spec.inference.operator.ScaleOperator"
-                  scaleFactor="0.75" weight="15" parameter="@popSizes"/>
-        <operator id="groupSizesDelta" spec="beast.base.spec.inference.operator.DeltaExchangeOperator"
-                  delta="1" weight="3" ivparameter="@groupSizes"/>
-        <operator id="treeScaler" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"
-                  scaleFactor="0.75" weight="3" tree="@tree"/>
-
+        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
+        <operator id='frequenciesDelta' spec='DeltaExchangeOperator' delta="0.01" weight="0.1"
+                  parameter="@hky.frequencies"/>
+        <operator id='popSizesScaler' spec='ScaleOperator' scaleFactor="0.75" weight="15" parameter="@popSizes"/>
+        <operator id='groupSizesDelta' spec='DeltaExchangeOperator' delta="1" weight="3" integer="true"
+                  intparameter="@groupSizes"/>
+        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree"/>
         <operator spec='Uniform' weight="30" tree="@tree"/>
         <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree"/>
         <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree"/>
         <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree"/>
         <operator spec='WilsonBalding' weight="1" tree="@tree"/>
-        <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
+        <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
             <model idref='posterior'/>
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testBirthDeathAsYule.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testBirthDeathAsYule.xml
similarity index 89%
rename from beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testBirthDeathAsYule.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testBirthDeathAsYule.xml
index 974f8597..329c847d 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testBirthDeathAsYule.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testBirthDeathAsYule.xml
@@ -1,12 +1,7 @@
 <?xml version="1.0" standalone="yes"?>
 <!-- test Yule birth model and Birth Death model per Gernhard 2008-->
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
-       beast.evolution.nuc:beast.base.evolution.alignment:
-       beast.base.evolution.operator:beast.base.spec.inference.operator:
-       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
-       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
-       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
+       namespace='beast.base.evolution.speciation:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
 
     <data id="alignment" dataType="nucleotide">
         <sequence taxon="tip1">A</sequence>
@@ -117,16 +112,16 @@
 
     <!-- A prior on the distribution node heights defined given                  -->
     <!-- a Yule speciation process (a pure birth process).                       -->
-    <input spec='beast.base.spec.evolution.speciation.BirthDeathGernhard08Model' id="birthDeath">
+    <input spec='BirthDeathGernhard08Model' id="birthDeath">
         <birthDiffRate idref="birthRate"/>
         <relativeDeathRate idref='relativeDeathRate'/>
         <sampleProbability idref="sampleProbability"/>
         <tree idref='tree'/>
     </input>
 
-    <parameter id="birthRate" value="1.0" spec="RealScalarParam" domain="PositiveReal"/>
-    <parameter id="relativeDeathRate" value="0.0" spec="RealScalarParam" domain="NonNegativeReal"/>
-    <parameter id="sampleProbability" value="1.0" spec="RealScalarParam" domain="UnitInterval"/>
+    <parameter id="birthRate" value="1.0" lower="0.0" upper="1000000.0"/>
+    <parameter id='relativeDeathRate' value='0.0' lower="0.0" upper="1.0"/>
+    <parameter id="sampleProbability" value="1.0"/>
 
     <run spec='MCMC' chainLength="1000000">
         <state>
@@ -136,11 +131,12 @@
 
         <distribution spec="CompoundDistribution" id="posterior">
             <distribution id="birthDeath.prior" idref='birthDeath'/>
-            <distribution id="birthRate.prior" spec="beast.base.spec.beast2vs1.OneOnX" param="@birthRate"/>
+            <distribution id="birthRate.prior" spec="beast.base.inference.distribution.Prior" x="@birthRate">
+                <distr id="OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX"/>
+            </distribution>
         </distribution>
 
-        <operator id='birthScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
-                  scaleFactor="0.75" weight="1" parameter="@birthRate"/>
+        <operator id='birthScaler' spec='ScaleOperator' scaleFactor="0.75" weight="1" parameter="@birthRate"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
             <model idref='posterior'/>
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testBirthDeathModel_10taxa.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testBirthDeathModel_10taxa.xml
similarity index 68%
rename from beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testBirthDeathModel_10taxa.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testBirthDeathModel_10taxa.xml
index 65ae16e3..0d1376f3 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testBirthDeathModel_10taxa.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testBirthDeathModel_10taxa.xml
@@ -1,12 +1,7 @@
 <?xml version="1.0" standalone="yes"?>
 <!-- test Yule birth model and Birth Death model per Gernhard 2008-->
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
-       beast.evolution.nuc:beast.base.evolution.alignment:
-       beast.base.evolution.operator:beast.base.spec.inference.operator:
-       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
-       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
-       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
+       namespace='beast.base.evolution.speciation:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
 
     <data id="alignment" dataType="nucleotide">
         <sequence taxon="A">A</sequence>
@@ -21,20 +16,20 @@
         <sequence taxon="J">A</sequence>
     </data>
 
-    <input spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+    <input spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
         <taxa idref='alignment'/>
     </input>
 
     <!-- A prior on the distribution node heights defined given                  -->
     <!-- a Yule speciation process (a pure birth process).                       -->
-    <input spec='beast.base.spec.evolution.speciation.BirthDeathGernhard08Model' id="birthDeath">
+    <input spec='BirthDeathGernhard08Model' id="birthDeath">
         <birthDiffRate idref="birthRate"/>
         <relativeDeathRate idref='relativeDeathRate'/>
         <tree idref='tree'/>
     </input>
 
-    <parameter id="birthRate" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
-    <parameter id="relativeDeathRate" value="0.5" spec="RealScalarParam" domain="PositiveReal"/>
+    <parameter id="birthRate" value="2.0" lower="0.0" upper="1000000.0"/>
+    <parameter id='relativeDeathRate' value='0.5' lower="0.0" upper="100.0"/>
 
     <run spec='MCMC' chainLength="2000000">
         <state>
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testCalibration.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testCalibration.xml
similarity index 71%
rename from beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testCalibration.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testCalibration.xml
index ad037d6c..f1505d82 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testCalibration.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testCalibration.xml
@@ -1,12 +1,8 @@
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
-       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
-       beast.base.evolution.operator:beast.base.spec.inference.operator:
-       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
-       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
-       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
+       namespace='beast.base.evolution.alignment:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
 
-<!-- The sequence alignment                                                  -->
+
+    <!-- The sequence alignment                                                  -->
     <!-- ntax=6 nchar=768                                                        -->
     <!-- npatterns=69                                                            -->
     <data id="alignment" dataType="nucleotide">
@@ -30,56 +26,45 @@
         </sequence>
     </data>
 
-    <parameter id="hky.kappa" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
-    <parameter dimension="4" id="hky.frequencies" spec="SimplexParam" value="0.25"/>
-    <parameter id="popSize" value="17" spec="RealScalarParam" domain="PositiveReal"/>
 
     <run spec="MCMC" id="mcmc" chainLength="10000000"> <!--autoOptimize="true"-->
-        <init spec='beast.base.spec.evolution.tree.coalescent.RandomTree' id='randomTree' initial='@tree' taxa='@alignment'>
-            <populationModel spec='beast.base.spec.evolution.tree.coalescent.ConstantPopulation' popSize='@popSize'/>
+        <init spec='beast.base.evolution.tree.coalescent.RandomTree' id='randomTree' initial='@tree' taxa='@alignment'>
+            <populationModel spec='ConstantPopulation' popSize='@popSize'/>
         </init>
 
         <state>
-            <stateNode idref='hky.kappa'/>
-            <stateNode idref='hky.frequencies'/>
-            <stateNode idref='popSize'/>
+            <stateNode spec='parameter.RealParameter' id="hky.kappa" value="2.0" lower="0.0"/>
+            <stateNode spec='parameter.RealParameter' id="hky.frequencies" value="0.25" dimension="4" lower='0.0'/>
+            <stateNode spec='parameter.RealParameter' id="popSize" value="17" lower="0.0"/>
             <stateNode spec='beast.base.evolution.tree.Tree' id='tree'/>
         </state>
 
         <distribution spec='CompoundDistribution' id='posterior'>
             <distribution spec='CompoundDistribution' id='prior'>
-                <distribution id="hky.kappa.prior" spec='LogNormal' param='@hky.kappa' >
-                    <!-- M="1" S="1.25" />-->
-                    <M spec="RealScalarParam" domain="Real" value="1.0"/>
-                    <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>
+                <distribution id="hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@hky.kappa">
+                    <distr id="LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false"
+                                  spec="beast.base.inference.distribution.LogNormalDistributionModel"/>
+                </distribution>
+                <distribution id="hky.frequencies.prior" spec="beast.base.inference.distribution.Prior" x="@hky.frequencies">
+                    <distr id="Uniform" lower="0.0" upper="1.0" spec="beast.base.inference.distribution.Uniform"/>
                 </distribution>
-                <distribution id="hky.frequencies.prior" spec="beast.base.spec.inference.distribution.IID"
-                              param="@hky.frequencies">
-                    <distr id="Uniform" spec="beast.base.spec.inference.distribution.Uniform">
-                        <lower id="freqs.lower" spec="RealScalarParam" domain="Real" value="0.0"/>
-                        <upper id="freqs.upper" spec="RealScalarParam" domain="Real" value="1.0"/>
-                    </distr>
+                <distribution id="popSize.prior" spec="beast.base.inference.distribution.Prior" x="@popSize">
+                    <distr id="OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX"/>
                 </distribution>
-                <!-- OneOnX is deprecated, test only -->
-                <distribution id="popSize.prior" spec='beast.base.spec.beast2vs1.OneOnX'
-                              param='@popSize' />
 
-                <distribution spec='beast.base.spec.evolution.tree.MRCAPrior' tree='@tree' id='HumanChimpMRCA'>
+                <distribution spec='beast.base.evolution.tree.MRCAPrior' tree='@tree' id='HumanChimpMRCA'>
                     <taxonset spec='TaxonSet' id='human,chimp'>
                         <taxon spec='Taxon' id='human'/>
                         <taxon spec='Taxon' id='chimp'/>
                     </taxonset>
-                    <distr spec='beast.base.spec.inference.distribution.Normal'>
-                        <mean spec="RealScalarParam" domain="Real" value="6.0"/>
-                        <sigma spec="RealScalarParam" domain="PositiveReal" value="0.5"/>
-                    </distr>
+                    <distr spec='beast.base.inference.distribution.Normal' mean='6.0' sigma='0.5'/>
                 </distribution>
 
                 <distribution id="coalescent" spec="Coalescent">
                     <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
                         <tree idref="tree"/>
                     </treeIntervals>
-                    <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation" id='ConstantPopulation'>
+                    <populationModel spec="ConstantPopulation" id='ConstantPopulation'>
                         <parameter name="popSize" idref="popSize"/>
                     </populationModel>
                 </distribution>
@@ -95,20 +80,17 @@
             </distribution>
         </distribution>
 
-        <operator id='kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
-                  scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
-        <operator id='frequenciesDelta' spec='beast.base.spec.inference.operator.DeltaExchangeOperator'
-                  delta="0.01" weight="0.1" rvparameter="@hky.frequencies"/>
-        <operator id='popSizeScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
-                  scaleFactor="0.75" weight="3" parameter="@popSize"/>
-        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator'
-                  scaleFactor="0.75" weight="3" tree="@tree"/>
+        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
+        <operator id='frequenciesDelta' spec='DeltaExchangeOperator' delta="0.01" weight="0.1"
+                  parameter="@hky.frequencies"/>
+        <operator id='popSizeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize"/>
+        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree"/>
         <operator spec='Uniform' weight="30" tree="@tree"/>
         <operator spec='SubtreeSlide' weight="15" gaussian="true" size="1.7" tree="@tree"/>
         <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree"/>
         <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree"/>
         <operator spec='WilsonBalding' weight="1" tree="@tree"/>
-        <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
+        <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
             <model idref='posterior'/>
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testCalibrationMono.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testCalibrationMono.xml
similarity index 70%
rename from beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testCalibrationMono.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testCalibrationMono.xml
index a33fc581..62ecbc91 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testCalibrationMono.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testCalibrationMono.xml
@@ -1,10 +1,6 @@
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
-       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
-       beast.base.evolution.operator:beast.base.spec.inference.operator:
-       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
-       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
-       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
+       namespace='beast.base.evolution.alignment:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
+
 
     <!-- The sequence alignment                                                  -->
     <!-- ntax=6 nchar=768                                                        -->
@@ -30,45 +26,36 @@
         </sequence>
     </data>
 
-    <parameter id="hky.kappa" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
-    <parameter dimension="4" id="hky.frequencies" spec="SimplexParam" value="0.25"/>
-    <parameter id="popSize" value="17" spec="RealScalarParam" domain="PositiveReal"/>
 
     <run spec="MCMC" id="mcmc" chainLength="10000000"> <!--autoOptimize="true"-->
-        <init spec='beast.base.spec.evolution.tree.coalescent.RandomTree' id='randomTree' initial='@tree' taxa='@alignment'>
-            <populationModel spec='beast.base.spec.evolution.tree.coalescent.ConstantPopulation' popSize='@popSize'/>
+        <init spec='beast.base.evolution.tree.coalescent.RandomTree' id='randomTree' initial='@tree' taxa='@alignment'>
+            <populationModel spec='ConstantPopulation' popSize='@popSize'/>
         </init>
 
         <state>
-            <stateNode idref='hky.kappa'/>
-            <stateNode idref='hky.frequencies'/>
-            <stateNode idref='popSize'/>
+            <stateNode spec='parameter.RealParameter' id="hky.kappa" value="2.0" lower="0.0"/>
+            <stateNode spec='parameter.RealParameter' id="hky.frequencies" value="0.25" dimension="4" lower='0.0'/>
+            <stateNode spec='parameter.RealParameter' id="popSize" value="17" lower="0.0"/>
             <stateNode spec='beast.base.evolution.tree.Tree' id='tree'/>
         </state>
 
         <distribution spec='CompoundDistribution' id='posterior'>
             <distribution spec='CompoundDistribution' id='prior'>
-                <distribution id="hky.kappa.prior" spec='LogNormal' param='@hky.kappa' >
-                    <!-- M="1" S="1.25" />-->
-                    <M spec="RealScalarParam" domain="Real" value="1.0"/>
-                    <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>
+                <distribution id="hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@hky.kappa">
+                    <distr id="LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false"
+                                  spec="beast.base.inference.distribution.LogNormalDistributionModel"/>
                 </distribution>
-                <distribution id="hky.frequencies.prior" spec="beast.base.spec.inference.distribution.IID"
-                              param="@hky.frequencies">
-                    <distr id="Uniform" spec="beast.base.spec.inference.distribution.Uniform">
-                        <lower id="freqs.lower" spec="RealScalarParam" domain="Real" value="0.0"/>
-                        <upper id="freqs.upper" spec="RealScalarParam" domain="Real" value="1.0"/>
-                    </distr>
+                <distribution id="hky.frequencies.prior" spec="beast.base.inference.distribution.Prior" x="@hky.frequencies">
+                    <distr id="Uniform" lower="0.0" upper="1.0" spec="beast.base.inference.distribution.Uniform"/>
+                </distribution>
+                <distribution id="popSize.prior" spec="beast.base.inference.distribution.Prior" x="@popSize">
+                    <distr id="OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX"/>
                 </distribution>
-                <!-- OneOnX is deprecated, test only -->
-                <distribution id="popSize.prior" spec='beast.base.spec.beast2vs1.OneOnX'
-                              param='@popSize' />
 
-                <distribution spec='beast.base.spec.evolution.tree.MRCAPrior' tree='@tree' id='mrcaPrior2'
-                              taxonset='@human,chimp' monophyletic='true'>
-                    <distr spec='beast.base.spec.inference.distribution.Normal'>
-                        <mean spec="RealScalarParam" domain="Real" value="6.0"/>
-                        <sigma spec="RealScalarParam" domain="PositiveReal" value="0.5"/>
+                <distribution spec='beast.base.evolution.tree.MRCAPrior' tree='@tree' id='mrcaPrior2' taxonset='@human,chimp' monophyletic='true'>
+                    <distr spec='beast.base.inference.distribution.Normal'>
+                        <parameter name='mean' value='6.0'/>
+                        <parameter name='sigma' value='0.5'/>
                     </distr>
                 </distribution>
 
@@ -76,7 +63,7 @@
                     <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
                         <tree idref="tree"/>
                     </treeIntervals>
-                    <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation" id='ConstantPopulation'>
+                    <populationModel spec="ConstantPopulation" id='ConstantPopulation'>
                         <parameter name="popSize" idref="popSize"/>
                     </populationModel>
                 </distribution>
@@ -92,27 +79,24 @@
             </distribution>
         </distribution>
 
-        <operator id='kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
-                  scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
-        <operator id='frequenciesDelta' spec='beast.base.spec.inference.operator.DeltaExchangeOperator'
-                  delta="0.01" weight="0.1" rvparameter="@hky.frequencies"/>
-        <operator id='popSizeScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
-                  scaleFactor="0.75" weight="3" parameter="@popSize"/>
-        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator'
-                  scaleFactor="0.75" weight="3" tree="@tree"/>
+        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
+        <operator id='frequenciesDelta' spec='DeltaExchangeOperator' delta="0.01" weight="0.1"
+                  parameter="@hky.frequencies"/>
+        <operator id='popSizeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize"/>
+        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree"/>
         <operator spec='Uniform' weight="30" tree="@tree"/>
         <operator spec='SubtreeSlide' weight="15" gaussian="true" size="1.7" tree="@tree"/>
         <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree"/>
         <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree"/>
         <operator spec='WilsonBalding' weight="1" tree="@tree"/>
-        <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
+        <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
             <model idref='posterior'/>
             <log idref="posterior"/>
             <log idref="prior"/>
             <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree'/>
-            <log spec='beast.base.spec.evolution.tree.MRCAPrior' tree='@tree' id='HumanChimpMRCA'>
+            <log spec='beast.base.evolution.tree.MRCAPrior' tree='@tree' id='HumanChimpMRCA'>
                 <taxonset spec='TaxonSet' id='human,chimp'>
                     <taxon spec='Taxon' id='human'/>
                     <taxon spec='Taxon' id='chimp'/>
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testCoalescentNoClock.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testCoalescentNoClock.xml
similarity index 75%
rename from beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testCoalescentNoClock.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testCoalescentNoClock.xml
index 39465000..66ecccf3 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testCoalescentNoClock.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testCoalescentNoClock.xml
@@ -1,10 +1,5 @@
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
-       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
-       beast.base.evolution.operator:beast.base.spec.inference.operator:
-       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
-       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
-       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
     <!-- equivalent to testCoalescentNoClock.xml in BEAST 1          -->
 
     <!-- The sequence alignment (each sequence refers to a taxon above).         -->
@@ -33,8 +28,8 @@
 
     <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
     <input spec='HKY' id="hky">
-        <kappa idref='hky.kappa'/>
-        <frequencies id='freqs' spec='Frequencies' frequencies='@hky.frequencies'/>
+        <parameter name='kappa' idref='hky.kappa'/>
+        <input id='freqs' name='frequencies' spec='Frequencies' frequencies='@hky.frequencies'/>
     </input>
 
     <!-- site model                                                              -->
@@ -49,14 +44,14 @@
         <siteModel idref="siteModel"/>
     </input>
 
-   <input spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+   <input spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
         <!--trait idref='rateCategories'/-->
         <taxa idref='alignment'/>
     </input>
 
-    <parameter id="hky.kappa" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
-    <parameter dimension="4" id="hky.frequencies" spec="SimplexParam" value="0.25"/>
-    <parameter id="popSize" value="0.077" spec="RealScalarParam" domain="PositiveReal"/>
+    <parameter id="hky.kappa" value="2.0" lower="0.0"/>
+    <parameter id="hky.frequencies" value="0.25" dimension="4"/>
+    <parameter id="popSize" value="0.077" lower="0.0"/>
 
     <run spec="MCMC" id="mcmc" chainLength="10000000"> <!--autoOptimize="true"-->
         <state>
@@ -68,50 +63,40 @@
 
         <distribution spec="CompoundDistribution" id="posterior">
             <distribution spec="CompoundDistribution" id="prior">
-                <distribution id="hky.kappa.prior" spec='LogNormal' param='@hky.kappa' >
-                    <!-- M="1" S="1.25" />-->
-                    <M spec="RealScalarParam" domain="Real" value="1.0"/>
-                    <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>
+                <distribution id="hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@hky.kappa">
+                    <distr id="LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false"
+                                  spec="beast.base.inference.distribution.LogNormalDistributionModel"/>
                 </distribution>
-
-                <distribution id="hky.frequencies.prior" spec="beast.base.spec.inference.distribution.IID"
-                              param="@hky.frequencies">
-                    <distr id="Uniform" spec="beast.base.spec.inference.distribution.Uniform">
-                        <lower id="freqs.lower" spec="RealScalarParam" domain="Real" value="0.0"/>
-                        <upper id="freqs.upper" spec="RealScalarParam" domain="Real" value="1.0"/>
-                    </distr>
+                <distribution id="hky.frequencies.prior" spec="beast.base.inference.distribution.Prior" x="@hky.frequencies">
+                    <distr id="Uniform" lower="0.0" upper="1.0" spec="beast.base.inference.distribution.Uniform"/>
+                </distribution>
+                <distribution id="popSize.prior" spec="beast.base.inference.distribution.Prior" x="@popSize">
+                    <distr id="OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX"/>
                 </distribution>
-
-                <!-- OneOnX is deprecated, test only -->
-                <distribution id="popSize.prior" spec='beast.base.spec.beast2vs1.OneOnX'
-                              param='@popSize' />
 
                 <distribution id="coalescent" spec="Coalescent">
                     <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
                         <tree idref="tree"/>
                     </treeIntervals>
-                    <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation" id='ConstantPopulation'>
-                        <popSize idref="popSize"/>
+                    <populationModel spec="ConstantPopulation" id='ConstantPopulation'>
+                        <parameter name="popSize" idref="popSize"/>
                     </populationModel>
                 </distribution>
             </distribution>
             <distribution id='likelihood' idref="treeLikelihood"/>
         </distribution>
 
-        <operator id='kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
-                  scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
-        <operator id='frequenciesDelta' spec='beast.base.spec.inference.operator.DeltaExchangeOperator'
-                  delta="0.01" weight="0.1" rvparameter="@hky.frequencies"/>
-        <operator id='popSizeScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
-                  scaleFactor="0.75" weight="3" parameter="@popSize"/>
-        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator'
-                  scaleFactor="0.75" weight="3" tree="@tree"/>
+        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
+        <operator id='frequenciesDelta' spec='DeltaExchangeOperator' delta="0.01" weight="0.1"
+                  parameter="@hky.frequencies"/>
+        <operator id='popSizeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize"/>
+        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree"/>
         <operator spec='Uniform' weight="30" tree="@tree"/>
         <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree"/>
         <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree"/>
         <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree"/>
         <operator spec='WilsonBalding' weight="1" tree="@tree"/>
-        <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
+        <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
             <model idref='posterior'/>
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testCoalescentNoClock1.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testCoalescentNoClock1.xml
similarity index 84%
rename from beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testCoalescentNoClock1.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testCoalescentNoClock1.xml
index 5974a9b9..48954761 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testCoalescentNoClock1.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testCoalescentNoClock1.xml
@@ -1,11 +1,6 @@
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
-       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
-       beast.base.evolution.operator:beast.base.spec.inference.operator:
-       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
-       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
-       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
-    <!-- equivalent to testCoalescentNoClock1.xml in BEAST 1 -->
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
+    <!-- equivalent to testCoalescentNoClock1.xml in BEAST 1          -->
 
     <!-- The sequence alignment (each sequence refers to a taxon above).         -->
     <!-- ntax=6 nchar=768                                                        -->
@@ -57,10 +52,10 @@
           taxa='@alignment'/>
 
 
-    <!-- Parameters -->
-    <parameter id="hky.kappa" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
-    <parameter id="hky.frequencies" dimension="4" value="0.25" spec="SimplexParam"/>
-    <parameter id="popSize" value="0.077" spec="RealScalarParam" domain="PositiveReal"/>
+    <parameter id="hky.kappa" value="2.0" lower="0.0"/>
+    <parameter id="hky.frequencies" value="0.25" dimension="4"/>
+    <parameter id="popSize" value="0.077" lower="0.0"/>
+
 
     <run spec="MCMC" id="mcmc" chainLength="20000000"> <!--autoOptimize="true"-->
         <state>
@@ -75,28 +70,25 @@
                 <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
                     <tree idref="tree"/>
                 </treeIntervals>
-                <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation" id='ConstantPopulation'>
+                <populationModel spec="ConstantPopulation" id='ConstantPopulation'>
                     <popSize idref="popSize"/>
                 </populationModel>
             </distribution>
             <distribution id='likelihood' idref="treeLikelihood"/>
         </distribution>
 
-        <operator id='kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
-                  scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
-        <operator id='frequenciesDelta' spec='beast.base.spec.inference.operator.DeltaExchangeOperator'
-                  delta="0.01" weight="0.1" rvparameter="@hky.frequencies"/>
-        <operator id='popSizeScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
-                  scaleFactor="0.75" weight="3" parameter="@popSize"/>
-        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator'
-                  scaleFactor="0.75" weight="3" tree="@tree"/>
-
+        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
+        <operator id='frequenciesDelta' spec='DeltaExchangeOperator' delta="0.01" weight="0.1"
+                  parameter="@hky.frequencies"/>
+        <operator id='popSizeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize"/>
+        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree"/>
         <operator spec='Uniform' weight="30" tree="@tree"/>
         <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree"/>
         <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree"/>
         <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree"/>
         <operator spec='WilsonBalding' weight="1" tree="@tree"/>
 
+
         <logger logEvery="1000" fileName="test.$(seed).log">
             <model idref='posterior'/>
             <log idref="posterior"/>
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testCoalescentTipDates.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testCoalescentTipDates.xml
similarity index 74%
rename from beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testCoalescentTipDates.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testCoalescentTipDates.xml
index 08f4e4b9..d4a01f57 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testCoalescentTipDates.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testCoalescentTipDates.xml
@@ -1,10 +1,5 @@
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
-       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
-       beast.base.evolution.operator:beast.base.spec.inference.operator:
-       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
-       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
-       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
 
     <data id="alignment" dataType="nucleotide">
         <sequence taxon="A">
@@ -21,7 +16,7 @@
         </sequence>
     </data>
 
-   <tree spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+   <tree spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
         <trait spec='beast.base.evolution.tree.TraitSet' traitname='date-forward' units='day'
                value='
 		A  = 5000,
@@ -33,7 +28,7 @@
         <taxa idref='alignment'/>
     </tree>
 
-    <parameter id="popSize" value="10000" spec="RealScalarParam" domain="PositiveReal"/>
+    <parameter id="popSize" value="10000" lower="0.0"/>
 
     <run spec="MCMC" id="mcmc" chainLength="1000000"> <!--autoOptimize="true"-->
         <state>
@@ -45,7 +40,7 @@
                 <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
                      <tree idref="tree"/>
                 </treeIntervals>
-                <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation" id='ConstantPopulation'>
+                <populationModel spec="ConstantPopulation" id='ConstantPopulation'>
                     <popSize idref="popSize"/>
                 </populationModel>
             </distribution>
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testCoalescentTipDates1.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testCoalescentTipDates1.xml
similarity index 74%
rename from beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testCoalescentTipDates1.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testCoalescentTipDates1.xml
index 71a7b7c6..437d0dc2 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testCoalescentTipDates1.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testCoalescentTipDates1.xml
@@ -1,10 +1,5 @@
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
-       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
-       beast.base.evolution.operator:beast.base.spec.inference.operator:
-       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
-       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
-       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
 
     <data id="alignment" dataType="nucleotide">
         <sequence taxon="A">
@@ -21,7 +16,7 @@
         </sequence>
     </data>
 
-   <tree spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+   <tree spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
         <trait spec='beast.base.evolution.tree.TraitSet' traitname='date-forward' units='day'
                value='
 		A  = 0,
@@ -33,7 +28,7 @@
 		<taxa idref='alignment'/>
     </tree>
 
-    <parameter id="popSize" value="10000" spec="RealScalarParam" domain="PositiveReal"/>
+    <parameter id="popSize" value="10000" lower="0.0"/>
 
     <run spec="MCMC" id="mcmc" chainLength="1000000"> <!--autoOptimize="true"-->
         <state>
@@ -45,7 +40,7 @@
                 <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
                      <tree idref="tree"/>
                 </treeIntervals>
-                <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation" id='ConstantPopulation'>
+                <populationModel spec="ConstantPopulation" id='ConstantPopulation'>
                     <popSize idref="popSize"/>
                 </populationModel>
             </distribution>
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testCoalescentTipDatesSampling.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testCoalescentTipDatesSampling.xml
similarity index 63%
rename from beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testCoalescentTipDatesSampling.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testCoalescentTipDatesSampling.xml
index ca707c76..eb346874 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testCoalescentTipDatesSampling.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testCoalescentTipDatesSampling.xml
@@ -1,10 +1,5 @@
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
-       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
-       beast.base.evolution.operator:beast.base.spec.inference.operator:
-       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
-       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
-       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
+       namespace='beast.base.math:beast.base.evolution.alignment:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
 
     <data id="alignment" dataType="nucleotide">
         <sequence taxon="A">
@@ -21,19 +16,19 @@
         </sequence>
     </data>
 
-   <tree spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+   <tree spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
         <trait spec='beast.base.evolution.tree.TraitSet' traitname='date-backward' units='day'
                value='
 		A  = 5000,
 		B  = 5000,
 		C  = 5000,
-		D  = 19999'>
+		D  = 5000'>
 			<taxa spec='beast.base.evolution.alignment.TaxonSet' alignment='@alignment'/>
         </trait>
 		<taxa idref='alignment'/>
     </tree>
 
-    <parameter id="popSize" value="10000" spec="RealScalarParam" domain="PositiveReal"/>
+    <parameter id="popSize" value="1000000" lower="0.0"/>
 
     <run spec="MCMC" id="mcmc" chainLength="10000000"> <!--autoOptimize="true"-->
         <state>
@@ -45,37 +40,28 @@
                 <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
                      <tree idref="tree"/>
                 </treeIntervals>
-                <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation" id='ConstantPopulation'>
+                <populationModel spec="ConstantPopulation" id='ConstantPopulation'>
                     <popSize idref="popSize"/>
                 </populationModel>
             </distribution>
 
-            <distribution id="tipDateA" monophyletic="false" spec="beast.base.spec.evolution.tree.MRCAPrior" tipsonly="true" tree="@tree">
+            <distribution id="tipDateA" monophyletic="false" spec="beast.base.evolution.tree.MRCAPrior" tipsonly="true" tree="@tree">
                 <taxonset id="TaxonSetA" spec="TaxonSet">
                     <taxon id="A" spec="Taxon"/>
                 </taxonset>
-                <distr id="Uniform0" spec="beast.base.spec.inference.distribution.Uniform">
-                    <lower id="Uniform0.lower" spec="RealScalarParam" domain="Real" value="4999"/>
-                    <upper id="Uniform0.upper" spec="RealScalarParam" domain="Real" value="5001"/>
-                </distr>
+                <distr id="Uniform0" lower="4999" offset="0.0" spec="distribution.Uniform" upper="5001"/>
             </distribution>
 
-            <distribution id="tipDateB" monophyletic="false" spec="beast.base.spec.evolution.tree.MRCAPrior" tipsonly="true" tree="@tree">
+            <distribution id="tipDateB" monophyletic="false" spec="beast.base.evolution.tree.MRCAPrior" tipsonly="true" tree="@tree">
                 <taxonset id="TaxonSetB" spec="TaxonSet">
                     <taxon id="B" spec="Taxon"/>
                 </taxonset>
-                <distr id="Normal0" spec="beast.base.spec.inference.distribution.Normal">
-                    <mean id="Normal0.mean" spec="RealScalarParam" domain="Real" value="5000"/>
-                    <sigma id="Normal0.sigma" spec="RealScalarParam" domain="PositiveReal" value="1"/>
-                </distr>
+                <distr id="Noraml0" offset="0.0" spec="distribution.Normal" mean="5000" sigma="1"/>
             </distribution>
 
-            <distribution id="rootHeight" monophyletic="false" spec="beast.base.spec.evolution.tree.MRCAPrior" tipsonly="false" tree="@tree">
+            <distribution id="rootHeight" monophyletic="false" spec="beast.base.evolution.tree.MRCAPrior" tipsonly="false" tree="@tree">
                 <taxonset id="TaxonSetAll" spec="TaxonSet" alignment="@alignment"/>
-                <distr id="Normal1" spec="beast.base.spec.inference.distribution.Normal">
-                    <mean id="Normal1.mean" spec="RealScalarParam" domain="Real" value="20000"/>
-                    <sigma id="Normal1.sigma" spec="RealScalarParam" domain="PositiveReal" value="1"/>
-                </distr>
+                <distr id="Noraml1" offset="0.0" spec="distribution.Normal" mean="20000" sigma="1"/>
             </distribution>
 
             <!--<distribution id="tipDateD" monophyletic="false" spec="beast.base.evolution.tree.MRCAPrior" tipsonly="true" tree="@tree">-->
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testEBSP.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testEBSP.xml
similarity index 93%
rename from beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testEBSP.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testEBSP.xml
index 878208ba..c9174c98 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testEBSP.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testEBSP.xml
@@ -1,11 +1,7 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
-       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
-       beast.base.evolution.operator:beast.base.spec.inference.operator:
-       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
-       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
-       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
+<beast namespace="beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood:beast.base.inference.parameter:beast.base.inference.distribution"
+       version="2.0">
+
 
     <data dataType="nucleotide" id="alignment.26" name="taxa">
         <sequence id="seq_Orthogeomys_heterodus" taxon="Orthogeomys_heterodus" totalcount="4"
@@ -179,20 +175,20 @@
         <!-- site model                                                              -->
         <input spec='SiteModel' id="siteModel$(n)" substModel='@hky$(n)'/>
 
-        <tree spec='beast.base.spec.evolution.tree.ClusterTree' id='tree$(n)' clusterType='upgma' taxa='@alignment$(n)'/>
+        <tree spec='beast.base.evolution.tree.ClusterTree' id='tree$(n)' clusterType='upgma' taxa='@alignment$(n)'/>
 
         <input spec='TreeLikelihood' id="treeLikelihood$(n)"
                data="@alignment$(n)"
                tree="@tree$(n)"
                siteModel="@siteModel$(n)"/>
 
-        <parameter id="hky.kappa$(n)" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
-        <parameter id="hky.frequencies$(n)" value="0.25" dimension="4" spec="SimplexParam"/>
+        <parameter id="hky.kappa$(n)" value="2.0" lower="0.0"/>
+        <parameter id="hky.frequencies$(n)" value="0.25" dimension="4"/>
     </plate>
 
-    <parameter id="popSizes" dimension="3" value="0.017" spec="RealVectorParam" domain="PositiveReal"/>
-    <parameter id='indicators' dimension="3" spec='BoolVectorParam' value="false"/>
-    <parameter id="populationMean" value="0.017" spec="RealScalarParam" domain="PositiveReal"/>
+    <parameter id="popSizes" value="0.017" lower="0.0"/>
+    <input name="indicators" spec='BooleanParameter' id='indicators' value="false"/>
+    <parameter id="populationMean" value="0.017" lower="0.0"/>
 
     <run spec="MCMC" id="mcmc" chainLength="10000000"> <!--autoOptimize="true"-->
         <state>
@@ -208,36 +204,30 @@
 
         <distribution id="posterior" spec="CompoundDistribution">
             <distribution id="prior" spec="CompoundDistribution">
-                <!-- OneOnX is deprecated, test only -->
-                <distribution id="populationMean.prior" spec='beast.base.spec.beast2vs1.OneOnX'
-                              param='@populationMean' />
-                <!-- Prior on sum(indicators) -->
-                <distribution spec="beast.base.spec.inference.distribution.Poisson">
-                    <lambda estimate="true" spec="RealScalarParam" domain="PositiveReal" value="0.6931471805599453"/>
-                    <param id="indsSun" spec="beast.base.spec.inference.util.AsIntScalar" domain="NonNegativeInt" >
-                         <arg spec="beast.base.spec.evolution.IntSum" arg="@indicators" />
-                    </param>
+                <distribution spec="Prior" x="@populationMean">
+                    <distr offset="0.0" spec="OneOnX"/>
                 </distribution>
-
-                <!-- Prior on popSizes -->
-                <distribution id="popPriorDist" spec="beast.base.spec.inference.distribution.IID"
-                              param="@popSizes">
-                    <distr id="popSizesExponential" spec="beast.base.spec.inference.distribution.Exponential">
-                        <mean idref="populationMean"/>
+                <distribution spec="Prior">
+                    <x arg="@indicators" id="indsSun" spec="beast.base.evolution.Sum"/>
+                    <distr offset="0.0" spec="Poisson">
+                        <parameter dimension="1" estimate="true" lower="0.0" name="lambda" upper="0.0" value="0.6931471805599453"/>
                     </distr>
                 </distribution>
+                <distribution id="populationMeanPrior" spec="Prior" x="@popSizes">
+                    <distr id="popPriorDist" mean="@populationMean" offset="0.0" spec="Exponential"/>
+                </distribution>
 
                 <distribution id="coalescent" spec="CompoundDistribution">
                     <distribution id="Coal.26" spec="Coalescent" treeIntervals="@TreeIntervals.26">
-                        <populationModel id="scaledDemo4" spec="beast.base.spec.evolution.tree.coalescent.ScaledPopulationFunction">
+                        <populationModel id="scaledDemo4" spec="beast.base.evolution.tree.coalescent.ScaledPopulationFunction">
                             <population id="demographic" populationIndicators="@indicators" populationSizes="@popSizes"
-                                        spec="beast.base.spec.evolution.tree.coalescent.CompoundPopulationFunction" type="linear"
+                                        spec="beast.base.evolution.tree.coalescent.CompoundPopulationFunction" type="linear"
                                         useIntervalsMiddle="false">
                                 <plate spec='Plate' var='n' range='.26,.29,.47'>
                                     <itree id="TreeIntervals$(n)" spec="beast.base.evolution.tree.TreeIntervals" tree="@tree$(n)"/>
                                 </plate>
                             </population>
-                            <factor value="3" spec="RealScalarParam" domain="PositiveReal"/>
+                            <parameter dimension="1" estimate="true" lower="0.0" name="factor" upper="0.0" value="3"/>
                         </populationModel>
                     </distribution>
 
@@ -246,16 +236,11 @@
                 </distribution>
 
                 <plate spec='Plate' var='n' range='.26,.29,.47'>
-                    <distribution spec="LogNormal" param="@hky.kappa$(n)">
-                        <M spec="RealScalarParam" domain="Real" value="1.0"/>
-                        <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>
+                    <distribution spec="Prior" x="@hky.kappa$(n)">
+                        <distr M="1.0" S="1.25" meanInRealSpace="false" spec="LogNormalDistributionModel"/>
                     </distribution>
-                    <distribution spec="beast.base.spec.inference.distribution.IID"
-                                  param="@hky.frequencies$(n)">
-                        <distr spec="beast.base.spec.inference.distribution.Uniform">
-                            <lower spec="RealScalarParam" domain="Real" value="0.0"/>
-                            <upper spec="RealScalarParam" domain="Real" value="1.0"/>
-                        </distr>
+                    <distribution spec="Prior" x="@hky.frequencies$(n)">
+                        <distr lower="0.0" upper="1.0" spec="beast.base.inference.distribution.Uniform"/>
                     </distribution>
                 </plate>
             </distribution>
@@ -267,17 +252,14 @@
             </distribution>
         </distribution>
 
-<!-- TODO check SampleOffValues -->
-        <operator spec="beast.base.spec.inference.operator.SampleOffValues"
-                  dist="@popSizesExponential" indicators="@indicators" values="@popSizes" weight="15.0"/>
 
-        <operator id="bitflip" parameter="@indicators" spec="beast.base.spec.inference.operator.BitFlipOperator"
-                  uniform="true" weight="30.0"/>
+        <operator id="bitflip" parameter="@indicators" spec="BitFlipOperator" uniform="true" weight="30.0"/>
+        <operator dist="@popPriorDist" indicators="@indicators" spec="beast.base.evolution.tree.coalescent.SampleOffValues"
+                  values="@popSizes" weight="15.0"/>
         <operator degreesOfFreedom="1" indicator="@indicators" parameter="@popSizes" scaleAll="false"
-                  scaleAllIndependently="false" scaleFactor="0.5" spec="beast.base.spec.inference.operator.ScaleOperator" weight="6.0"/>
-        <operator spec='beast.base.spec.inference.operator.ScaleOperator'
-                  scaleFactor="0.9" weight="3" parameter="@populationMean"/>
-        <operator scaleFactor="0.7" spec="beast.base.spec.evolution.operator.UpDownOperator" weight="30.0">
+                  scaleAllIndependently="false" scaleFactor="0.5" spec="ScaleOperator" weight="6.0"/>
+        <operator spec='ScaleOperator' scaleFactor="0.9" weight="3" parameter="@populationMean"/>
+        <operator scaleFactor="0.7" spec="UpDownOperator" weight="30.0">
             <down idref="popSizes"/>
             <down idref="populationMean"/>
             <plate spec='Plate' var='n' range='.26,.29,.47'>
@@ -286,15 +268,15 @@
         </operator>
 
         <plate spec='Plate' var='n' range='.26,.29,.47'>
-            <operator spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa$(n)"/>
-            <operator spec='beast.base.spec.inference.operator.DeltaExchangeOperator' delta="0.01" weight="0.1" parameter="@hky.frequencies$(n)"/>
-            <operator spec='beast.base.spec.evolution.operator.ScaleTreeOperator' scaleFactor="0.75" weight="3" tree="@tree$(n)"/>
+            <operator spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa$(n)"/>
+            <operator spec='DeltaExchangeOperator' delta="0.01" weight="0.1" parameter="@hky.frequencies$(n)"/>
+            <operator spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree$(n)"/>
             <operator spec='Uniform' weight="30" tree="@tree$(n)"/>
             <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree$(n)"/>
             <operator spec='Exchange' isNarrow='true' weight="15" tree="@tree$(n)"/>
             <operator spec='Exchange' isNarrow='false' weight="3" tree="@tree$(n)"/>
             <operator spec='WilsonBalding' weight="1" tree="@tree$(n)"/>
-            <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" down="@tree$(n)"/>
+            <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" down="@tree$(n)"/>
         </plate>
 
         <logger logEvery="100000" mode="autodetect">
@@ -302,7 +284,7 @@
             <log idref="prior"/>
             <log idref="likelihood"/>
             <log idref="populationMean"/>
-            <log spec="beast.base.spec.evolution.Sum" arg="@indicators"/>
+            <log spec="beast.base.evolution.Sum" arg="@indicators"/>
             <log idref="indicators"/>
             <plate spec='Plate' var='n' range='.26,.29,.47'>
                 <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree$(n)'/>
@@ -319,7 +301,7 @@
             <log idref="prior"/>
             <log idref="likelihood"/>
             <log idref="populationMean"/>
-            <log spec="beast.base.spec.evolution.Sum" arg="@indicators"/>
+            <log spec="beast.base.evolution.Sum" arg="@indicators"/>
             <log idref="indicators"/>
             <plate spec='Plate' var='n' range='.26,.29,.47'>
                 <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree$(n)'/>
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testExponentialGrowth.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testExponentialGrowth.xml
similarity index 73%
rename from beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testExponentialGrowth.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testExponentialGrowth.xml
index 66136c9e..ff659be5 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testExponentialGrowth.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testExponentialGrowth.xml
@@ -1,12 +1,8 @@
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
-       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
-       beast.base.evolution.operator:beast.base.spec.inference.operator:
-       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
-       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
-       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
-
-<!-- The sequence alignment (each sequence refers to a taxon above).         -->
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
+
+
+    <!-- The sequence alignment (each sequence refers to a taxon above).         -->
     <!-- ntax=6 nchar=768                                                        -->
     <!-- npatterns=69                                                            -->
     <data id="alignment" dataType="nucleotide">
@@ -49,15 +45,15 @@
     </input>
 
 
-    <input spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+    <input spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
         <taxa idref='alignment'/>
     </input>
 
-    <!-- Parameters -->
-    <parameter id="hky.kappa" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
-    <parameter id="hky.frequencies" dimension="4" value="0.25" spec="SimplexParam"/>
-    <parameter id="popSize" value="0.077" spec="RealScalarParam" domain="PositiveReal"/>
-    <parameter id="growthRate" value="7.7E-5" spec="RealScalarParam" domain="Real"/>
+    <parameter id="hky.kappa" value="2.0" lower="0.0"/>
+    <parameter id="hky.frequencies" value="0.25" dimension="4" lower='0.0'/>
+    <parameter id="popSize" value="0.077" lower="0.0"/>
+    <parameter id="growthRate" value="7.7E-5"/>
+
 
     <run spec="MCMC" id="mcmc" chainLength="10000000"> <!--autoOptimize="true"-->
         <state>
@@ -76,63 +72,48 @@
 
         <distribution spec="CompoundDistribution" id="posterior">
             <distribution spec="CompoundDistribution" id="prior">
-                <!-- kappa prior -->
-                <distribution id="hky.kappa.prior" spec="LogNormal" param="@hky.kappa">
-                    <M spec="RealScalarParam" domain="Real" value="1.0"/>
-                    <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>
+                <distribution id="hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@hky.kappa">
+                    <distr id="LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false"
+                                  spec="beast.base.inference.distribution.LogNormalDistributionModel"/>
                 </distribution>
-
-                <!-- frequencies prior -->
-                <distribution id="hky.frequencies.prior" spec="beast.base.spec.inference.distribution.IID" param="@hky.frequencies">
-                    <distr spec="beast.base.spec.inference.distribution.Uniform">
-                        <lower spec="RealScalarParam" domain="Real" value="0.0"/>
-                        <upper spec="RealScalarParam" domain="Real" value="1.0"/>
-                    </distr>
+                <distribution id="hky.frequencies.prior" spec="beast.base.inference.distribution.Prior" x="@hky.frequencies">
+                    <distr id="Uniform" lower="0.0" upper="1.0" spec="beast.base.inference.distribution.Uniform"/>
+                </distribution>
+                <distribution id="popSize.prior" spec="beast.base.inference.distribution.Prior" x="@popSize">
+                    <distr id="OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX"/>
                 </distribution>
 
-                <!-- popSize prior -->
-                <distribution id="popSize.prior" spec="beast.base.spec.beast2vs1.OneOnX" param="@popSize"/>
-
-                <!-- growthRate prior -->
-                <distribution id="growthRate.prior" spec="beast.base.spec.inference.distribution.Laplace"
-                              param="@growthRate">
-                    <mu spec="RealScalarParam" domain="Real" value="0.001"/>
-                    <scale spec="RealScalarParam" domain="PositiveReal" value="119.61481002566472"/>
+                <distribution id="growthRate.prior" spec="beast.base.inference.distribution.Prior" x="@growthRate">
+                    <distr id="LaplaceDistribution" mu="0.001" scale="119.61481002566472"
+                                  spec="beast.base.inference.distribution.LaplaceDistribution"/>
                 </distribution>
 
-                <!-- Coalescent -->
                 <distribution id="coalescent" spec="Coalescent">
-                    <treeIntervals spec="beast.base.evolution.tree.TreeIntervals">
+                    <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
                         <tree idref="tree"/>
                     </treeIntervals>
-                    <populationModel spec="beast.base.spec.evolution.tree.coalescent.ExponentialGrowth">
-                        <popSize idref="popSize"/>
-                        <growthRate idref="growthRate"/>
+                    <populationModel spec="ExponentialGrowth">
+                        <parameter name="popSize" idref="popSize"/>
+                        <parameter name="growthRate" idref="growthRate"/>
                     </populationModel>
                 </distribution>
-
             </distribution>
-
             <distribution id='likelihood' idref="treeLikelihood"/>
         </distribution>
 
-        <operator id='kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
-                  scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
-        <operator id='frequenciesDelta' spec='beast.base.spec.inference.operator.DeltaExchangeOperator'
-                  delta="0.01" weight="0.1" rvparameter="@hky.frequencies"/>
-        <operator id='popSizeScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
-                  scaleFactor="0.75" weight="3" parameter="@popSize"/>
-        <operator id='growthRateRandomWalk' spec='beast.base.spec.inference.operator.RealRandomWalkOperator'
-                  windowSize="1.0" weight="3" scalar="@growthRate"/>
-        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator'
-                  scaleFactor="0.75" weight="3" tree="@tree"/>
-
+        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
+        <operator id='frequenciesDelta' spec='DeltaExchangeOperator' delta="0.01" weight="0.1"
+                  parameter="@hky.frequencies"/>
+        <operator id='popSizeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize"/>
+        <operator id='growthRateRandomWalk' spec='RealRandomWalkOperator' windowSize="1.0" weight="3"
+                  parameter="@growthRate"/>
+        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree"/>
         <operator spec='Uniform' weight="30" tree="@tree"/>
         <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree"/>
         <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree"/>
         <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree"/>
         <operator spec='WilsonBalding' weight="1" tree="@tree"/>
-        <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
+        <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
             <model idref='posterior'/>
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testHKY.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testHKY.xml
similarity index 86%
rename from beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testHKY.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testHKY.xml
index f3219c5e..0461eabe 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testHKY.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testHKY.xml
@@ -1,10 +1,5 @@
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
-       beast.base.evolution.tree.coalescent:beast.evolution.nuc:
-       beast.base.evolution.operator:beast.base.spec.inference.operator:
-       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
-       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
-       beast.base.spec.evolution.likelihood'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
 
     <!-- same as testMCMC.xml in BEAST 1                                         -->
     <!-- The sequence alignment                                                  -->
@@ -31,11 +26,6 @@
         </sequence>
     </data>
 
-    <input id="hky.kappa" spec="RealScalarParam" domain="PositiveReal" value="1.0"/>
-<!--    <parameter id="hky.kappa" value="1.0" lower="0.0"/>-->
-
-<!--    <input id="freqs" spec="SimplexParam" dimension="4" value="0.25 0.25 0.25 0.25"/>-->
-
     <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
     <input spec='HKY' id='hky'>
         <kappa idref='hky.kappa'/>
@@ -55,8 +45,9 @@
         <siteModel idref="siteModel"/>
     </input>
 
+    <parameter id="hky.kappa" value="1.0" lower="0.0"/>
 
-    <tree spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+    <tree spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
         <taxa idref='alignment'/>
     </tree>
 
@@ -69,8 +60,8 @@
 
         <distribution id='likelihood' idref="treeLikelihood"/>
 
-        <operator id='kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.5" weight="1" parameter="@hky.kappa"/>
-        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator' scaleFactor="0.5" weight="1" tree="@tree"/>
+        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" parameter="@hky.kappa"/>
+        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" tree="@tree"/>
         <operator spec='Uniform' weight="10" tree="@tree"/>
         <operator spec='SubtreeSlide' weight="5" gaussian="true" size="1.0" tree="@tree"/>
         <operator id='narrow' spec='Exchange' isNarrow='true' weight="1" tree="@tree"/>
@@ -86,12 +77,12 @@
 <!--         <logger logEvery="1000" fileName="test.$(seed).trees">
             <log idref="tree"/>
         </logger>       -->
-        <logger logEvery="100000">
+        <logger logEvery="10000">
 	        <model idref='likelihood'/>
             <log idref="likelihood"/>
-    	    <ESS spec='beast.base.spec.inference.util.ESS' name='log' arg="@likelihood"/>
+    	    <ESS spec='ESS' name='log' arg="@likelihood"/>
             <log idref='hky.kappa'/>
-    	    <ESS spec='beast.base.spec.inference.util.ESS' name='log' arg="@hky.kappa"/>
+    	    <ESS spec='ESS' name='log' arg="@hky.kappa"/>
         </logger>
     </run>
 
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testMultiSubstModel.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testMultiSubstModel.xml
similarity index 79%
rename from beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testMultiSubstModel.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testMultiSubstModel.xml
index 71b3f9b7..12457576 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testMultiSubstModel.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testMultiSubstModel.xml
@@ -1,11 +1,4 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
-       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
-       beast.base.evolution.operator:beast.base.spec.inference.operator:
-       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
-       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
-       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
+<?xml version="1.0" encoding="UTF-8" standalone="no"?><beast namespace="beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.alignment:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood" version="2.0">
 
 
     <data dataType="nucleotide" filter="1-449" id="firsthalf" name="alignment" spec="FilteredAlignment" strip="false">
@@ -31,42 +24,39 @@
     <distribution id="posterior" spec="CompoundDistribution" useThreads="false">
         <distribution id="prior" spec="CompoundDistribution" useThreads="false">
             <distribution id="CoalescentConstant.firsthalf" spec="Coalescent">
-                <populationModel id="ConstantPopulation.firsthalf" spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
-                    <popSize id="popSize.firsthalf" spec="RealScalarParam" domain="PositiveReal" value="1.0" estimate="true"/>
+                <populationModel id="ConstantPopulation.firsthalf" spec="ConstantPopulation">
+                    <parameter dimension="1" estimate="true" id="popSize.firsthalf" name="popSize" value="1"/>
                 </populationModel>
                 <treeIntervals id="TreeIntervals.firsthalf" spec="beast.base.evolution.tree.TreeIntervals" tree="@Tree.firsthalf"/>
             </distribution>
-            <distribution id="KappaPrior.firsthalf" spec='LogNormal' param='@kappa.firsthalf' >
-                <!-- M="1" S="1.25" />-->
-                <M spec="RealScalarParam" domain="Real" value="1.0"/>
-                <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>
-            </distribution>
-            <distribution id="KappaPrior.secondhalf" spec='LogNormal' param='@kappa.secondhalf' >
-                <M spec="RealScalarParam" domain="Real" value="1.0"/>
-                <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>
-            </distribution>
-<!-- OneOnX is deprecated, test only -->
-            <distribution id="popSize.prior" spec='beast.base.spec.beast2vs1.OneOnX'
-                          param='@popSize.firsthalf' />
+            <distribution id="KappaPrior.firsthalf" spec="beast.base.inference.distribution.Prior" x="@kappa.firsthalf">
+                    <distr id="LogNormalDistributionModel.firsthalf" M="1.0" S="1.25" meanInRealSpace="false" spec="beast.base.inference.distribution.LogNormalDistributionModel"/>
+                </distribution>
+            <distribution id="KappaPrior.secondhalf" spec="beast.base.inference.distribution.Prior" x="@kappa.secondhalf">
+                    <distr id="LogNormalDistributionModel.secondhalf" M="1.0" S="1.25" meanInRealSpace="false" spec="beast.base.inference.distribution.LogNormalDistributionModel"/>
+                </distribution>
+            <distribution id="popSize.prior" spec="beast.base.inference.distribution.Prior" x="@popSize.firsthalf">
+                    <distr id="OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX"/>
+                </distribution>
         </distribution>
         <distribution id="likelihood" spec="CompoundDistribution" useThreads="false">
             <distribution data="@firsthalf" id="treeLikelihood.firsthalf" spec="TreeLikelihood" tree="@Tree.firsthalf" useAmbiguities="false">
                 <siteModel gammaCategoryCount="0" id="SiteModel.firsthalf" spec="SiteModel">
-                    <parameter estimate="false" id="mutationRate.firsthalf" name="mutationRate" spec="RealScalarParam" domain="PositiveReal" value="1.0"/>
-                    <parameter estimate="false" id="gammaShape.firsthalf" name="shape" spec="RealScalarParam" domain="PositiveReal" value="1.0"/>
-                    <parameter estimate="false" id="proportionInvariant.firsthalf" name="proportionInvariant" spec="RealScalarParam" domain="UnitInterval" value="0.0"/>
+                    <parameter dimension="1" estimate="false" id="mutationRate.firsthalf" name="mutationRate" value="1.0"/>
+                    <parameter dimension="1" estimate="false" id="gammaShape.firsthalf" name="shape" value="1.0"/>
+                    <parameter dimension="1" estimate="false" id="proportionInvariant.firsthalf" name="proportionInvariant" value="0.0"/>
                     <substModel id="hky.firsthalf" kappa="@kappa.firsthalf" spec="HKY">
                         <frequencies estimate="true" frequencies="@freqParameter.firsthalf" id="estimatedFreqs.firsthalf" spec="Frequencies"/>
                     </substModel>
                 </siteModel>
-                <branchRateModel clock.rate="@clockRate.firsthalf" id="StrictClock.firsthalf" spec="beast.base.spec.evolution.branchratemodel.StrictClockModel"/>
+                <branchRateModel clock.rate="@clockRate.firsthalf" id="StrictClock.firsthalf" spec="beast.base.evolution.branchratemodel.StrictClockModel"/>
             </distribution>
             <distribution branchRateModel="@StrictClock.firsthalf" id="treeLikelihood.secondhalf" spec="TreeLikelihood" tree="@Tree.firsthalf" useAmbiguities="false">
                 <data idref="secondhalf"/>
                 <siteModel gammaCategoryCount="0" id="SiteModel.secondhalf" spec="SiteModel">
-                    <parameter estimate="false" id="mutationRate.secondhalf" name="mutationRate" spec="RealScalarParam" domain="PositiveReal" value="1.0"/>
-                    <parameter estimate="false" id="gammaShape.secondhalf" name="shape" spec="RealScalarParam" domain="PositiveReal" value="1.0"/>
-                    <parameter estimate="false" id="proportionInvariant.secondhalf" name="proportionInvariant" spec="RealScalarParam" domain="UnitInterval" value="0.0"/>
+                    <parameter dimension="1" estimate="false" id="mutationRate.secondhalf" name="mutationRate" value="1.0"/>
+                    <parameter dimension="1" estimate="false" id="gammaShape.secondhalf" name="shape" value="1.0"/>
+                    <parameter dimension="1" estimate="false" id="proportionInvariant.secondhalf" name="proportionInvariant" value="0.0"/>
                     <substModel id="hky.secondhalf" kappa="@kappa.secondhalf" spec="HKY">
                         <frequencies estimate="true" frequencies="@freqParameter.secondhalf" id="estimatedFreqs.secondhalf" spec="Frequencies"/>
                     </substModel>
@@ -75,7 +65,7 @@
         </distribution>
     </distribution>
 
-<parameter id="clockRate.firsthalf" spec="RealScalarParam" domain="PositiveReal" value="1.0"/>
+<parameter dimension="1" id="clockRate.firsthalf" value="1.0"/>
     
 <run chainLength="10000000" id="mcmc" preBurnin="0" sampleFromPrior="false" spec="MCMC" storeEvery="-1">
     <state id="state" storeEvery="100000">
@@ -85,17 +75,15 @@
             </taxonset>
         </tree>
         <stateNode idref='popSize.firsthalf'/>
-        <parameter estimate="true" id="kappa.firsthalf" spec="RealScalarParam" domain="PositiveReal" name="stateNode" value="1.0"/>
-        <parameter dimension="4" estimate="true" id="freqParameter.firsthalf" spec="SimplexParam" name="stateNode" value="0.25"/>
-        <parameter estimate="true" id="kappa.secondhalf" spec="RealScalarParam" domain="PositiveReal" name="stateNode" value="1.0"/>
-        <parameter dimension="4" estimate="true" id="freqParameter.secondhalf" spec="SimplexParam" name="stateNode" value="0.25"/>
+        <parameter dimension="1" estimate="true" id="kappa.firsthalf" lower="0.0" name="stateNode" value="1.0"/>
+        <parameter dimension="4" estimate="true" id="freqParameter.firsthalf" lower="0.0" name="stateNode" upper="1.0" value="0.25"/>
+        <parameter dimension="1" estimate="true" id="kappa.secondhalf" lower="0.0" name="stateNode" value="1.0"/>
+        <parameter dimension="4" estimate="true" id="freqParameter.secondhalf" lower="0.0" name="stateNode" upper="1.0" value="0.25"/>
     </state>
 
     <distribution idref="posterior"/>
 
-    <operator degreesOfFreedom="1" id="treeScaler.firsthalf" optimise="true" rootOnly="false"
-              scaleAll="false" scaleAllIndependently="false" scaleFactor="0.75"
-              spec="ScaleOperator" tree="@Tree.firsthalf" weight="3.0"/>
+    <operator degreesOfFreedom="1" id="treeScaler.firsthalf" optimise="true" rootOnly="false" scaleAll="false" scaleAllIndependently="false" scaleFactor="0.75" spec="ScaleOperator" tree="@Tree.firsthalf" weight="3.0"/>
 
     <operator id="UniformOperator.firsthalf" spec="Uniform" tree="@Tree.firsthalf" weight="30.0"/>
 
@@ -107,25 +95,21 @@
 
     <operator id="WilsonBalding.firsthalf" spec="WilsonBalding" tree="@Tree.firsthalf" weight="3.0"/>
 
-    <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" down="@Tree.firsthalf"/>
+    <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" down="@Tree.firsthalf"/>
 
-    <operator id="KappaScaler.firsthalf" parameter="@kappa.firsthalf" scaleFactor="0.75"
-              spec="beast.base.spec.inference.operator.ScaleOperator" weight="1.0"/>
+    <operator degreesOfFreedom="1" id="KappaScaler.firsthalf" optimise="true" parameter="@kappa.firsthalf" rootOnly="false" scaleAll="false" scaleAllIndependently="false" scaleFactor="0.75" spec="ScaleOperator" weight="1.0"/>
 
-    <operator autoOptimize="true" delta="0.01" id="FrequenciesExchanger.firsthalf"
-              integer="false" spec="beast.base.spec.inference.operator.DeltaExchangeOperator" weight="0.1">
+    <operator autoOptimize="true" delta="0.01" id="FrequenciesExchanger.firsthalf" integer="false" spec="DeltaExchangeOperator" weight="0.1">
         <parameter idref="freqParameter.firsthalf"/>
     </operator>
 
-    <operator id="KappaScaler.secondhalf" parameter="@kappa.secondhalf" scaleFactor="0.75"
-              spec="beast.base.spec.inference.operator.ScaleOperator" weight="1.0"/>
+    <operator degreesOfFreedom="1" id="KappaScaler.secondhalf" optimise="true" parameter="@kappa.secondhalf" rootOnly="false" scaleAll="false" scaleAllIndependently="false" scaleFactor="0.75" spec="ScaleOperator" weight="1.0"/>
 
-    <operator autoOptimize="true" delta="0.01" id="FrequenciesExchanger.secondhalf"
-              integer="false" spec="beast.base.spec.inference.operator.DeltaExchangeOperator" weight="0.1">
+    <operator autoOptimize="true" delta="0.01" id="FrequenciesExchanger.secondhalf" integer="false" spec="DeltaExchangeOperator" weight="0.1">
         <parameter idref="freqParameter.secondhalf"/>
     </operator>
 
-    <operator id='popSizeScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize.firsthalf"/>
+    <operator id='popSizeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize.firsthalf"/>
 
     <logger fileName="test.$(seed).log" id="tracelog" logEvery="1000" mode="autodetect" model="@posterior">
         <distribution idref="posterior" name="log"/>
@@ -143,14 +127,14 @@
         <parameter idref="popSize.firsthalf" name="log"/>
     </logger>
 
-    <logger id="screenlog" logEvery="100000" mode="autodetect">
+    <logger id="screenlog" logEvery="10000" mode="autodetect">
         <distribution idref="posterior" name="log"/>
-        <log arg="@posterior" id="ESS.0" spec="beast.base.spec.inference.util.ESS"/>
+        <log arg="@posterior" id="ESS.0" spec="util.ESS"/>
         <distribution idref="likelihood" name="log"/>
         <distribution idref="prior" name="log"/>
     </logger>
 
-    <tree estimate="false" id="RandomTree.firsthalf" initial="@Tree.firsthalf" name="init" populationModel="@ConstantPopulation.firsthalf" spec="beast.base.spec.evolution.tree.coalescent.RandomTree" taxa="@firsthalf"/>
+    <tree estimate="false" id="RandomTree.firsthalf" initial="@Tree.firsthalf" name="init" populationModel="@ConstantPopulation.firsthalf" spec="beast.base.evolution.tree.coalescent.RandomTree" taxa="@firsthalf"/>
 
 </run>
 
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testRandomLocalClock.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testRandomLocalClock.xml
similarity index 70%
rename from beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testRandomLocalClock.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testRandomLocalClock.xml
index d455bde3..c084eff7 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testRandomLocalClock.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testRandomLocalClock.xml
@@ -1,12 +1,8 @@
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
-       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
-       beast.base.evolution.operator:beast.base.spec.inference.operator:
-       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
-       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
-       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter'>
 
-<!-- The sequence alignment (each sequence refers to a taxon above).         -->
+
+    <!-- The sequence alignment (each sequence refers to a taxon above).         -->
     <!-- ntax=6 nchar=768                                                        -->
     <!-- npatterns=69                                                            -->
     <data id="alignment" dataType="nucleotide">
@@ -32,7 +28,7 @@
 
     <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
     <input spec='HKY' id="hky">
-        <kappa idref='hky.kappa'/>
+        <parameter name='kappa' idref='hky.kappa'/>
         <input id='freqs' name='frequencies' spec='Frequencies' frequencies='@hky.frequencies'/>
     </input>
 
@@ -42,14 +38,14 @@
         <substModel idref='hky'/>
     </input>
 
-    <input spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+    <input spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
         <taxa idref='alignment'/>
     </input>
 
-    <input spec='beast.base.spec.evolution.branchratemodel.RandomLocalClockModel' id="branchRates" ratesAreMultipliers="false">
+    <input spec='RandomLocalClockModel' id="branchRates" ratesAreMultipliers="false">
         <!--<parameter name='mutationRate'>1.0</parameter>-->
-        <rates idref='rates'/>
-        <indicators idref='indicators'/>
+        <parameter name='rates' id='rates' value="1.0" lower='0.0'/>
+        <input name="indicators" spec='BooleanParameter' id='indicators' value="false"/>
         <tree idref="tree"/>
     </input>
 
@@ -60,11 +56,9 @@
         <branchRateModel idref="branchRates"/>
     </input>
 
-    <parameter id="hky.kappa" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
-    <parameter dimension="4" id="hky.frequencies" spec="SimplexParam" value="0.25"/>
-    <parameter id="popSize" value="0.077" spec="RealScalarParam" domain="PositiveReal"/>
-    <parameter id="rates" value="1.0" spec="RealVectorParam" domain="PositiveReal"/>
-    <parameter id='indicators' spec='BoolVectorParam' value="false"/>
+    <parameter id="hky.kappa" value="2.0" lower="0.0"/>
+    <parameter id="hky.frequencies" value="0.25" dimension="4" lower='0.0'/>
+    <parameter id="popSize" value="0.077" lower="0.0"/>
 
     <run spec="MCMC" id="mcmc" chainLength="10000000"> <!--autoOptimize="true"-->
         <state>
@@ -78,31 +72,19 @@
 
         <distribution spec="CompoundDistribution" id="posterior">
             <distribution spec="CompoundDistribution" id="prior">
-                <distribution id="hky.kappa.prior" spec='LogNormal' param='@hky.kappa' >
-                    <!-- M="1" S="1.25" />-->
-                    <M spec="RealScalarParam" domain="Real" value="1.0"/>
-                    <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>
+                <distribution id="hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@hky.kappa">
+                    <distr id="LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false"
+                                  spec="beast.base.inference.distribution.LogNormalDistributionModel"/>
                 </distribution>
-                <distribution id="hky.frequencies.prior" spec="beast.base.spec.inference.distribution.IID"
-                              param="@hky.frequencies">
-                    <distr id="Uniform" spec="beast.base.spec.inference.distribution.Uniform">
-                        <lower id="freqs.lower" spec="RealScalarParam" domain="Real" value="0.0"/>
-                        <upper id="freqs.upper" spec="RealScalarParam" domain="Real" value="1.0"/>
-                    </distr>
+                <distribution id="hky.frequencies.prior" spec="beast.base.inference.distribution.Prior" x="@hky.frequencies">
+                    <distr id="Uniform" lower="0.0" upper="1.0" spec="beast.base.inference.distribution.Uniform"/>
                 </distribution>
-                <!-- OneOnX is deprecated, test only -->
-                <distribution id="popSize.prior" spec='beast.base.spec.beast2vs1.OneOnX'
-                              param='@popSize' />
-
-                <distribution id="rates.prior" spec="beast.base.spec.inference.distribution.IID"
-                              param="@rates">
-                    <distr id="Gamma" spec="beast.base.spec.inference.distribution.Gamma">
-                        <alpha id="Gamma.alpha" spec="RealScalarParam" domain="PositiveReal" value="0.5"/>
-                        <!-- Shape–Scale -->
-                        <theta id="Gamma.theta" spec="RealScalarParam" domain="PositiveReal" value="2.0"/>
-                    </distr>
+                <distribution id="popSize.prior" spec="beast.base.inference.distribution.Prior" x="@popSize">
+                    <distr id="OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX"/>
+                </distribution>
+                <distribution id="rates.prior" spec="beast.base.inference.distribution.Prior" x="@rates">
+                    <distr id="Gamma" alpha="0.5" beta="2.0" spec="beast.base.inference.distribution.Gamma"/>
                 </distribution>
-
                 <!--<distribution id="indicators.prior" spec="beast.base.inference.distribution.Prior" x="@indicators">
                     <distribution id="Poisson" lambda="0.6931471805599453" spec="beast.base.inference.distribution.Poisson"/>
                 </distribution>-->
@@ -111,7 +93,7 @@
                     <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
                         <tree idref="tree"/>
                     </treeIntervals>
-                    <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation" id='ConstantPopulation'>
+                    <populationModel spec="ConstantPopulation" id='ConstantPopulation'>
                         <popSize idref="popSize"/>
                     </populationModel>
                 </distribution>
@@ -119,25 +101,20 @@
             <distribution id='likelihood' idref="treeLikelihood"/>
         </distribution>
 
-        <operator id="indicatorsBitFlip" spec="beast.base.spec.inference.operator.BitFlipOperator"
-                  weight="15" parameter="@indicators"/>
-        <operator id='rateScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
-                  scaleFactor="0.75" weight="15" parameter="@rates"/>
+        <operator id="indicatorsBitFlip" spec="BitFlipOperator" weight="15" parameter="@indicators"/>
+        <operator id='rateScaler' spec='ScaleOperator' scaleFactor="0.75" weight="15" parameter="@rates"/>
 
-        <operator id='kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
-                  scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
-        <operator id='frequenciesDelta' spec='beast.base.spec.inference.operator.DeltaExchangeOperator'
-                  delta="0.01" weight="0.1" rvparameter="@hky.frequencies"/>
-        <operator id='popSizeScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
-                  scaleFactor="0.75" weight="3" parameter="@popSize"/>
-        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator'
-                  scaleFactor="0.75" weight="3" tree="@tree"/>
+        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
+        <operator id='frequenciesDelta' spec='DeltaExchangeOperator' delta="0.01" weight="0.1"
+                  parameter="@hky.frequencies"/>
+        <operator id='popSizeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize"/>
+        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree"/>
         <operator spec='Uniform' weight="30" tree="@tree"/>
         <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree"/>
         <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree"/>
         <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree"/>
         <operator spec='WilsonBalding' weight="1" tree="@tree"/>
-        <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
+        <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
             <model idref='posterior'/>
diff --git a/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testSRD06CP12_3.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testSRD06CP12_3.xml
new file mode 100644
index 00000000..f0f7c97c
--- /dev/null
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testSRD06CP12_3.xml
@@ -0,0 +1,171 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<beast namespace="beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood:beast.base.evolution.branchratemodel"
+       version="2.0">
+    <!-- SRD06 model: split sequences in first together with seconds and thirds of all sites -->
+    <data id="alignment" dataType="nucleotide">
+        <sequence taxon="human">
+            AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCCTTATTTCTACTAGGACTATGAGAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTG-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCGGAGCTTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGGCCTCCATGACTTTTTCAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAATTATAGGCT-AAATCCTATATATCTTA-CACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACACCTCTTTACAGTGA
+        </sequence>
+        <sequence taxon="chimp">
+            AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTCAAATCCCCTTATTTCTACTAGGACTATAAGAATCGAACTCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTAAGCACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCTCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AACCCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCGACACCTCTTTACAGTGA
+        </sequence>
+        <sequence taxon="bonobo">
+            AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTTAAATCCCCTTATTTCTACTAGGACTATGAGAGTCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCTCTCAGTAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAGC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTTGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCCCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCAACACCTCTTTACAGTGA
+        </sequence>
+        <sequence taxon="gorilla">
+            AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGAGGTTTAAACCCCCTTATTTCTACTAGGACTATGAGAATTGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTGTCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTCACATCCTTCCCGTACTAAGAAATTTAGGTTAAACATAGACCAAGAGCCTTCAAAGCCCTTAGTAAGTTA-CAACACTTAATTTCTGTAAGGACTGCAAAACCCTACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCAATGGGACTCAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAT-TCACCTCGGAGCTTGGTAAAAAGAGGCCCAGCCTCTGTCTTTAGATTTACAGTCCAATGCCTTA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGACCTTCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAGGTTAAATTACGGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCGTTAACCTTTTAAGTTAAAGATTAAGAGTATCGGCACCTCTTTGCAGTGA
+        </sequence>
+        <sequence taxon="orangutan">
+            AGAAATATGTCTGACAAAAGAGTTACTTTGATAGAGTAAAAAATAGAGGTCTAAATCCCCTTATTTCTACTAGGACTATGGGAATTGAACCCACCCCTGAGAATCCAAAATTCTCCGTGCCACCCATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTA--CACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTCA-CAGCACTTAATTTCTGTAAGGACTGCAAAACCCCACTTTGCATCAACTGAGCGCAAATCAGCCACTTTAATTAAGCTAAGCCCTCCTAGACCGATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAT-TGGCTTCAGTCCAAAGCCCCGGCAGGCCTTAAAGCTGCTCCTTCGAATTTGCAATTCAACATGACAA-TCACCTCAGGGCTTGGTAAAAAGAGGTCTGACCCCTGTTCTTAGATTTACAGCCTAATGCCTTAACTCGGCCATTTTACCGCAAAAAAGGAAGGAATCGAACCTCCTAAAGCTGGTTTCAAGCCAACCCCATAACCCCCATGACTTTTTCAAAAGGTACTAGAAAAACCATTTCGTAACTTTGTCAAAGTTAAATTACAGGTC-AGACCCTGTGTATCTTA-CATTGCAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACCAGCCTCTCTTTGCAATGA
+        </sequence>
+        <sequence taxon="siamang">
+            AGAAATACGTCTGACGAAAGAGTTACTTTGATAGAGTAAATAACAGGGGTTTAAATCCCCTTATTTCTACTAGAACCATAGGAGTCGAACCCATCCTTGAGAATCCAAAACTCTCCGTGCCACCCGTCGCACCCTGTTCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCATACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTAACAAAACTTAATTTCTGCAAGGGCTGCAAAACCCTACTTTGCATCAACCGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCGATGGGACTTAAACCCATAAAAATTTAGTTAACAGCTAAACACCCTAAACAACCTGGCTTCAATCTAAAGCCCCGGCAGA-GTTGAAGCTGCTTCTTTGAACTTGCAATTCAACGTGAAAAATCACTTCGGAGCTTGGCAAAAAGAGGTTTCACCTCTGTCCTTAGATTTACAGTCTAATGCTTTA-CTCAGCCACTTTACCACAAAAAAGGAAGGAATCGAACCCTCTAAAACCGGTTTCAAGCCAGCCCCATAACCTTTATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATCACAGGTCCAAACCCCGTATATCTTATCACTGTAGAGCTAGACCAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACTACCGCCTCTTTACAGTGA
+        </sequence>
+    </data>
+
+    <data data="@alignment" dataType="nucleotide" filter="1::3,2::3" id="CP12" name="taxa"
+          spec="beast.base.evolution.alignment.FilteredAlignment"/>
+    <data data="@alignment" dataType="nucleotide" filter="3::3" id="CP3" name="taxa"
+          spec="beast.base.evolution.alignment.FilteredAlignment"/>
+
+    <siteModel gammaCategoryCount="4" id="CP12.siteModel" spec="SiteModel">
+        <parameter dimension="1" id="CP12.mutationRate" name="mutationRate" value="1.0" lower="0.0"/>
+        <parameter dimension="1" id="CP12.gammaShape" name="shape" value="0.5" lower="0.0" upper="1000.0"/>
+        <substModel id="CP12.hky" kappa="@CP12.hky.kappa" spec="HKY">
+            <frequencies frequencies="@CP12.frequencies" id="CP12.freqs" spec="Frequencies"/>
+        </substModel>
+    </siteModel>
+
+    <siteModel gammaCategoryCount="4" id="CP3.siteModel" spec="SiteModel">
+        <parameter dimension="1" id="CP3.mutationRate" name="mutationRate" value="1.0" lower="0.0"/>
+        <parameter dimension="1" id="CP3.gammaShape" name="shape" value="0.5" lower="0.0" upper="1000.0"/>
+        <substModel id="CP3.hky" kappa="@CP3.hky.kappa" spec="HKY">
+            <frequencies frequencies="@CP3.frequencies" id="CP3.freqs" spec="Frequencies"/>
+        </substModel>
+    </siteModel>
+
+    <input spec='StrictClockModel' id="branchRates">
+        <parameter name='clock.rate' id='clockRate' value="1.0"/>
+    </input>
+
+    <input spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+        <!--trait idref='rateCategories'/-->
+        <taxa idref='alignment'/>
+    </input>
+
+    <input spec='TreeLikelihood' id="CP12.treeLikelihood">
+        <data idref="CP12"/>
+        <tree idref="tree"/>
+        <siteModel idref="CP12.siteModel"/>
+        <branchRateModel idref="branchRates"/>
+    </input>
+
+    <input spec='TreeLikelihood' id="CP3.treeLikelihood">
+        <data idref="CP3"/>
+        <tree idref="tree"/>
+        <siteModel idref="CP3.siteModel"/>
+        <branchRateModel idref="branchRates"/>
+    </input>
+
+    <parameter id="CP12.hky.kappa" value="2.0" lower="0.0"/>
+    <parameter id="CP3.hky.kappa" value="2.0" lower="0.0"/>
+    <parameter id="CP12.frequencies" value="0.25" dimension="4" lower="0.0" upper="1.0"/>
+    <parameter id="CP3.frequencies" value="0.25" dimension="4" lower="0.0" upper="1.0"/>
+    <parameter id="popSize" value="0.077" lower="0.0"/>
+
+    <run spec="MCMC" id="mcmc" chainLength="10000000"> <!--autoOptimize="true"-->
+
+        <distribution spec="CompoundDistribution" id="posterior">
+            <distribution spec="CompoundDistribution" id="prior">
+                <distribution id="CP12.hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@CP12.hky.kappa">
+                    <distr id="CP12.LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false"
+                           spec="beast.base.inference.distribution.LogNormalDistributionModel"/>
+                </distribution>
+                <distribution id="CP12.gammaShape.prior" spec="beast.base.inference.distribution.Prior" x="@CP12.gammaShape">
+                    <distr id="CP12.gammaShape.OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX"/>
+                </distribution>
+                <distribution id="CP3.hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@CP3.hky.kappa">
+                    <distr id="CP3.LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false"
+                           spec="beast.base.inference.distribution.LogNormalDistributionModel"/>
+                </distribution>
+                <distribution id="CP3.gammaShape.prior" spec="beast.base.inference.distribution.Prior" x="@CP3.gammaShape">
+                    <distr id="CP3.gammaShape.OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX"/>
+                </distribution>
+                <distribution id="popSize.prior" spec="beast.base.inference.distribution.Prior" x="@popSize">
+                    <distr id="OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX"/>
+                </distribution>
+
+                <distribution id="coalescent" spec="Coalescent">
+                    <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
+                        <tree idref="tree"/>
+                    </treeIntervals>
+                    <populationModel spec="ConstantPopulation">
+                        <popSize idref="popSize"/>
+                    </populationModel>
+                </distribution>
+            </distribution>
+            <distribution spec="CompoundDistribution" id='likelihood'>
+                <distribution idref="CP12.treeLikelihood"/>
+                <distribution idref="CP3.treeLikelihood"/>
+            </distribution>
+        </distribution>
+
+        <operator id='compMuDelta' spec='DeltaExchangeOperator' delta="0.75" weightvector="512 256" weight="2">
+            <parameter idref="CP12.mutationRate"/>
+            <parameter idref="CP3.mutationRate"/>
+        </operator>
+
+        <operator id='CP12kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1"
+                  parameter="@CP12.hky.kappa"/>
+        <operator id='CP12frequenciesDelta' spec='DeltaExchangeOperator' delta="0.01" weight="0.1"
+                  parameter="@CP12.frequencies"/>
+        <operator id='CP3kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@CP3.hky.kappa"/>
+        <operator id='CP3frequenciesDelta' spec='DeltaExchangeOperator' delta="0.01" weight="0.1"
+                  parameter="@CP3.frequencies"/>
+        <operator id='CP12alphaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1"
+                  parameter="@CP12.gammaShape"/>
+        <operator id='CP3alphaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@CP3.gammaShape"/>
+        <operator id='popSizeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize"/>
+        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree"/>
+        <operator spec='Uniform' weight="30" tree="@tree"/>
+        <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree"/>
+        <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree"/>
+        <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree"/>
+        <operator spec='WilsonBalding' weight="1" tree="@tree"/>
+        <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
+
+        <logger logEvery="1000" fileName="test.$(seed).log">
+            <model idref='posterior'/>
+            <log idref="posterior"/>
+            <log idref="prior"/>
+            <log idref="likelihood"/>
+            <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree'/>
+            <log idref="popSize"/>
+            <log idref="CP12.hky.kappa"/>
+            <log idref="CP3.hky.kappa"/>
+            <log idref="CP12.frequencies"/>
+            <log idref="CP3.frequencies"/>
+            <log idref="CP12.gammaShape"/>
+            <log idref="CP3.gammaShape"/>
+            <log idref="CP12.mutationRate"/>
+            <log idref="CP3.mutationRate"/>
+            <log idref="clockRate"/>
+            <log idref="CP12.treeLikelihood"/>
+            <log idref="CP3.treeLikelihood"/>
+            <log idref="coalescent"/>
+        </logger>
+        <!--         <logger logEvery="1000" fileName="test.$(seed).trees">
+    <log idref="tree"/>
+</logger>        -->
+        <logger logEvery="100000">
+            <model idref='posterior'/>
+            <log idref="posterior"/>
+            <log idref="prior"/>
+            <log idref="likelihood"/>
+            <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree'/>
+            <log idref="popSize"/>
+            <log idref="coalescent"/>
+        </logger>
+    </run>
+
+</beast>
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testSiteModelAlpha.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testSiteModelAlpha.xml
similarity index 91%
rename from beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testSiteModelAlpha.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testSiteModelAlpha.xml
index 911190a5..94ae74e2 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testSiteModelAlpha.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testSiteModelAlpha.xml
@@ -1,11 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
-       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
-       beast.base.evolution.operator:beast.base.spec.inference.operator:
-       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
-       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
-       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood:beast.base.evolution.branchratemodel'>
 
     <!-- 17 taxa, 1485 sites, 138 patterns -->
     <data dataType="nucleotide" id="alignment">
@@ -75,7 +70,7 @@
 
     </data>
 
-    <tree spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+    <tree spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
         <trait spec='beast.base.evolution.tree.TraitSet' traitname='date-forward' units='year'
                value='
 		TREESPARROW_HENAN_1_2004=2004.0,
@@ -99,22 +94,22 @@
 		PEREGRINEFALCON_HK_D0028_2004=2004.0,
 		TREESPARROW_HENAN_2_2004=2004.0,
 		HONGKONG_538_1997=1997.0'>
-            <taxa spec='beast.base.evolution.alignment.TaxonSet' alignment='@alignment'/>
+		<taxa spec='beast.base.evolution.alignment.TaxonSet' alignment='@alignment'/>
         </trait>
         <taxa idref='alignment'/>
     </tree>
 
     <siteModel spec='SiteModel' id="siteModel" gammaCategoryCount="4">
-        <parameter id='siteModel.alpha' name='shape' spec="RealScalarParam" domain="PositiveReal" value="0.05"/>
+        <parameter id='siteModel.alpha' name='shape' value="0.05" lower="0.0" upper="100.0"/>
 
         <substModel spec='HKY' id="hky">
-            <kappa id="hky.kappa" spec="RealScalarParam" domain="PositiveReal" value="2.0"/>
+            <parameter name='kappa' id="hky.kappa" value="2.0" lower="0.0" upper="100.0"/>
             <frequencies id='freqs' spec='Frequencies' data="@alignment"/>
         </substModel>
     </siteModel>
 
-    <input spec='beast.base.spec.evolution.branchratemodel.StrictClockModel' id="branchRates">
-        <parameter id="clockRate" name='clock.rate' spec="RealScalarParam" domain="PositiveReal" value="4.0E-4"/>
+    <input spec='StrictClockModel' id="branchRates">
+        <parameter name='clock.rate' id='clockRate' value="4.0E-4"/>
     </input>
 
     <input spec='TreeLikelihood' id="treeLikelihood">
@@ -124,7 +119,7 @@
         <branchRateModel idref="branchRates"/>
     </input>
 
-    <parameter id="popSize" spec="RealScalarParam" domain="PositiveReal" value="380.0"/>
+    <parameter id="popSize" value="380.0" lower="0.0" upper="38000.0"/>
 
     <run spec="MCMC" id="mcmc" chainLength="5000000"> <!--autoOptimize="true"-->
         <state>
@@ -136,43 +131,40 @@
         </state>
 
         <distribution spec="CompoundDistribution" id="posterior">
-<!--use Uniform or TruncatedDistribution to replace bounds -->
-<!--            <distribution id="shape.prior" spec="beast.base.spec.inference.distribution.Uniform" param="@siteModel.alpha">-->
-<!--                <lower id="shape.lower" spec="RealScalarParam" domain="Real" value="0.001"/>-->
-<!--                <upper id="shape.upper" spec="RealScalarParam" domain="Real" value="100.0"/>-->
-<!--            </distribution>-->
-<!--            <distribution id="kappa.prior" spec="beast.base.spec.inference.distribution.Uniform" param="@hky.kappa">-->
-<!--                <lower id="kappa.lower" spec="RealScalarParam" domain="Real" value="0.001"/>-->
-<!--                <upper id="kappa.upper" spec="RealScalarParam" domain="Real" value="100.0"/>-->
-<!--            </distribution>-->
-<!--            <distribution id="popSize.prior" spec="beast.base.spec.inference.distribution.Uniform" param="@popSize">-->
-<!--                <lower id="popSize.lower" spec="RealScalarParam" domain="Real" value="0.001"/>-->
-<!--                <upper id="popSize.upper" spec="RealScalarParam" domain="Real" value="38000.0"/>-->
-<!--            </distribution>-->
+            <!--<distribution spec="CompoundDistribution" id="prior">-->
+                <!--<distribution id="hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@hky.kappa">-->
+                <!--<distr id="LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false" spec="beast.base.inference.distribution.LogNormalDistributionModel"/>-->
+                <!--</distribution>-->
+                <!--<distribution id="hky.frequencies.prior" spec="beast.base.inference.distribution.Prior" x="@hky.frequencies">-->
+                <!--<distr id="Uniform" lower="0.0" upper="1.0" spec="beast.base.inference.distribution.Uniform"/>-->
+                <!--</distribution>-->
+                <!--<distribution id="popSize.prior" spec="beast.base.inference.distribution.Prior" x="@popSize">-->
+                <!--<distr id="OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX"/>-->
+                <!--</distribution>-->
 
-            <distribution id="coalescent" spec="Coalescent">
-                <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
-                    <tree idref="tree"/>
-                </treeIntervals>
-                <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
-                    <popSize idref="popSize"/>
-                </populationModel>
-            </distribution>
+                <distribution id="coalescent" spec="Coalescent">
+                    <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
+                        <tree idref="tree"/>
+                    </treeIntervals>
+                    <populationModel spec="ConstantPopulation">
+                        <popSize idref="popSize"/>
+                    </populationModel>
+                </distribution>
             <!--</distribution>-->
             <distribution id='likelihood' idref="treeLikelihood"/>
         </distribution>
 
-        <operator id='kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.75" weight="1" parameter="@hky.kappa"/>
-        <operator id='shapeScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.75" weight="1" parameter="@siteModel.alpha"/>
-        <operator id='clockRateScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.5" weight="1" parameter="@clockRate"/>
-        <operator id='popSizeScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize"/>
-        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator' scaleFactor="0.75" weight="3" tree="@tree"/>
+        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="1" parameter="@hky.kappa"/>
+        <operator id='shapeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="1" parameter="@siteModel.alpha"/>
+        <operator id='clockRateScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" parameter="@clockRate"/>
+        <operator id='popSizeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize"/>
+        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree"/>
         <operator spec='Uniform' weight="30" tree="@tree"/>
         <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree"/>
         <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree"/>
         <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree"/>
         <operator spec='WilsonBalding' weight="1" tree="@tree"/>
-        <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" up="@clockRate" down="@tree"/>
+        <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" up="@clockRate" down="@tree"/>
 
         <logger logEvery="500" fileName="test.$(seed).log">
             <model idref='posterior'/>
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testStarBEAST.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testStarBEAST.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/beast2vs1/testStarBEAST.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testStarBEAST.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testStarBEASTConstant.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testStarBEASTConstant.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/beast2vs1/testStarBEASTConstant.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testStarBEASTConstant.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testStarBEASTLinear.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testStarBEASTLinear.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/beast2vs1/testStarBEASTLinear.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testStarBEASTLinear.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testStarBEASTLinearConstRoot.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testStarBEASTLinearConstRoot.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/beast2vs1/testStarBEASTLinearConstRoot.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testStarBEASTLinearConstRoot.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testStarBeast2.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testStarBeast2.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/beast2vs1/testStarBeast2.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testStarBeast2.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testStrictClock.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testStrictClock.xml
similarity index 75%
rename from beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testStrictClock.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testStrictClock.xml
index 774e2fd5..15d3e93a 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testStrictClock.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testStrictClock.xml
@@ -1,12 +1,7 @@
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
-       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
-       beast.base.evolution.operator:beast.base.spec.inference.operator:
-       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
-       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
-       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter'>
 
-<!-- same as testStrictClockNoDate.xml in BEAST 1                            -->
+    <!-- same as testStrictClockNoDate.xml in BEAST 1                            -->
     <!-- The sequence alignment (each sequence refers to a taxon above).         -->
     <!-- ntax=6 nchar=768                                                        -->
     <!-- npatterns=69                                                            -->
@@ -33,7 +28,7 @@
 
     <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
     <input spec='HKY' id="hky">
-        <kappa idref='hky.kappa'/>
+        <parameter name='kappa' idref='hky.kappa'/>
         <input id='freqs' name='frequencies' spec='Frequencies' frequencies='@hky.frequencies'/>
     </input>
 
@@ -43,8 +38,9 @@
         <substModel idref='hky'/>
     </input>
 
-    <input spec='beast.base.spec.evolution.branchratemodel.StrictClockModel' id="branchRates">
-        <clock.rate id='clockRate' value="1.0" spec="RealScalarParam" domain="PositiveReal"/>
+
+    <input spec='StrictClockModel' id="branchRates">
+        <parameter name='clock.rate' id='clockRate' value="1.0"/>
     </input>
 
     <input spec='TreeLikelihood' id="treeLikelihood">
@@ -54,14 +50,14 @@
         <branchRateModel idref="branchRates"/>
     </input>
 
-    <input spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+    <input spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
         <!--trait idref='rateCategories'/-->
         <taxa idref='alignment'/>
     </input>
 
-    <parameter id="hky.kappa" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
-    <parameter dimension="4" id="hky.frequencies" spec="SimplexParam" value="0.25"/>
-    <parameter id="popSize" value="0.077" spec="RealScalarParam" domain="PositiveReal"/>
+    <parameter id="hky.kappa" value="2.0" lower="0.0"/>
+    <parameter id="hky.frequencies" value="0.25" dimension="4"/>
+    <parameter id="popSize" value="0.077" lower="0.0"/>
 
     <run spec="MCMC" id="mcmc" chainLength="10000000"> <!--autoOptimize="true"-->
         <state>
@@ -73,29 +69,21 @@
 
         <distribution spec="CompoundDistribution" id="posterior">
             <distribution spec="CompoundDistribution" id="prior">
-                <distribution id="hky.kappa.prior" spec='LogNormal' param='@hky.kappa' >
-                    <!-- M="1" S="1.25" />-->
-                    <M spec="RealScalarParam" domain="Real" value="1.0"/>
-                    <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>
+                <distribution id="hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@hky.kappa">
+                    <distr id="LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false" spec="beast.base.inference.distribution.LogNormalDistributionModel"/>
                 </distribution>
-
-                <distribution id="hky.frequencies.prior" spec="beast.base.spec.inference.distribution.IID"
-                              param="@hky.frequencies">
-                    <distr id="Uniform" spec="beast.base.spec.inference.distribution.Uniform">
-                        <lower id="freqs.lower" spec="RealScalarParam" domain="Real" value="0.0"/>
-                        <upper id="freqs.upper" spec="RealScalarParam" domain="Real" value="1.0"/>
-                    </distr>
+                <distribution id="hky.frequencies.prior" spec="beast.base.inference.distribution.Prior" x="@hky.frequencies">
+                    <distr id="Uniform" lower="0.0" upper="1.0" spec="beast.base.inference.distribution.Uniform"/>
+                </distribution>
+                <distribution id="popSize.prior" spec="beast.base.inference.distribution.Prior" x="@popSize">
+                    <distr id="OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX"/>
                 </distribution>
-
-                <!-- OneOnX is deprecated, test only -->
-                <distribution id="popSize.prior" spec='beast.base.spec.beast2vs1.OneOnX'
-                              param='@popSize' />
 
                 <distribution id="coalescent" spec="Coalescent">
                     <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
                         <tree idref="tree"/>
                     </treeIntervals>
-                    <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation" id='ConstantPopulation'>
+                    <populationModel spec="ConstantPopulation">
                         <popSize idref="popSize"/>
                     </populationModel>
                 </distribution>
@@ -103,20 +91,17 @@
             <distribution id='likelihood' idref="treeLikelihood"/>
         </distribution>
 
-        <operator id='kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
-                  scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
-        <operator id='frequenciesDelta' spec='beast.base.spec.inference.operator.DeltaExchangeOperator'
-                  delta="0.01" weight="0.1" rvparameter="@hky.frequencies"/>
-        <operator id='popSizeScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
-                  scaleFactor="0.75" weight="3" parameter="@popSize"/>
-        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator'
-                  scaleFactor="0.75" weight="3" tree="@tree"/>
+        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
+        <operator id='frequenciesDelta' spec='DeltaExchangeOperator' delta="0.01" weight="0.1"
+                  parameter="@hky.frequencies"/>
+        <operator id='popSizeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize"/>
+        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree"/>
         <operator spec='Uniform' weight="30" tree="@tree"/>
         <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree"/>
         <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree"/>
         <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree"/>
         <operator spec='WilsonBalding' weight="1" tree="@tree"/>
-        <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
+        <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
             <model idref='posterior'/>
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testStrictClock2.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testStrictClock2.xml
similarity index 79%
rename from beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testStrictClock2.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testStrictClock2.xml
index 470e124b..e8507116 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testStrictClock2.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testStrictClock2.xml
@@ -1,12 +1,7 @@
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
-       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
-       beast.base.evolution.operator:beast.base.spec.inference.operator:
-       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
-       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
-       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter'>
 
-<!-- same as testStrictClockNoDate2.xml in BEAST 1                            -->
+    <!-- same as testStrictClockNoDate2.xml in BEAST 1                            -->
     <!-- The sequence alignment (each sequence refers to a taxon above).         -->
     <!-- ntax=6 nchar=768                                                        -->
     <!-- npatterns=69                                                            -->
@@ -33,7 +28,7 @@
 
     <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
     <input spec='HKY' id="hky">
-        <kappa idref='hky.kappa'/>
+        <parameter name='kappa' idref='hky.kappa'/>
         <frequencies id='freqs' spec='Frequencies'>
             <data idref='alignment'/>
         </frequencies>
@@ -46,8 +41,8 @@
     </input>
 
 
-    <input spec='beast.base.spec.evolution.branchratemodel.StrictClockModel' id="branchRates">
-        <clock.rate id='clockRate' value="1.0" spec="RealScalarParam" domain="PositiveReal"/>
+    <input spec='StrictClockModel' id="branchRates">
+        <parameter name='clock.rate' id='clockRate' value="1.0"/>
     </input>
 
     <input spec='TreeLikelihood' id="treeLikelihood">
@@ -57,13 +52,13 @@
         <branchRateModel idref="branchRates"/>
     </input>
 
-    <input spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+    <input spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
         <!--trait idref='rateCategories'/-->
         <taxa idref='alignment'/>
     </input>
 
-    <parameter id="hky.kappa" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
-    <parameter id="popSize" value="0.077" spec="RealScalarParam" domain="PositiveReal"/>
+    <parameter id="hky.kappa" value="2.0" lower="0.0"/>
+    <parameter id="popSize" value="0.077" lower="0.0"/>
 
     <run spec="MCMC" id="mcmc" chainLength="10000000"> <!--autoOptimize="true"-->
         <state>
@@ -74,21 +69,19 @@
 
         <distribution spec="CompoundDistribution" id="posterior">
             <distribution spec="CompoundDistribution" id="prior">
-                <distribution id="hky.kappa.prior" spec='LogNormal' param='@hky.kappa' >
-                    <!-- M="1" S="1.25" />-->
-                    <M spec="RealScalarParam" domain="Real" value="1.0"/>
-                    <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>
+                <distribution id="hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@hky.kappa">
+                    <distr id="LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false"
+                                  spec="beast.base.inference.distribution.LogNormalDistributionModel"/>
+                </distribution>
+                <distribution id="popSize.prior" spec="beast.base.inference.distribution.Prior" x="@popSize">
+                    <distr id="OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX"/>
                 </distribution>
-
-                <!-- OneOnX is deprecated, test only -->
-                <distribution id="popSize.prior" spec='beast.base.spec.beast2vs1.OneOnX'
-                              param='@popSize' />
 
                 <distribution id="coalescent" spec="Coalescent">
                     <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
                         <tree idref="tree"/>
                     </treeIntervals>
-                    <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation" id='ConstantPopulation'>
+                    <populationModel spec="ConstantPopulation">
                         <popSize idref="popSize"/>
                     </populationModel>
                 </distribution>
@@ -96,18 +89,15 @@
             <distribution id='likelihood' idref="treeLikelihood"/>
         </distribution>
 
-        <operator id='kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
-                  scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
-        <operator id='popSizeScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
-                  scaleFactor="0.75" weight="3" parameter="@popSize"/>
-        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator'
-                  scaleFactor="0.75" weight="3" tree="@tree"/>
+        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
+        <operator id='popSizeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize"/>
+        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree"/>
         <operator spec='Uniform' weight="30" tree="@tree"/>
         <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree"/>
         <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree"/>
         <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree"/>
         <operator spec='WilsonBalding' weight="1" tree="@tree"/>
-        <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
+        <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
             <model idref='posterior'/>
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testStrictClockTipDatesSampling.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testStrictClockTipDatesSampling.xml
similarity index 91%
rename from beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testStrictClockTipDatesSampling.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testStrictClockTipDatesSampling.xml
index 1198b0ac..c0de665a 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testStrictClockTipDatesSampling.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testStrictClockTipDatesSampling.xml
@@ -1,12 +1,7 @@
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
-       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
-       beast.base.evolution.operator:beast.base.spec.inference.operator:
-       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
-       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
-       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
-
-<!-- 17 taxa, 1485 sites, 138 patterns -->
+       namespace='beast.base.math:beast.base.evolution.alignment:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter'>
+
+    <!-- 17 taxa, 1485 sites, 138 patterns -->
     <data dataType="nucleotide" id="alignment">
         <sequence taxon="TREESPARROW_HENAN_1_2004">
             ATGGAGAAAATAGTGCTTCTTCGTGCAATGATCAATCTTGTTAAAAGTGATCAGATTGGCGTTGGTTACCATGCAGACTACTCGACAGAGCAGGGTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATATTGGAAAAGACACACAACGGGAAGCTCTGCGACCTAGATGGAGTGAAGCCTCTAATTTTGAAAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTGACGAATTCATCAATGTGCCGGAGTGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAAAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCGATCATGAAGCCTCATCAGGGGTGAGCTCAGCATGTCCATACCTGGGGAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTACATACCCAACAATAAAGAGGGGCTACAATAATACCAACCCAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGGAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCAAAGTAAATGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGACGCTATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACCAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACAGGGCTCAGAAATAGCCCTCAAAGAGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAAGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAAAATTTAAACAAGAAGATGGAGGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGAAAAGGTCCGACTACAACTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT
@@ -74,7 +69,7 @@
 
     </data>
 
-    <tree spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+    <tree spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
         <trait spec='beast.base.evolution.tree.TraitSet' traitname='date-forward' units='year'
                value='
 		TREESPARROW_HENAN_1_2004=2004.0,
@@ -115,7 +110,7 @@
         <substModel idref='hky'/>
     </input>
 
-    <input spec='beast.base.spec.evolution.branchratemodel.StrictClockModel' id="branchRates">
+    <input spec='StrictClockModel' id="branchRates">
         <clock.rate idref='clockRate'/>
     </input>
 
@@ -126,13 +121,12 @@
         <branchRateModel idref="branchRates"/>
     </input>
 
-    <parameter id='clockRate' value="2.3E-5" spec="RealScalarParam" domain="PositiveReal" />
-    <parameter id="hky.kappa" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
-    <parameter dimension="4" id="hky.frequencies" spec="SimplexParam" value="0.25"/>
-    <parameter id="popSize" value="380.0" spec="RealScalarParam" domain="PositiveReal"/>
+    <parameter id="hky.kappa" value="2.0" lower="0.0"/>
+    <parameter id="hky.frequencies" value="0.25" dimension="4"/>
+    <parameter id="popSize" value="380.0" lower="0.0" upper="38000.0"/>
+    <parameter id='clockRate' value="2.3E-5" lower="0.0" upper="100.0"/>
 
-    <distribution id="tipDateB" monophyletic="false" spec="beast.base.spec.evolution.tree.MRCAPrior"
-                  tipsonly="true" tree="@tree">
+    <distribution id="tipDateB" monophyletic="false" spec="beast.base.evolution.tree.MRCAPrior" tipsonly="true" tree="@tree">
         <taxonset id="age(CHICKEN_HONGKONG_915_1997)" spec="TaxonSet">
             <taxon id="CHICKEN_HONGKONG_915_1997" spec="Taxon"/>
         </taxonset>
@@ -149,43 +143,33 @@
 
         <distribution spec="CompoundDistribution" id="posterior">
             <distribution spec="CompoundDistribution" id="prior">
-                <distribution id="hky.kappa.prior" spec='LogNormal' param='@hky.kappa' >
-                    <!-- M="1" S="1.25" />-->
-                    <M spec="RealScalarParam" domain="Real" value="1.0"/>
-                    <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>
+                <distribution id="hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@hky.kappa">
+                    <distr id="LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false"
+                           spec="beast.base.inference.distribution.LogNormalDistributionModel"/>
                 </distribution>
-                <distribution id="hky.frequencies.prior" spec="beast.base.spec.inference.distribution.IID"
-                              param="@hky.frequencies">
-                    <distr id="Uniform" spec="beast.base.spec.inference.distribution.Uniform">
-                        <lower id="freqs.lower" spec="RealScalarParam" domain="Real" value="0.0"/>
-                        <upper id="freqs.upper" spec="RealScalarParam" domain="Real" value="1.0"/>
-                    </distr>
+                <distribution id="hky.frequencies.prior" spec="beast.base.inference.distribution.Prior" x="@hky.frequencies">
+                    <distr id="Uniform" lower="0.0" upper="1.0" spec="beast.base.inference.distribution.Uniform"/>
                 </distribution>
-                <!-- OneOnX is deprecated, test only -->
-                <distribution id="popSize.prior" spec='beast.base.spec.beast2vs1.OneOnX'
-                              param='@popSize' />
-                <distribution id="clockRate.prior" spec="beast.base.spec.inference.distribution.Uniform"
-                              param="@clockRate">
-                    <lower id="clockRate.lower" spec="RealScalarParam" domain="Real" value="0.0"/>
-                    <upper id="clockRate.upper" spec="RealScalarParam" domain="Real" value="100.0"/>
+                <distribution id="popSize.prior" spec="beast.base.inference.distribution.Prior" x="@popSize">
+                    <distr id="OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX"/>
                 </distribution>
+                <!--<distribution id="clockRate.prior" spec="beast.base.inference.distribution.Prior" x="@clockRate">-->
+                <!--<distr id="Uniform2" lower="0.0" upper="100.0" spec="beast.base.inference.distribution.Uniform"/>-->
+                <!--</distribution>-->
 
-                <distribution id="tipDateA" monophyletic="false" spec="beast.base.spec.evolution.tree.MRCAPrior" tipsonly="true"
+                <distribution id="tipDateA" monophyletic="false" spec="beast.base.evolution.tree.MRCAPrior" tipsonly="true"
                               tree="@tree">
                     <taxonset id="age(TREESPARROW_HENAN_1_2004)" spec="TaxonSet">
                         <taxon id="TREESPARROW_HENAN_1_2004" spec="Taxon"/>
                     </taxonset>
-                    <distr id="Uniform0" spec="beast.base.spec.inference.distribution.Uniform">
-<!--                        <lower id="Uniform0.lower" spec="RealScalarParam" domain="Real" value="0.0"/>-->
-                        <upper id="Uniform0.upper" spec="RealScalarParam" domain="Real" value="2500.0"/>
-                    </distr>
+                    <distr id="Uniform0" offset="0.0" spec="distribution.Uniform" upper="2005"/>
                 </distribution>
 
                 <distribution id="coalescent" spec="Coalescent">
                     <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
                         <tree idref="tree"/>
                     </treeIntervals>
-                    <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
+                    <populationModel spec="ConstantPopulation">
                         <popSize idref="popSize"/>
                     </populationModel>
                 </distribution>
@@ -198,22 +182,18 @@
         <operator id="TipDatesRandomWalkerB" windowSize="1" spec="TipDatesRandomWalker"
                   taxonset="@age(CHICKEN_HONGKONG_915_1997)" tree="@tree" weight="1.0"/>
 
-        <operator id='kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
-                  scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
-        <operator id='frequenciesDelta' spec='beast.base.spec.inference.operator.DeltaExchangeOperator'
-                  delta="0.01" weight="0.1" rvparameter="@hky.frequencies"/>
-        <operator id='popSizeScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
-                  scaleFactor="0.75" weight="3" parameter="@popSize"/>
-        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator'
-                  scaleFactor="0.75" weight="3" tree="@tree"/>
+        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
+        <operator id='frequenciesDelta' spec='DeltaExchangeOperator' delta="0.01" weight="0.1"
+                  parameter="@hky.frequencies"/>
+        <operator id='popSizeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize"/>
+        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree"/>
         <operator spec='Uniform' weight="30" tree="@tree"/>
         <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree"/>
         <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree"/>
         <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree"/>
         <operator spec='WilsonBalding' weight="3" tree="@tree"/>
-        <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" up="@clockRate" down="@tree"/>
-        <operator id='clockRateScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
-                  scaleFactor="0.75" weight="3" parameter="@clockRate" />
+        <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" up="@clockRate" down="@tree"/>
+        <operator id='clockRateScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@clockRate"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
             <model idref='posterior'/>
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testStrictClockTipTime.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testStrictClockTipTime.xml
similarity index 89%
rename from beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testStrictClockTipTime.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testStrictClockTipTime.xml
index 891ceb16..db32ae41 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testStrictClockTipTime.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testStrictClockTipTime.xml
@@ -1,10 +1,5 @@
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
-       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
-       beast.base.evolution.operator:beast.base.spec.inference.operator:
-       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
-       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
-       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
+	namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter'>
 
 	<data dataType="nucleotide" id="alignment">
 		<sequence taxon="D4Brazi82">
@@ -72,7 +67,7 @@
 		<substModel idref='hky' />
 	</input>
 	
-	<input spec='beast.base.spec.evolution.branchratemodel.StrictClockModel' id="branchRates">
+	<input spec='StrictClockModel' id="branchRates">
 		<clock.rate idref='clockRate' />
 	</input>
 
@@ -83,7 +78,7 @@
 		<branchRateModel idref="branchRates" />
 	</input>
 
-	<input spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
+	<input spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
 		<trait spec='beast.base.evolution.tree.TraitSet' traitname='date-forward' units='year'
 			value='
         D4Brazi82  = 1982, D4ElSal83  = 1983, D4ElSal94  = 1994, D4Indon76  = 1976, D4Indon77  = 1977,
@@ -95,11 +90,10 @@
 		<taxa idref='alignment' />
 	</input>
 
-
-	<parameter id='clockRate' value="2.3E-5" spec="RealScalarParam" domain="PositiveReal" />
-    <parameter id="hky.kappa" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
-    <parameter dimension="4" id="hky.frequencies" spec="SimplexParam" value="0.25"/>
-    <parameter id="popSize" value="380.0" spec="RealScalarParam" domain="PositiveReal"/>
+	<parameter id="hky.kappa" value="2.0" lower="0.0" />
+	<parameter id="hky.frequencies" value="0.25" dimension="4" />
+	<parameter id="popSize" value="380.0" lower="0.0" upper="38000.0" />
+	<parameter id='clockRate' value="2.3E-5" lower="0.0" upper="100.0" />
 
 	<run spec="MCMC" id="mcmc" chainLength="10000000"> <!--autoOptimize="true" -->
 		<state>
@@ -112,33 +106,25 @@
 
 		<distribution spec="CompoundDistribution" id="posterior">
 			<distribution spec="CompoundDistribution" id="prior">
-                <distribution id="hky.kappa.prior" spec='LogNormal' param='@hky.kappa' >
-                    <!-- M="1" S="1.25" />-->
-                    <M spec="RealScalarParam" domain="Real" value="1.0"/>
-                    <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>
-                </distribution>
-                <distribution id="hky.frequencies.prior" spec="beast.base.spec.inference.distribution.IID"
-                              param="@hky.frequencies">
-                    <distr id="Uniform" spec="beast.base.spec.inference.distribution.Uniform">
-                        <lower id="freqs.lower" spec="RealScalarParam" domain="Real" value="0.0"/>
-                        <upper id="freqs.upper" spec="RealScalarParam" domain="Real" value="1.0"/>
-                    </distr>
-                </distribution>
-                <!-- OneOnX is deprecated, test only -->
-                <distribution id="popSize.prior" spec='beast.base.spec.beast2vs1.OneOnX'
-                              param='@popSize' />
-
-				<distribution id="clockRate.prior" spec="beast.base.spec.inference.distribution.Uniform"
-                              param="@clockRate">
-                    <lower id="clockRate.lower" spec="RealScalarParam" domain="Real" value="0.0"/>
-                    <upper id="clockRate.upper" spec="RealScalarParam" domain="Real" value="100.0"/>
+				<distribution id="hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@hky.kappa">
+					<distr id="LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false"
+						spec="beast.base.inference.distribution.LogNormalDistributionModel" />
+				</distribution>
+				<distribution id="hky.frequencies.prior" spec="beast.base.inference.distribution.Prior" x="@hky.frequencies">
+					<distr id="Uniform" lower="0.0" upper="1.0" spec="beast.base.inference.distribution.Uniform" />
+				</distribution>
+				<distribution id="popSize.prior" spec="beast.base.inference.distribution.Prior" x="@popSize">
+					<distr id="OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX" />
+				</distribution>
+				<distribution id="clockRate.prior" spec="beast.base.inference.distribution.Prior" x="@clockRate">
+					<distr id="Uniform2" lower="0.0" upper="100.0" spec="beast.base.inference.distribution.Uniform" />
 				</distribution>
 
 				<distribution id="coalescent" spec="Coalescent">
 					<treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
 						<tree idref="tree" />
 					</treeIntervals>
-					<populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
+					<populationModel spec="ConstantPopulation">
 						<popSize idref="popSize" />
 					</populationModel>
 				</distribution>
@@ -146,22 +132,17 @@
 			<distribution id='likelihood' idref="treeLikelihood" />
 		</distribution>
 
-        <operator id='kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
-                  scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
-        <operator id='frequenciesDelta' spec='beast.base.spec.inference.operator.DeltaExchangeOperator'
-                  delta="0.01" weight="0.1" rvparameter="@hky.frequencies"/>
-        <operator id='popSizeScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
-                  scaleFactor="0.75" weight="3" parameter="@popSize"/>
-        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator'
-                  scaleFactor="0.75" weight="3" tree="@tree"/>
-        <operator spec='Uniform' weight="30" tree="@tree"/>
-        <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree" />
+		<operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa" />
+		<operator id='frequenciesDelta' spec='DeltaExchangeOperator' delta="0.01" weight="0.1" parameter="@hky.frequencies" />
+		<operator id='popSizeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize" />
+		<operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree" />
+		<operator spec='Uniform' weight="30" tree="@tree" />
+		<operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree" />
 		<operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree" />
 		<operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree" />
 		<operator spec='WilsonBalding' weight="3" tree="@tree" />
-		<operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" up="@clockRate" down="@tree" />
-		<operator id='clockRateScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
-                  scaleFactor="0.75" weight="3" parameter="@clockRate" />
+		<operator spec='UpDownOperator' scaleFactor="0.75" weight="3" up="@clockRate" down="@tree" />
+		<operator id='clockRateScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@clockRate" />
 
 		<logger logEvery="1000" fileName="test.$(seed).log">
 			<model idref='posterior' />
diff --git a/beast-base/src/test/resources/beast.base/examples/beast2vs1/testTipDates.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testTipDates.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/beast2vs1/testTipDates.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testTipDates.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testUCRelaxedClockLogNormal.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testUCRelaxedClockLogNormal.xml
similarity index 67%
rename from beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testUCRelaxedClockLogNormal.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testUCRelaxedClockLogNormal.xml
index 0e881147..25472084 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testUCRelaxedClockLogNormal.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testUCRelaxedClockLogNormal.xml
@@ -1,12 +1,8 @@
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
-       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:
-       beast.base.evolution.operator:beast.base.spec.inference.operator:
-       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
-       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
-       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
-
-<!-- The sequence alignment (each sequence refers to a taxon above). -->
+    namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter'>
+
+
+    <!-- The sequence alignment (each sequence refers to a taxon above). -->
     <!-- ntax=6 nchar=768 -->
     <!-- npatterns=69 -->
     <data id="alignment" dataType="nucleotide">
@@ -32,7 +28,7 @@
 
     <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985) -->
     <input spec='HKY' id="hky">
-        <kappa idref='hky.kappa'/>
+        <parameter name='kappa' idref='hky.kappa' />
         <input id='freqs' name='frequencies' spec='Frequencies' frequencies='@hky.frequencies' />
     </input>
 
@@ -43,13 +39,13 @@
     </input>
 
 
-    <input spec='beast.base.spec.evolution.branchratemodel.UCRelaxedClockModel' id="branchRates">
+    <input spec='UCRelaxedClockModel' id="branchRates">
         <!-- <parameter name='mutationRate'>1.0</parameter> -->
-        <distr id='lognormal' spec="beast.base.spec.inference.distribution.LogNormal" meanInRealSpace="true">
-            <M id='M' spec="RealScalarParam" domain="Real" value="1.0"/>
-            <S id='S' spec="RealScalarParam" domain="PositiveReal" value="0.3333333333333333"/>
+        <distr id='lognormal' spec="beast.base.inference.distribution.LogNormalDistributionModel" meanInRealSpace="true">
+            <parameter name='M' id='M' value="1" lower="0.0" />
+            <parameter name='S' id='S' value="0.3333333333333333" lower="0" />
         </distr>
-        <rateCategories spec='IntVectorParam' domain="NonNegativeInt" id='rateCategories' dimension="11" value="1" />
+        <parameter spec='IntegerParameter' name='rateCategories' id='rateCategories' dimension="11" value="1" />
         <tree idref="tree" />
     </input> 
 
@@ -66,69 +62,57 @@
         :0.009871782435416254);'
           taxa='@alignment'/>
 
-    <parameter id="hky.kappa" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
-    <parameter dimension="4" id="hky.frequencies" spec="SimplexParam" value="0.25"/>
-    <parameter id="popSize" value="0.077" spec="RealScalarParam" domain="PositiveReal"/>
+    <parameter id="hky.kappa" value="2.0" lower="0.0" />
+    <parameter id="hky.frequencies" value="0.25" dimension="4" />
+    <parameter id="popSize" value="0.077" lower="0.0" />
 
     <run spec="MCMC" id="mcmc" chainLength="10000000"> <!--autoOptimize="true" -->
 
         <distribution spec="CompoundDistribution" id="posterior">
             <distribution spec="CompoundDistribution" id="prior">
-                <distribution id="hky.kappa.prior" spec='LogNormal' param='@hky.kappa' >
-                    <!-- M="1" S="1.25" />-->
-                    <M spec="RealScalarParam" domain="Real" value="1.0"/>
-                    <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>
+                <distribution id="hky.kappa.prior" spec="beast.base.inference.distribution.Prior" x="@hky.kappa">
+                    <distr id="LogNormalDistributionModel" M="1.0" S="1.25" meanInRealSpace="false"
+                        spec="beast.base.inference.distribution.LogNormalDistributionModel" />
                 </distribution>
-                <distribution id="hky.frequencies.prior" spec="beast.base.spec.inference.distribution.IID"
-                              param="@hky.frequencies">
-                    <distr id="Uniform" spec="beast.base.spec.inference.distribution.Uniform">
-                        <lower id="freqs.lower" spec="RealScalarParam" domain="Real" value="0.0"/>
-                        <upper id="freqs.upper" spec="RealScalarParam" domain="Real" value="1.0"/>
-                    </distr>
+                <distribution id="hky.frequencies.prior" spec="beast.base.inference.distribution.Prior" x="@hky.frequencies">
+                    <distr id="Uniform" lower="0.0" upper="1.0" spec="beast.base.inference.distribution.Uniform" />
                 </distribution>
-                <!-- OneOnX is deprecated, test only -->
-                <distribution id="popSize.prior" spec='beast.base.spec.beast2vs1.OneOnX'
-                              param='@popSize' />
-                <distribution id="S.prior" spec="beast.base.spec.inference.distribution.Exponential"
-                              param="@S">
-                    <mean spec="RealScalarParam" domain="PositiveReal" value="0.3333333333333333"/>
+                <distribution id="popSize.prior" spec="beast.base.inference.distribution.Prior" x="@popSize">
+                    <distr id="OneOnX" offset="0.0" spec="beast.base.inference.distribution.OneOnX" />
+                </distribution>
+                <distribution id="S.prior" spec="beast.base.inference.distribution.Prior" x="@S">
+                    <distr id="Exponential" mean="0.3333333333333333" spec="beast.base.inference.distribution.Exponential" />
                 </distribution>   
 
                 <distribution id="coalescent" spec="Coalescent">
                     <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>
                         <tree idref="tree" />
                     </treeIntervals>
-                    <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation" id='ConstantPopulation'>
-                        <popSize idref="popSize"/>
+                    <populationModel spec="ConstantPopulation">
+                        <popSize idref="popSize" />
                     </populationModel>
                 </distribution>
             </distribution>
             <distribution id='likelihood' idref="treeLikelihood" />
         </distribution>
 
-        <operator id='SScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
-                  parameter="@S" scaleFactor="0.75" weight="3"/>
-        <operator id="CategoriesRandomWalk" spec="beast.base.spec.inference.operator.IntRandomWalkOperator"
-                  parameter="@rateCategories" windowSize='1' weight="10" />
-        <operator id='CategoriesSwapOperator' spec='beast.base.spec.inference.operator.SwapOperator'
-                  intparameter='@rateCategories' howMany="1" weight="10" />
-        <operator id='CategoriesUniform' spec='beast.base.spec.inference.operator.uniform.IntUniformOperator'
-                  parameter='@rateCategories' weight="10"/>
-
-        <operator id='kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
-                  scaleFactor="0.75" weight="0.1" parameter="@hky.kappa"/>
-        <operator id='frequenciesDelta' spec='beast.base.spec.inference.operator.DeltaExchangeOperator'
-                  delta="0.01" weight="0.1" rvparameter="@hky.frequencies"/>
-        <operator id='popSizeScaler' spec='beast.base.spec.inference.operator.ScaleOperator'
-                  scaleFactor="0.75" weight="3" parameter="@popSize"/>
-        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator'
-                  scaleFactor="0.75" weight="3" tree="@tree"/>
+        <operator id='SScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3">
+            <parameter idref="S" />
+        </operator>  
+        <operator id="CategoriesRandomWalk" spec="IntRandomWalkOperator" windowSize='1' weight="10" parameter="@rateCategories" />
+        <operator id='CategoriesSwapOperator' spec='SwapOperator' howMany="1" weight="10" intparameter='@rateCategories' />
+        <operator id='CategoriesUniform' spec='UniformOperator' weight="10" parameter='@rateCategories' /> 
+
+        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.75" weight="0.1" parameter="@hky.kappa" />
+        <operator id='frequenciesDelta' spec='DeltaExchangeOperator' delta="0.01" weight="0.1" parameter="@hky.frequencies" />
+        <operator id='popSizeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" parameter="@popSize" />
+        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.75" weight="3" tree="@tree" />
         <operator spec='Uniform' weight="30" tree="@tree" />
         <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree" />
         <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree" />
         <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree" />
         <operator spec='WilsonBalding' weight="1" tree="@tree" />
-        <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" down="@tree" />
+        <operator spec='UpDownOperator' scaleFactor="0.75" weight="3" down="@tree" /> 
 
         <logger logEvery="10000" fileName="test.$(seed).log">
             <model idref='posterior' />
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testYuleModel_10taxa.xml b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testYuleModel_10taxa.xml
similarity index 68%
rename from beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testYuleModel_10taxa.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testYuleModel_10taxa.xml
index 989bfa01..b4053489 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testYuleModel_10taxa.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/beast2vs1/testYuleModel_10taxa.xml
@@ -1,12 +1,7 @@
 <?xml version="1.0" standalone="yes"?>
 <!-- test Yule birth model and Birth Death model per Gernhard 2008-->
 <beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:
-       beast.evolution.nuc:beast.base.evolution.alignment:
-       beast.base.evolution.operator:beast.base.spec.inference.operator:
-       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:
-       beast.base.spec.inference.parameter:beast.base.spec.inference.util:
-       beast.base.spec.inference.distribution:beast.base.spec.evolution.likelihood'>
+       namespace='beast.base.evolution.speciation:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
 
     <data id="alignment" dataType="nucleotide">
         <sequence taxon="A">A</sequence>
@@ -21,18 +16,18 @@
         <sequence taxon="J">A</sequence>
     </data>
 
-    <input spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma' allowSampledAncestors='false' isUltrametric='true'>
+    <input spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>
         <taxa idref='alignment'/>
     </input>
 
     <!-- A prior on the distribution node heights defined given                  -->
     <!-- a Yule speciation process (a pure birth process).                       -->
-    <input spec='beast.base.spec.evolution.speciation.YuleModel' id="yule">
+    <input spec='YuleModel' id="yule">
         <birthDiffRate idref="birthRate"/>
         <tree idref='tree'/>
     </input>
 
-    <parameter id="birthRate" value="2.0" spec="RealScalarParam" domain="PositiveReal"/>
+    <parameter id="birthRate" value="2.0" lower="0.0" upper="100.0"/>
 
     <run spec='MCMC' chainLength="2000000">
         <state>
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/1/experiment.sh b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/1/experiment.sh
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/1/experiment.sh
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/1/experiment.sh
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/1/testHKY1044.xml b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/1/testHKY1044.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/1/testHKY1044.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/1/testHKY1044.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/1/testHKY1366.xml b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/1/testHKY1366.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/1/testHKY1366.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/1/testHKY1366.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/1/testHKY1510.xml b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/1/testHKY1510.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/1/testHKY1510.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/1/testHKY1510.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/1/testHKY1748.xml b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/1/testHKY1748.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/1/testHKY1748.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/1/testHKY1748.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/1/testHKY1749.xml b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/1/testHKY1749.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/1/testHKY1749.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/1/testHKY1749.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/1/testHKY1809.xml b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/1/testHKY1809.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/1/testHKY1809.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/1/testHKY1809.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/1/testHKY336.xml b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/1/testHKY336.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/1/testHKY336.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/1/testHKY336.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/1/testHKY3475.xml b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/1/testHKY3475.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/1/testHKY3475.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/1/testHKY3475.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/1/testHKY501.xml b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/1/testHKY501.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/1/testHKY501.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/1/testHKY501.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/1/testHKY520.xml b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/1/testHKY520.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/1/testHKY520.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/1/testHKY520.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/1/testHKY755.xml b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/1/testHKY755.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/1/testHKY755.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/1/testHKY755.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/1/testHKY767.xml b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/1/testHKY767.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/1/testHKY767.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/1/testHKY767.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/II/experiment.sh b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/II/experiment.sh
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/II/experiment.sh
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/II/experiment.sh
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/II/testHKY1044.xml b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/II/testHKY1044.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/II/testHKY1044.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/II/testHKY1044.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/II/testHKY1366.xml b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/II/testHKY1366.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/II/testHKY1366.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/II/testHKY1366.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/II/testHKY1510.xml b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/II/testHKY1510.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/II/testHKY1510.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/II/testHKY1510.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/II/testHKY1748.xml b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/II/testHKY1748.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/II/testHKY1748.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/II/testHKY1748.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/II/testHKY1749.xml b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/II/testHKY1749.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/II/testHKY1749.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/II/testHKY1749.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/II/testHKY1809.xml b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/II/testHKY1809.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/II/testHKY1809.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/II/testHKY1809.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/II/testHKY336.xml b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/II/testHKY336.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/II/testHKY336.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/II/testHKY336.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/II/testHKY3475.xml b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/II/testHKY3475.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/II/testHKY3475.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/II/testHKY3475.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/II/testHKY501.xml b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/II/testHKY501.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/II/testHKY501.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/II/testHKY501.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/II/testHKY520.xml b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/II/testHKY520.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/II/testHKY520.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/II/testHKY520.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/II/testHKY755.xml b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/II/testHKY755.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/II/testHKY755.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/II/testHKY755.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/II/testHKY767.xml b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/II/testHKY767.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/II/testHKY767.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/II/testHKY767.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/experiment.sh b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/mrbayes/experiment.sh
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/experiment.sh
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/mrbayes/experiment.sh
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/run1044.nex b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/mrbayes/run1044.nex
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/run1044.nex
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/mrbayes/run1044.nex
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/run1366.nex b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/mrbayes/run1366.nex
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/run1366.nex
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/mrbayes/run1366.nex
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/run1510.nex b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/mrbayes/run1510.nex
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/run1510.nex
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diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/run1748.nex b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/mrbayes/run1748.nex
similarity index 100%
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diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/run1749.nex b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/mrbayes/run1749.nex
similarity index 100%
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diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/run1809.nex b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/mrbayes/run1809.nex
similarity index 100%
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diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/run336.nex b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/mrbayes/run336.nex
similarity index 100%
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diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/run3475.nex b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/mrbayes/run3475.nex
similarity index 100%
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diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/run501.nex b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/mrbayes/run501.nex
similarity index 100%
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diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/run520.nex b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/mrbayes/run520.nex
similarity index 100%
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diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/run755.nex b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/mrbayes/run755.nex
similarity index 100%
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diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/run767.nex b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/mrbayes/run767.nex
similarity index 100%
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diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/testHKY1044.nex b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/mrbayes/testHKY1044.nex
similarity index 100%
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diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/testHKY1366.nex b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/mrbayes/testHKY1366.nex
similarity index 100%
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diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/testHKY1510.nex b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/mrbayes/testHKY1510.nex
similarity index 100%
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diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/testHKY1748.nex b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/mrbayes/testHKY1748.nex
similarity index 100%
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diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/testHKY1749.nex b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/mrbayes/testHKY1749.nex
similarity index 100%
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diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/testHKY1809.nex b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/mrbayes/testHKY1809.nex
similarity index 100%
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diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/testHKY336.nex b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/mrbayes/testHKY336.nex
similarity index 100%
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diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/testHKY3475.nex b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/mrbayes/testHKY3475.nex
similarity index 100%
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diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/testHKY501.nex b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/mrbayes/testHKY501.nex
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/testHKY501.nex
rename to beast-base/src/test/resources/beast.base/examples/legacy/benchmark/mrbayes/testHKY501.nex
diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/testHKY520.nex b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/mrbayes/testHKY520.nex
similarity index 100%
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diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/testHKY755.nex b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/mrbayes/testHKY755.nex
similarity index 100%
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diff --git a/beast-base/src/test/resources/beast.base/examples/benchmark/mrbayes/testHKY767.nex b/beast-base/src/test/resources/beast.base/examples/legacy/benchmark/mrbayes/testHKY767.nex
similarity index 100%
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diff --git a/beast-base/src/test/resources/beast.base/examples/legacy/bitflip.xml b/beast-base/src/test/resources/beast.base/examples/legacy/bitflip.xml
new file mode 100644
index 00000000..5991c100
--- /dev/null
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/bitflip.xml
@@ -0,0 +1,22 @@
+<beast version='2.0'
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter'>
+
+    <parameter spec='BooleanParameter' name='indicators' id='indicators' dimension="5" value="false"/>
+
+    <run spec="MCMC" id="mcmc" chainLength="100000"> <!--autoOptimize="true"-->
+        <state>
+            <input name='stateNode' idref='indicators'/>
+        </state>
+	
+	<distribution spec="CompoundDistribution" id="posterior"/>
+
+        <operator id="bitflip" spec="BitFlipOperator" weight="1">
+            <input name="parameter" idref="indicators"/>
+        </operator>
+
+        <logger logEvery="10" fileName="bitflip.log">
+            <log idref="indicators"/>
+        </logger>
+    </run>
+
+</beast>
diff --git a/beast-base/src/test/resources/beast.base/examples/parameterised/README.md b/beast-base/src/test/resources/beast.base/examples/legacy/parameterised/README.md
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/parameterised/README.md
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diff --git a/beast-base/src/test/resources/beast.base/examples/parameterised/RSV2.json b/beast-base/src/test/resources/beast.base/examples/legacy/parameterised/RSV2.json
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/parameterised/RSV2.json
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diff --git a/beast-base/src/test/resources/beast.base/examples/parameterised/RSV2.xml b/beast-base/src/test/resources/beast.base/examples/legacy/parameterised/RSV2.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/parameterised/RSV2.xml
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diff --git a/beast-base/src/test/resources/beast.base/examples/starbeastinit/sbi-01.xml b/beast-base/src/test/resources/beast.base/examples/legacy/starbeastinit/sbi-01.xml
similarity index 100%
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diff --git a/beast-base/src/test/resources/beast.base/examples/starbeastinit/sbi-02.xml b/beast-base/src/test/resources/beast.base/examples/legacy/starbeastinit/sbi-02.xml
similarity index 100%
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diff --git a/beast-base/src/test/resources/beast.base/examples/starbeastinit/sbi-03.xml b/beast-base/src/test/resources/beast.base/examples/legacy/starbeastinit/sbi-03.xml
similarity index 100%
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diff --git a/beast-base/src/test/resources/beast.base/examples/testBSP.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testBSP.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/testBSP.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/testBSP.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/testCalYule_5t_2c.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testCalYule_5t_2c.xml
similarity index 100%
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diff --git a/beast-base/src/test/resources/beast.base/examples/testCalibration.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testCalibration.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/testCalibration.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/testCalibration.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/testClassicRootCalibrationPrior.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testClassicRootCalibrationPrior.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/testClassicRootCalibrationPrior.xml
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diff --git a/beast-base/src/test/resources/beast.base/examples/testCoalescent.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testCoalescent.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/testCoalescent.xml
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diff --git a/beast-base/src/test/resources/beast.base/examples/testConditionalRootCalibrationPrior.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testConditionalRootCalibrationPrior.xml
similarity index 100%
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diff --git a/beast-base/src/test/resources/beast.base/examples/testDirectSimulator.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testDirectSimulator.xml
similarity index 100%
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diff --git a/beast-base/src/test/resources/beast.base/examples/testDirectSimulator2.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testDirectSimulator2.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/testDirectSimulator2.xml
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diff --git a/beast-base/src/test/resources/beast.base/examples/testDirectSimulatorHierarchical.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testDirectSimulatorHierarchical.xml
similarity index 100%
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diff --git a/beast-base/src/test/resources/beast.base/examples/testDirichlet/plotResults.R b/beast-base/src/test/resources/beast.base/examples/legacy/testDirichlet/plotResults.R
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/testDirichlet/plotResults.R
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diff --git a/beast-base/src/test/resources/beast.base/examples/testDirichlet/testDirichlet.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testDirichlet/testDirichlet.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/testDirichlet/testDirichlet.xml
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diff --git a/beast-base/src/test/resources/beast.base/examples/testDirichlet/testDirichlet2.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testDirichlet/testDirichlet2.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/testDirichlet/testDirichlet2.xml
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diff --git a/beast-base/src/test/resources/beast.base/examples/testDirichlet/testDirichletBact.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testDirichlet/testDirichletBact.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/testDirichlet/testDirichletBact.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/testDirichlet/testDirichletBact.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/testDirichlet/testDirichletMarginalDensity2.pdf b/beast-base/src/test/resources/beast.base/examples/legacy/testDirichlet/testDirichletMarginalDensity2.pdf
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/testDirichlet/testDirichletMarginalDensity2.pdf
rename to beast-base/src/test/resources/beast.base/examples/legacy/testDirichlet/testDirichletMarginalDensity2.pdf
diff --git a/beast-base/src/test/resources/beast.base/examples/testDirichlet/testDirichletNoPrior.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testDirichlet/testDirichletNoPrior.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/testDirichlet/testDirichletNoPrior.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/testDirichlet/testDirichletNoPrior.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/testEBSP.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testEBSP.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/testEBSP.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/testEBSP.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/testExponentialGrowth.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testExponentialGrowth.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/testExponentialGrowth.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/testExponentialGrowth.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/legacy/testGTR.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testGTR.xml
new file mode 100644
index 00000000..c39a57d2
--- /dev/null
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/testGTR.xml
@@ -0,0 +1,211 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<beast beautitemplate='Standard' beautistatus=''
+       namespace="beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.alignment:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood"
+       version="2.0">
+
+
+    <data id="primate-mtDNA">
+        <sequence id="seq_Lemur_catta" taxon="Lemur_catta" totalcount="4"
+                  value="AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATTCTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGGGATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCTAGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTCATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTCCCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAACCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATTTACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAACACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATGTATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGATAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTATAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTGCATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAACAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT"/>
+        <sequence id="seq_Homo_sapiens" taxon="Homo_sapiens" totalcount="4"
+                  value="AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
+        <sequence id="seq_Pan" taxon="Pan" totalcount="4"
+                  value="AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATTCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCTCGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAAGCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TATAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCACCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCGCGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAGCTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
+        <sequence id="seq_Gorilla" taxon="Gorilla" totalcount="4"
+                  value="AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGGACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCTCGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTCCTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTCCCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAAACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCTATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CGTAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTACCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCGCATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAGCTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT"/>
+        <sequence id="seq_Pongo" taxon="Pongo" totalcount="4"
+                  value="AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGGCCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCTTGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTCTTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTCTCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAAACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTTATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAACATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGATAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAACAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCGCTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCGCATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAACCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT"/>
+        <sequence id="seq_Hylobates" taxon="Hylobates" totalcount="4"
+                  value="AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATTCTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGGGCTCCAAGCCTTACTCCCACTGATAGCCTTCTGATGACTCGCAGCAAGCCTCGCTAACCTCGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTCCTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTCCCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAAACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCTAACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAACATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CACAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAGCCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTGCCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAACCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT"/>
+        <sequence id="seq_Macaca_fuscata" taxon="Macaca_fuscata" totalcount="4"
+                  value="AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGGACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTCCTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTCTCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAAGCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAACACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT"/>
+        <sequence id="seq_M._mulatta" taxon="M._mulatta" totalcount="4"
+                  value="AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGGACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTCCTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTCCCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCTATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAACATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CGCGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT"/>
+        <sequence id="seq_M._fascicularis" taxon="M._fascicularis" totalcount="4"
+                  value="AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTTCTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGTACCATACTACTATCCCGAGGACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTCCTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTCTCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAACATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTGCCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAATATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAACAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT"/>
+        <sequence id="seq_M._sylvanus" taxon="M._sylvanus" totalcount="4"
+                  value="AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTTCTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGCATCATACTACTATCCCGAGGACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCTTGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTCCTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTCTCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAAACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCTATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAACATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TGCAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCGCTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAATATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAACAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT"/>
+        <sequence id="seq_Saimiri_sciureus" taxon="Saimiri_sciureus" totalcount="4"
+                  value="AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTCTATGCTATTCTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAATAACATTTACTCGAGGGCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCTCGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTCTTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTCACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAAACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCTTACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAACATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CGCAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGATAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAATA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAGCTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCATCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAATCAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT"/>
+        <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4"
+                  value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
+    </data>
+
+
+    <map name="Beta">beast.base.inference.distribution.Beta</map>
+    <map name="Exponential">beast.base.inference.distribution.Exponential</map>
+    <map name="InverseGamma">beast.base.inference.distribution.InverseGamma</map>
+    <map name="LogNormal">beast.base.inference.distribution.LogNormalDistributionModel</map>
+    <map name="Gamma">beast.base.inference.distribution.Gamma</map>
+    <map name="Uniform">beast.base.inference.distribution.Uniform</map>
+    <map name="prior">beast.base.inference.distribution.Prior</map>
+    <map name="LaplaceDistribution">beast.base.inference.distribution.LaplaceDistribution</map>
+    <map name="OneOnX">beast.base.inference.distribution.OneOnX</map>
+    <map name="Normal">beast.base.inference.distribution.Normal</map>
+
+
+    <run chainLength="5000000" id="mcmc" spec="MCMC">
+        <state id="state" storeEvery="5000">
+            <tree id="Tree.t:primate" name="stateNode">
+                <taxonset id="TaxonSet.coding" spec="TaxonSet">
+                    <alignment filter="2-457,660-896" id="coding" spec="FilteredAlignment">
+                        <data idref="primate-mtDNA"/>
+                    </alignment>
+                </taxonset>
+            </tree>
+            <parameter id="birthRate.t:primate" name="stateNode" value="1.0"/>
+            <parameter id="rateAC.s:primate" lower="0.0" name="stateNode" value="1.0"/>
+            <parameter id="rateAG.s:primate" lower="0.0" name="stateNode" value="1.0"/>
+            <parameter id="rateAT.s:primate" lower="0.0" name="stateNode" value="1.0"/>
+            <parameter id="rateCG.s:primate" lower="0.0" name="stateNode" value="1.0"/>
+            <parameter id="rateGT.s:primate" lower="0.0" name="stateNode" value="1.0"/>
+            <parameter dimension="4" id="freqParameter.s:primate" lower="0.0" name="stateNode" upper="1.0"
+                       value="0.25"/>
+        </state>
+
+        <init estimate="false" id="RandomTree.t:primate" initial="@Tree.t:primate"
+              spec="beast.base.evolution.tree.coalescent.RandomTree" taxa="@coding">
+            <populationModel id="ConstantPopulation0.t:primate" spec="ConstantPopulation">
+                <parameter id="randomPopSize.t:primate" name="popSize" value="1"/>
+            </populationModel>
+        </init>
+
+        <distribution id="posterior" spec="CompoundDistribution">
+            <distribution id="prior" spec="CompoundDistribution">
+                <distribution birthDiffRate="@birthRate.t:primate" id="YuleModel.t:primate"
+                              spec="beast.base.evolution.speciation.YuleModel" tree="@Tree.t:primate"/>
+                <prior id="YuleBirthRatePrior.t:primate" name="distribution" x="@birthRate.t:primate">
+                    <Uniform id="Uniform.0" name="distr" upper="Infinity"/>
+                </prior>
+                <prior id="RateACPrior.s:primate" name="distribution" x="@rateAC.s:primate">
+                    <LogNormal id="LogNormalDistributionModel.0" name="distr">
+                        <parameter estimate="false" id="RealParameter.0" name="M" value="0"/>
+                        <parameter estimate="false" id="RealParameter.01" lower="0.0" name="S" upper="5.0"
+                                   value="1.25"/>
+                    </LogNormal>
+                </prior>
+                <prior id="RateAGPrior.s:primate" name="distribution" x="@rateAG.s:primate">
+                    <LogNormal id="LogNormalDistributionModel.01" name="distr">
+                        <parameter estimate="false" id="RealParameter.02" name="M" value="0"/>
+                        <parameter estimate="false" id="RealParameter.03" lower="0.0" name="S" upper="5.0"
+                                   value="1.25"/>
+                    </LogNormal>
+                </prior>
+                <prior id="RateATPrior.s:primate" name="distribution" x="@rateAT.s:primate">
+                    <LogNormal id="LogNormalDistributionModel.02" name="distr">
+                        <parameter estimate="false" id="RealParameter.04" name="M" value="0"/>
+                        <parameter estimate="false" id="RealParameter.05" lower="0.0" name="S" upper="5.0"
+                                   value="1.25"/>
+                    </LogNormal>
+                </prior>
+                <prior id="RateCGPrior.s:primate" name="distribution" x="@rateCG.s:primate">
+                    <LogNormal id="LogNormalDistributionModel.03" name="distr">
+                        <parameter estimate="false" id="RealParameter.06" name="M" value="0"/>
+                        <parameter estimate="false" id="RealParameter.07" lower="0.0" name="S" upper="5.0"
+                                   value="1.25"/>
+                    </LogNormal>
+                </prior>
+                <prior id="RateGTPrior.s:primate" name="distribution" x="@rateGT.s:primate">
+                    <LogNormal id="LogNormalDistributionModel.04" name="distr">
+                        <parameter estimate="false" id="RealParameter.08" name="M" value="0"/>
+                        <parameter estimate="false" id="RealParameter.09" lower="0.0" name="S" upper="5.0"
+                                   value="1.25"/>
+                    </LogNormal>
+                </prior>
+            </distribution>
+            <distribution id="likelihood" spec="CompoundDistribution">
+                <distribution data="@coding" id="treeLikelihood.coding" spec="TreeLikelihood" tree="@Tree.t:primate">
+                    <siteModel id="SiteModel.s:primate" spec="SiteModel">
+                        <parameter estimate="false" id="mutationRate.s:primate" name="mutationRate" value="1.0"/>
+                        <parameter estimate="false" id="gammaShape.s:primate" name="shape" value="1.0"/>
+                        <parameter estimate="false" id="proportionInvariant.s:primate" lower="0.0"
+                                   name="proportionInvariant" upper="1.0" value="0.0"/>
+                        <substModel id="gtr.s:primate" rateAC="@rateAC.s:primate" rateAG="@rateAG.s:primate"
+                                    rateAT="@rateAT.s:primate" rateCG="@rateCG.s:primate" rateGT="@rateGT.s:primate"
+                                    spec="GTR">
+                            <parameter estimate="false" id="rateCT.s:primate" lower="0.0" name="rateCT" value="1.0"/>
+                            <frequencies frequencies="@freqParameter.s:primate" id="estimatedFreqs.s:primate"
+                                         spec="Frequencies"/>
+                        </substModel>
+                    </siteModel>
+                    <branchRateModel id="StrictClock.c:primate" spec="beast.base.evolution.branchratemodel.StrictClockModel">
+                        <parameter estimate="false" id="clockRate.c:primate" name="clock.rate" value="1.0"/>
+                    </branchRateModel>
+                </distribution>
+                <distribution branchRateModel="@StrictClock.c:primate" id="treeLikelihood.noncoding"
+                              siteModel="@SiteModel.s:primate" spec="TreeLikelihood" tree="@Tree.t:primate">
+                    <data data="@primate-mtDNA" filter="1,458-659,897-898" id="noncoding" spec="FilteredAlignment"/>
+                </distribution>
+            </distribution>
+        </distribution>
+
+        <operator id="YuleBirthRateScaler.t:primate" parameter="@birthRate.t:primate" scaleFactor="0.75"
+                  spec="ScaleOperator" weight="3.0"/>
+
+        <operator id="treeScaler.t:primate" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:primate" weight="3.0"/>
+
+        <operator id="treeRootScaler.t:primate" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator"
+                  tree="@Tree.t:primate" weight="3.0"/>
+
+        <operator id="UniformOperator.t:primate" spec="Uniform" tree="@Tree.t:primate" weight="30.0"/>
+
+        <operator id="SubtreeSlide.t:primate" spec="SubtreeSlide" tree="@Tree.t:primate" weight="15.0"/>
+
+        <operator id="narrow.t:primate" spec="Exchange" tree="@Tree.t:primate" weight="15.0"/>
+
+        <operator id="wide.t:primate" isNarrow="false" spec="Exchange" tree="@Tree.t:primate" weight="3.0"/>
+
+        <operator id="WilsonBalding.t:primate" spec="WilsonBalding" tree="@Tree.t:primate" weight="3.0"/>
+
+        <operator id="RateACScaler.s:primate" parameter="@rateAC.s:primate" scaleFactor="0.5" spec="ScaleOperator"
+                  weight="0.1"/>
+
+        <operator id="RateAGScaler.s:primate" parameter="@rateAG.s:primate" scaleFactor="0.5" spec="ScaleOperator"
+                  weight="0.1"/>
+
+        <operator id="RateATScaler.s:primate" parameter="@rateAT.s:primate" scaleFactor="0.5" spec="ScaleOperator"
+                  weight="0.1"/>
+
+        <operator id="RateCGScaler.s:primate" parameter="@rateCG.s:primate" scaleFactor="0.5" spec="ScaleOperator"
+                  weight="0.1"/>
+
+        <operator id="RateGTScaler.s:primate" parameter="@rateGT.s:primate" scaleFactor="0.5" spec="ScaleOperator"
+                  weight="0.1"/>
+
+        <operator delta="0.01" id="FrequenciesExchanger.s:primate" spec="DeltaExchangeOperator" weight="0.1">
+            <parameter idref="freqParameter.s:primate"/>
+        </operator>
+
+        <logger fileName="primate-mtDNA.log" id="tracelog" logEvery="5000" model="@posterior" sanitiseHeaders="true"
+                sort="smart">
+            <log idref="posterior"/>
+            <log idref="likelihood"/>
+            <log idref="prior"/>
+            <log idref="treeLikelihood.noncoding"/>
+            <log idref="treeLikelihood.coding"/>
+            <log id="TreeHeight.t:primate" spec="beast.base.evolution.tree.TreeStatLogger" tree="@Tree.t:primate"/>
+            <log idref="YuleModel.t:primate"/>
+            <parameter idref="birthRate.t:primate" name="log"/>
+            <parameter idref="rateAC.s:primate" name="log"/>
+            <parameter idref="rateAG.s:primate" name="log"/>
+            <parameter idref="rateAT.s:primate" name="log"/>
+            <parameter idref="rateCG.s:primate" name="log"/>
+            <parameter idref="rateGT.s:primate" name="log"/>
+            <parameter idref="freqParameter.s:primate" name="log"/>
+        </logger>
+
+        <logger id="screenlog" logEvery="5000">
+            <log idref="posterior"/>
+            <log arg="@posterior" id="ESS.0" spec="util.ESS"/>
+            <log idref="likelihood"/>
+            <log idref="prior"/>
+        </logger>
+
+        <logger fileName="$(tree).trees" id="treelog.t:primate" logEvery="5000" mode="tree">
+            <log id="TreeWithMetaDataLogger.t:primate" spec="beast.base.evolution.TreeWithMetaDataLogger"
+                 tree="@Tree.t:primate"/>
+        </logger>
+
+    </run>
+
+</beast>
diff --git a/beast-base/src/test/resources/beast.base/examples/legacy/testHKY.json b/beast-base/src/test/resources/beast.base/examples/legacy/testHKY.json
new file mode 100644
index 00000000..12172ffa
--- /dev/null
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/testHKY.json
@@ -0,0 +1,86 @@
+{version: "2.7",
+namespace: "beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.alignment:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood",
+
+// this is a comment, which is non-standard JSON
+// only commenst after double slashes are supported
+// but /* bla */ comments are not
+
+map: [
+	{name: "stateNode", value: "parameter.RealParameter"}
+],
+
+beast: [
+	{id: "alignment",
+	 spec: "Alignment",
+	 sequence: [
+		 {spec: "Sequence", totalcount: 4, taxon: "human", value: "\n AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCCTTATTTCTACTAGGACTATGAGAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTG-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCGGAGCTTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGGCCTCCATGACTTTTTCAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAATTATAGGCT-AAATCCTATATATCTTA-CACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACACCTCTTTACAGTGA\n " },
+		 {spec: "Sequence", totalcount: 4, taxon: "chimp", value: "\n AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTCAAATCCCCTTATTTCTACTAGGACTATAAGAATCGAACTCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTAAGCACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCTCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AACCCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCGACACCTCTTTACAGTGA\n " },
+		 {spec: "Sequence", totalcount: 4, taxon: "bonobo", value: "\n AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTTAAATCCCCTTATTTCTACTAGGACTATGAGAGTCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCTCTCAGTAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAGC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTTGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCCCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCAACACCTCTTTACAGTGA\n " },
+		 {spec: "Sequence", totalcount: 4, taxon: "gorilla", value: "\n AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGAGGTTTAAACCCCCTTATTTCTACTAGGACTATGAGAATTGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTGTCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTCACATCCTTCCCGTACTAAGAAATTTAGGTTAAACATAGACCAAGAGCCTTCAAAGCCCTTAGTAAGTTA-CAACACTTAATTTCTGTAAGGACTGCAAAACCCTACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCAATGGGACTCAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAT-TCACCTCGGAGCTTGGTAAAAAGAGGCCCAGCCTCTGTCTTTAGATTTACAGTCCAATGCCTTA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGACCTTCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAGGTTAAATTACGGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCGTTAACCTTTTAAGTTAAAGATTAAGAGTATCGGCACCTCTTTGCAGTGA\n " },
+		 {spec: "Sequence", totalcount: 4, taxon: "orangutan", value: "\n AGAAATATGTCTGACAAAAGAGTTACTTTGATAGAGTAAAAAATAGAGGTCTAAATCCCCTTATTTCTACTAGGACTATGGGAATTGAACCCACCCCTGAGAATCCAAAATTCTCCGTGCCACCCATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTA--CACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTCA-CAGCACTTAATTTCTGTAAGGACTGCAAAACCCCACTTTGCATCAACTGAGCGCAAATCAGCCACTTTAATTAAGCTAAGCCCTCCTAGACCGATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAT-TGGCTTCAGTCCAAAGCCCCGGCAGGCCTTAAAGCTGCTCCTTCGAATTTGCAATTCAACATGACAA-TCACCTCAGGGCTTGGTAAAAAGAGGTCTGACCCCTGTTCTTAGATTTACAGCCTAATGCCTTAACTCGGCCATTTTACCGCAAAAAAGGAAGGAATCGAACCTCCTAAAGCTGGTTTCAAGCCAACCCCATAACCCCCATGACTTTTTCAAAAGGTACTAGAAAAACCATTTCGTAACTTTGTCAAAGTTAAATTACAGGTC-AGACCCTGTGTATCTTA-CATTGCAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACCAGCCTCTCTTTGCAATGA\n " },
+		 {spec: "Sequence", totalcount: 4, taxon: "siamang", value: "\n AGAAATACGTCTGACGAAAGAGTTACTTTGATAGAGTAAATAACAGGGGTTTAAATCCCCTTATTTCTACTAGAACCATAGGAGTCGAACCCATCCTTGAGAATCCAAAACTCTCCGTGCCACCCGTCGCACCCTGTTCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCATACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTAACAAAACTTAATTTCTGCAAGGGCTGCAAAACCCTACTTTGCATCAACCGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCGATGGGACTTAAACCCATAAAAATTTAGTTAACAGCTAAACACCCTAAACAACCTGGCTTCAATCTAAAGCCCCGGCAGA-GTTGAAGCTGCTTCTTTGAACTTGCAATTCAACGTGAAAAATCACTTCGGAGCTTGGCAAAAAGAGGTTTCACCTCTGTCCTTAGATTTACAGTCTAATGCTTTA-CTCAGCCACTTTACCACAAAAAAGGAAGGAATCGAACCCTCTAAAACCGGTTTCAAGCCAGCCCCATAACCTTTATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATCACAGGTCCAAACCCCGTATATCTTATCACTGTAGAGCTAGACCAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACTACCGCCTCTTTACAGTGA\n " }
+	  ]
+	},
+
+	{id: "mcmc",
+	 spec: "MCMC", chainLength: "5000000", preBurnin: 50000,
+	 init: [
+		{id: "coalescentSimulator",
+		 spec: "beast.base.evolution.tree.coalescent.RandomTree", taxa: "@alignment",
+			 populationModel: {spec: "ConstantPopulation", popSize: "1.0" },
+			 initial: {id: "tree", spec: "beast.base.evolution.tree.Tree" }
+		}
+	  ],
+	 distribution: {id: "posterior",
+		 spec: "CompoundDistribution",
+		 distribution: [
+			{spec: "beast.base.inference.distribution.Prior",
+				 x: {id: "hky.kappa", spec: "parameter.RealParameter", lower: 0.0, value: [ 1.0 ] },
+				 distr: {spec: "beast.base.inference.distribution.OneOnX" }
+			},
+			{id: "treeLikelihood",
+			 spec: "TreeLikelihood", data: "@alignment", tree: "@tree",
+			 siteModel: {id: "siteModel",
+				 spec: "SiteModel", gammaCategoryCount: 1,
+				 substModel: {id: "hky",
+					 spec: "HKY", kappa: "@hky.kappa",
+						 frequencies: {id: "freqs", spec: "Frequencies", data: "@alignment" }
+					}
+				}
+			}
+		  ]
+		},
+	 operator: [
+		 {id: "kappaScaler", spec: "ScaleOperator", parameter: "@hky.kappa", scaleFactor: 0.5, weight: 1.0 },
+		 {id: "treeScaler", spec: "ScaleOperator", tree: "@tree", scaleFactor: 0.5, weight: 1.0 },
+		 {id: "subtreeSlide", spec: "SubtreeSlide", tree: "@tree", weight: 5.0 },
+		 {id: "uniform", spec: "Uniform", tree: "@tree", weight: 10.0 },
+		 {id: "narrow", spec: "Exchange", tree: "@tree", weight: 1.0 },
+		 {id: "wide", spec: "Exchange", isNarrow: false, tree: "@tree", weight: 1.0 },
+		 {id: "wilsonBalding", spec: "WilsonBalding", tree: "@tree", weight: 1.0 }
+	  ],
+	 logger: [
+		{spec: "Logger", fileName: "test.$(seed).log", logEvery: 10000, model: "@treeLikelihood",
+		 log: [
+			 {idref: "treeLikelihood" },
+			 {idref: "hky.kappa" },
+			 {spec: "beast.base.evolution.tree.TreeStatLogger", tree: "@tree" }
+		  ]
+		},
+		{spec: "Logger", fileName: "test.$(seed).trees", logEvery: 10000,
+		 log: [
+			 {idref: "tree" }
+		  ]
+		},
+		{spec: "Logger", logEvery: 10000, model: "@treeLikelihood",
+		 log: [
+			 {idref: "treeLikelihood" },
+			 {spec: "beast.base.inference.util.ESS", arg: "@treeLikelihood" },
+			 {idref: "hky.kappa" },
+			 {spec: "beast.base.inference.util.ESS", arg: "@hky.kappa" }
+		  ]
+		}
+	  ]
+	}
+]
+}
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/testHKY.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testHKY.xml
similarity index 65%
rename from beast-base/src/test/resources/beast.base/examples/spec/testHKY.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/testHKY.xml
index a6a83b28..4377e018 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/testHKY.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/testHKY.xml
@@ -1,6 +1,6 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<beast version="2.8"
-       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt">
+<beast version='2.0'
+       namespace='beast.base.evolution.alignment:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
+
 
     <!-- The sequence alignment                                                  -->
     <!-- ntax=6 nchar=768                                                        -->
@@ -27,74 +27,77 @@
     </data>
 
     <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
-    <input spec="beast.base.spec.evolution.substitutionmodel.HKY" id="hky">
-        <kappa idref="hky.kappa"/>
-        <frequencies id="freqs" spec="beast.base.spec.evolution.substitutionmodel.Frequencies">
-            <data idref="alignment"/>
+    <input spec='HKY' id='hky'>
+        <kappa idref='hky.kappa'/>
+        <frequencies id='freqs' spec='Frequencies'>
+            <data idref='alignment'/>
         </frequencies>
     </input>
 
     <!-- site model                                                              -->
-    <input spec="beast.base.spec.evolution.sitemodel.SiteModel" id="siteModel" gammaCategoryCount="1">
+    <input spec='SiteModel' id="siteModel" gammaCategoryCount='1'>
         <!--
             <parameter name='shape' id='shape' value='0.5'/>
             <parameter name='proportionInvariant' id='propInvar' value='0.2'/>
         -->
-        <substModel idref="hky"/>
+        <substModel idref='hky'/>
     </input>
 
-    <input spec="beast.base.spec.evolution.likelihood.TreeLikelihood" id="treeLikelihood">
+    <input spec='TreeLikelihood' id="treeLikelihood">
         <data idref="alignment"/>
         <tree idref="tree"/>
         <siteModel idref="siteModel"/>
     </input>
 
-    <parameter id="hky.kappa" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+    <parameter id="hky.kappa" value="1.0" lower="0.0"/>
 
-    <tree id="tree"/>
+    <tree id='tree'/>
 
-    <tree spec="beast.base.spec.evolution.tree.ClusterTree" id="upgmatree" clusterType="upgma" initial="@tree">
-        <taxa idref="alignment"/>
+    <tree spec='beast.base.evolution.tree.ClusterTree' id='upgmatree' clusterType='upgma' initial='@tree'>
+        <taxa idref='alignment'/>
     </tree>
-    <tree spec="beast.base.spec.evolution.tree.coalescent.RandomTree" id="coalescentSimulator" initial="@tree" taxa="@alignment">
-        <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
-            <popSize value="1" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+    <tree spec='beast.base.evolution.tree.coalescent.RandomTree' id='coalescentSimulator' initial='@tree' taxa='@alignment'>
+        <populationModel spec='ConstantPopulation'>
+            <popSize spec='parameter.RealParameter' value='1'/>
         </populationModel>
     </tree>
 
+
     <run spec="MCMC" id="mcmc" chainLength="5000000" preBurnin="50000">
 
-        <init idref="coalescentSimulator"/>
-        <distribution spec="CompoundDistribution" id="posterior">
-            <distribution spec="beast.base.spec.inference.distribution.LogNormal" param="@hky.kappa"><M spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real" value="1.0"/><S spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal" value="0.5"/></distribution>
-            <distribution id="likelihood" idref="treeLikelihood"/>
+        <init idref='coalescentSimulator'/>
+        <distribution spec='CompoundDistribution' id='posterior'>
+            <distribution spec='beast.base.inference.distribution.Prior' x='@hky.kappa'>
+                <distr spec='beast.base.inference.distribution.OneOnX'/>
+            </distribution>
+            <distribution id='likelihood' idref="treeLikelihood"/>
         </distribution>
 
-        <operator id="kappaScaler" scaleFactor="0.5" weight="1" parameter="@hky.kappa" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-        <operator id="treeScaler" scaleFactor="0.5" weight="1" tree="@tree" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
+        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" parameter="@hky.kappa"/>
+        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" tree="@tree"/>
 
-        <operator id="subtreeSlide" spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" weight="5" size="1.0" tree="@tree"/>
+        <operator id='subtreeSlide' spec='SubtreeSlide' weight="5" gaussian="true" size="1.0" tree="@tree"/>
 
-        <operator id="uniform" weight="10" tree="@tree" spec="beast.base.evolution.operator.Uniform"/>
-        <operator id="narrow" spec="Exchange" isNarrow="true" weight="1" tree="@tree"/>
-        <operator id="wide" spec="Exchange" isNarrow="false" weight="1" tree="@tree"/>
-        <operator id="wilsonBalding" spec="WilsonBalding" weight="1" tree="@tree"/>
+        <operator id='uniform' spec='Uniform' weight="10" tree="@tree"/>
+        <operator id='narrow' spec='Exchange' isNarrow='true' weight="1" tree="@tree"/>
+        <operator id='wide' spec='Exchange' isNarrow='false' weight="1" tree="@tree"/>
+        <operator id='wilsonBalding' spec='WilsonBalding' weight="1" tree="@tree"/>
 
         <logger logEvery="10000" fileName="test.$(seed).log">
-            <model idref="likelihood"/>
+            <model idref='likelihood'/>
             <log idref="likelihood"/>
-            <log idref="hky.kappa"/>
-            <log spec="beast.base.evolution.tree.TreeStatLogger" tree="@tree"/>
+            <log idref='hky.kappa'/>
+            <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree'/>
         </logger>
         <logger logEvery="10000" fileName="test.$(seed).trees">
             <log idref="tree"/>
         </logger>
         <logger logEvery="10000">
-            <model idref="likelihood"/>
+            <model idref='likelihood'/>
             <log idref="likelihood"/>
-            <ESS spec="beast.base.spec.inference.util.ESS" name="log" arg="@likelihood"/>
-            <log idref="hky.kappa"/>
-            <ESS spec="beast.base.spec.inference.util.ESS" name="log" arg="@hky.kappa"/>
+            <ESS spec='ESS' name='log' arg="@likelihood"/>
+            <log idref='hky.kappa'/>
+            <ESS spec='ESS' name='log' arg="@hky.kappa"/>
         </logger>
     </run>
 
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantor.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testJukesCantor.xml
similarity index 72%
rename from beast-base/src/test/resources/beast.base/examples/spec/testJukesCantor.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/testJukesCantor.xml
index 559ba59a..3fcf586b 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantor.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/testJukesCantor.xml
@@ -1,6 +1,6 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<beast version="2.8"
-       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt">
+<beast version='2.0'
+       namespace='beast.base.evolution.alignment:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
+
 
     <!-- The sequence alignment                                                  -->
     <!-- ntax=6 nchar=768                                                        -->
@@ -27,58 +27,58 @@
     </data>
 
     <!-- The Jukes-Cantor substitution model (Jukes & Cantor, 1969)             -->
-    <input spec="beast.base.spec.evolution.substitutionmodel.JukesCantor" id="jc69"/>
+    <input spec='JukesCantor' id='jc69'/>
 
     <!-- site model                                                              -->
-    <input spec="beast.base.spec.evolution.sitemodel.SiteModel" id="siteModel" gammaCategoryCount="1">
-        <substModel idref="jc69"/>
+    <input spec='SiteModel' id="siteModel" gammaCategoryCount='1'>
+        <substModel idref='jc69'/>
     </input>
 
-    <input spec="beast.base.spec.evolution.likelihood.TreeLikelihood" id="treeLikelihood">
+    <input spec='TreeLikelihood' id="treeLikelihood">
         <data idref="alignment"/>
         <tree idref="tree"/>
         <siteModel idref="siteModel"/>
     </input>
 
-    <tree id="tree"/>
+    <tree id='tree'/>
 
-    <tree spec="beast.base.spec.evolution.tree.ClusterTree" id="upgmatree" clusterType="upgma" initial="@tree">
-        <taxa idref="alignment"/>
+    <tree spec='beast.base.evolution.tree.ClusterTree' id='upgmatree' clusterType='upgma' initial='@tree'>
+        <taxa idref='alignment'/>
     </tree>
-    <tree spec="beast.base.spec.evolution.tree.coalescent.RandomTree" id="coalescentSimulator" initial="@tree" taxa="@alignment">
-        <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
-            <popSize value="0.05" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+    <tree spec='beast.base.evolution.tree.coalescent.RandomTree' id='coalescentSimulator' initial='@tree' taxa='@alignment'>
+        <populationModel spec='ConstantPopulation'>
+            <popSize spec='parameter.RealParameter' value='0.05'/>
         </populationModel>
     </tree>
 
     <run spec="MCMC" id="mcmc" chainLength="5000000" preBurnin="50000">
 
-        <init idref="coalescentSimulator"/>
-        <distribution spec="CompoundDistribution" id="posterior">
-            <distribution id="likelihood" idref="treeLikelihood"/>
+        <init idref='coalescentSimulator'/>
+        <distribution spec='CompoundDistribution' id='posterior'>
+            <distribution id='likelihood' idref="treeLikelihood"/>
         </distribution>
 
-        <operator id="treeScaler" scaleFactor="0.5" weight="1" tree="@tree" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
+        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" tree="@tree"/>
 
-        <operator spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" weight="5" size="1.0" tree="@tree"/>
+        <operator spec='SubtreeSlide' weight="5" gaussian="true" size="1.0" tree="@tree"/>
 
-        <operator weight="10" tree="@tree" spec="beast.base.evolution.operator.Uniform"/>
-        <operator id="narrow" spec="Exchange" isNarrow="true" weight="1" tree="@tree"/>
-        <operator id="wide" spec="Exchange" isNarrow="false" weight="1" tree="@tree"/>
-        <operator spec="WilsonBalding" weight="1" tree="@tree"/>
+        <operator spec='Uniform' weight="10" tree="@tree"/>
+        <operator id='narrow' spec='Exchange' isNarrow='true' weight="1" tree="@tree"/>
+        <operator id='wide' spec='Exchange' isNarrow='false' weight="1" tree="@tree"/>
+        <operator spec='WilsonBalding' weight="1" tree="@tree"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
-            <model idref="likelihood"/>
+            <model idref='likelihood'/>
             <log idref="likelihood"/>
-            <log spec="beast.base.evolution.tree.TreeStatLogger" tree="@tree"/>
+            <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree'/>
         </logger>
         <logger logEvery="1000" fileName="test.$(seed).trees">
             <log idref="tree"/>
         </logger>
         <logger logEvery="20000">
-            <model idref="likelihood"/>
+            <model idref='likelihood'/>
             <log idref="likelihood"/>
-            <ESS spec="beast.base.spec.inference.util.ESS" name="log" arg="@likelihood"/>
+            <ESS spec='ESS' name='log' arg="@likelihood"/>
         </logger>
     </run>
 
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShort.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testJukesCantorShort.xml
similarity index 62%
rename from beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShort.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/testJukesCantorShort.xml
index ca09b44a..5975f6bd 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShort.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/testJukesCantorShort.xml
@@ -1,6 +1,6 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<beast version="2.8"
-       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt">
+<beast version='2.0'
+       namespace='beast.base.evolution.alignment:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
+
 
     <!-- A shortened version of the mitochondrial DNA alignment in testJukesCantor.xml, leading to higher uncertainty regarding the splits in the tree.  -->
     <!-- ntax=6 nchar=415                                                        -->
@@ -26,58 +26,58 @@
     </data>
 
     <!-- The Jukes-Cantor substitution model (Jukes & Cantor, 1969)             -->
-    <input spec="beast.base.spec.evolution.substitutionmodel.JukesCantor" id="jc69"/>
+    <input spec='JukesCantor' id='jc69'/>
 
     <!-- site model                                                              -->
-    <input spec="beast.base.spec.evolution.sitemodel.SiteModel" id="siteModel" gammaCategoryCount="1">
-        <substModel idref="jc69"/>
+    <input spec='SiteModel' id="siteModel" gammaCategoryCount='1'>
+        <substModel idref='jc69'/>
     </input>
 
-    <input spec="beast.base.spec.evolution.likelihood.TreeLikelihood" id="treeLikelihood">
+    <input spec='TreeLikelihood' id="treeLikelihood">
         <data idref="alignment"/>
         <tree idref="tree"/>
         <siteModel idref="siteModel"/>
     </input>
 
-    <tree id="tree"/>
+    <tree id='tree'/>
 
-    <tree spec="beast.base.spec.evolution.tree.ClusterTree" id="upgmatree" clusterType="upgma" initial="@tree">
-        <taxa idref="alignment"/>
+    <tree spec='beast.base.evolution.tree.ClusterTree' id='upgmatree' clusterType='upgma' initial='@tree'>
+        <taxa idref='alignment'/>
     </tree>
-    <tree spec="beast.base.spec.evolution.tree.coalescent.RandomTree" id="coalescentSimulator" initial="@tree" taxa="@alignment">
-        <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
-            <popSize value="0.05" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+    <tree spec='beast.base.evolution.tree.coalescent.RandomTree' id='coalescentSimulator' initial='@tree' taxa='@alignment'>
+        <populationModel spec='ConstantPopulation'>
+            <popSize spec='parameter.RealParameter' value='0.05'/>
         </populationModel>
     </tree>
 
     <run spec="MCMC" id="mcmc" chainLength="5000000" preBurnin="50000">
 
-        <init idref="coalescentSimulator"/>
-        <distribution spec="CompoundDistribution" id="posterior">
-            <distribution id="likelihood" idref="treeLikelihood"/>
+        <init idref='coalescentSimulator'/>
+        <distribution spec='CompoundDistribution' id='posterior'>
+            <distribution id='likelihood' idref="treeLikelihood"/>
         </distribution>
 
-        <operator id="treeScaler" scaleFactor="0.5" weight="1" tree="@tree" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
+        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" tree="@tree"/>
 
-        <operator spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" weight="5" size="1.0" tree="@tree"/>
+        <operator spec='SubtreeSlide' weight="5" gaussian="true" size="1.0" tree="@tree"/>
 
-        <operator weight="10" tree="@tree" spec="beast.base.evolution.operator.Uniform"/>
-        <operator id="narrow" spec="Exchange" isNarrow="true" weight="1" tree="@tree"/>
-        <operator id="wide" spec="Exchange" isNarrow="false" weight="1" tree="@tree"/>
-        <operator spec="WilsonBalding" weight="1" tree="@tree"/>
+        <operator spec='Uniform' weight="10" tree="@tree"/>
+        <operator id='narrow' spec='Exchange' isNarrow='true' weight="1" tree="@tree"/>
+        <operator id='wide' spec='Exchange' isNarrow='false' weight="1" tree="@tree"/>
+        <operator spec='WilsonBalding' weight="1" tree="@tree"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
-            <model idref="likelihood"/>
+            <model idref='likelihood'/>
             <log idref="likelihood"/>
-            <log spec="beast.base.evolution.tree.TreeStatLogger" tree="@tree"/>
+            <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree'/>
         </logger>
         <logger logEvery="1000" fileName="test.$(seed).trees">
             <log idref="tree"/>
         </logger>
         <logger logEvery="20000">
-            <model idref="likelihood"/>
+            <model idref='likelihood'/>
             <log idref="likelihood"/>
-            <ESS spec="beast.base.spec.inference.util.ESS" name="log" arg="@likelihood"/>
+            <ESS spec='ESS' name='log' arg="@likelihood"/>
         </logger>
     </run>
 
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShortUncertain.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testJukesCantorShortUncertain.xml
similarity index 96%
rename from beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShortUncertain.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/testJukesCantorShortUncertain.xml
index ed12c1b6..d9cc153d 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShortUncertain.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/testJukesCantorShortUncertain.xml
@@ -1,6 +1,6 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<beast version="2.8"
-       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt">
+<beast version='2.0'
+       namespace='beast.base.evolution.alignment:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
+
 
     <!-- The sequence alignment from testJukesCantorShort.xml, after converting to tip likelihoods.
 	These tip likelihoods denote the likelihood of observed data (e.g. read counts) given a particular base call.
@@ -37,58 +37,58 @@
     </data>
 
     <!-- The Jukes-Cantor substitution model (Jukes & Cantor, 1969)             -->
-    <input spec="beast.base.spec.evolution.substitutionmodel.JukesCantor" id="jc69"/>
+    <input spec='JukesCantor' id='jc69'/>
 
     <!-- site model                                                              -->
-    <input spec="beast.base.spec.evolution.sitemodel.SiteModel" id="siteModel" gammaCategoryCount="1">
-        <substModel idref="jc69"/>
+    <input spec='SiteModel' id="siteModel" gammaCategoryCount='1'>
+        <substModel idref='jc69'/>
     </input>
 
-    <input spec="beast.base.spec.evolution.likelihood.TreeLikelihood" id="treeLikelihood" useTipLikelihoods="true">
+    <input spec='TreeLikelihood' id="treeLikelihood" useTipLikelihoods="true">
         <data idref="alignment"/>
         <tree idref="tree"/>
         <siteModel idref="siteModel"/>
     </input>
 
-    <tree id="tree"/>
+    <tree id='tree'/>
 
-    <tree spec="beast.base.spec.evolution.tree.ClusterTree" id="upgmatree" clusterType="upgma" initial="@tree">
-        <taxa idref="alignment"/>
+    <tree spec='beast.base.evolution.tree.ClusterTree' id='upgmatree' clusterType='upgma' initial='@tree'>
+        <taxa idref='alignment'/>
     </tree>
-    <tree spec="beast.base.spec.evolution.tree.coalescent.RandomTree" id="coalescentSimulator" initial="@tree" taxa="@alignment">
-        <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
-            <popSize value="0.05" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+    <tree spec='beast.base.evolution.tree.coalescent.RandomTree' id='coalescentSimulator' initial='@tree' taxa='@alignment'>
+        <populationModel spec='ConstantPopulation'>
+            <popSize spec='parameter.RealParameter' value='0.05'/>
         </populationModel>
     </tree>
 
     <run spec="MCMC" id="mcmc" chainLength="5000000" preBurnin="50000">
 
-        <init idref="coalescentSimulator"/>
-        <distribution spec="CompoundDistribution" id="posterior">
-            <distribution id="likelihood" idref="treeLikelihood"/>
+        <init idref='coalescentSimulator'/>
+        <distribution spec='CompoundDistribution' id='posterior'>
+            <distribution id='likelihood' idref="treeLikelihood"/>
         </distribution>
 
-        <operator id="treeScaler" scaleFactor="0.5" weight="1" tree="@tree" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
+        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" tree="@tree"/>
 
-        <operator spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" weight="5" size="1.0" tree="@tree"/>
+        <operator spec='SubtreeSlide' weight="5" gaussian="true" size="1.0" tree="@tree"/>
 
-        <operator weight="10" tree="@tree" spec="beast.base.evolution.operator.Uniform"/>
-        <operator id="narrow" spec="Exchange" isNarrow="true" weight="1" tree="@tree"/>
-        <operator id="wide" spec="Exchange" isNarrow="false" weight="1" tree="@tree"/>
-        <operator spec="WilsonBalding" weight="1" tree="@tree"/>
+        <operator spec='Uniform' weight="10" tree="@tree"/>
+        <operator id='narrow' spec='Exchange' isNarrow='true' weight="1" tree="@tree"/>
+        <operator id='wide' spec='Exchange' isNarrow='false' weight="1" tree="@tree"/>
+        <operator spec='WilsonBalding' weight="1" tree="@tree"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
-            <model idref="likelihood"/>
+            <model idref='likelihood'/>
             <log idref="likelihood"/>
-            <log spec="beast.base.evolution.tree.TreeStatLogger" tree="@tree"/>
+            <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree'/>
         </logger>
         <logger logEvery="1000" fileName="test.$(seed).trees">
             <log idref="tree"/>
         </logger>
         <logger logEvery="20000">
-            <model idref="likelihood"/>
+            <model idref='likelihood'/>
             <log idref="likelihood"/>
-            <ESS spec="beast.base.spec.inference.util.ESS" name="log" arg="@likelihood"/>
+            <ESS spec='ESS' name='log' arg="@likelihood"/>
         </logger>
     </run>
 
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShortUncertain2.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testJukesCantorShortUncertain2.xml
similarity index 96%
rename from beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShortUncertain2.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/testJukesCantorShortUncertain2.xml
index 3f45e0dc..59e72041 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShortUncertain2.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/testJukesCantorShortUncertain2.xml
@@ -1,6 +1,6 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<beast version="2.8"
-       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt">
+<beast version='2.0'
+       namespace='beast.base.evolution.alignment:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
+
 
     <!-- The sequence alignment from testJukesCantorShort.xml, after converting to tip likelihoods.
 	These tip likelihoods denote the likelihood of observed data (e.g. read counts) given a particular base call.
@@ -38,58 +38,58 @@
 </data>
 
     <!-- The Jukes-Cantor substitution model (Jukes & Cantor, 1969)             -->
-    <input spec="beast.base.spec.evolution.substitutionmodel.JukesCantor" id="jc69"/>
+    <input spec='JukesCantor' id='jc69'/>
 
     <!-- site model                                                              -->
-    <input spec="beast.base.spec.evolution.sitemodel.SiteModel" id="siteModel" gammaCategoryCount="1">
-        <substModel idref="jc69"/>
+    <input spec='SiteModel' id="siteModel" gammaCategoryCount='1'>
+        <substModel idref='jc69'/>
     </input>
 
-    <input spec="beast.base.spec.evolution.likelihood.TreeLikelihood" id="treeLikelihood" useTipLikelihoods="true">
+    <input spec='TreeLikelihood' id="treeLikelihood" useTipLikelihoods="true">
         <data idref="alignment"/>
         <tree idref="tree"/>
         <siteModel idref="siteModel"/>
     </input>
 
-    <tree id="tree"/>
+    <tree id='tree'/>
 
-    <tree spec="beast.base.spec.evolution.tree.ClusterTree" id="upgmatree" clusterType="upgma" initial="@tree">
-        <taxa idref="alignment"/>
+    <tree spec='beast.base.evolution.tree.ClusterTree' id='upgmatree' clusterType='upgma' initial='@tree'>
+        <taxa idref='alignment'/>
     </tree>
-    <tree spec="beast.base.spec.evolution.tree.coalescent.RandomTree" id="coalescentSimulator" initial="@tree" taxa="@alignment">
-        <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
-            <popSize value="0.05" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+    <tree spec='beast.base.evolution.tree.coalescent.RandomTree' id='coalescentSimulator' initial='@tree' taxa='@alignment'>
+        <populationModel spec='ConstantPopulation'>
+            <popSize spec='parameter.RealParameter' value='0.05'/>
         </populationModel>
     </tree>
 
     <run spec="MCMC" id="mcmc" chainLength="5000000" preBurnin="50000">
 
-        <init idref="coalescentSimulator"/>
-        <distribution spec="CompoundDistribution" id="posterior">
-            <distribution id="likelihood" idref="treeLikelihood"/>
+        <init idref='coalescentSimulator'/>
+        <distribution spec='CompoundDistribution' id='posterior'>
+            <distribution id='likelihood' idref="treeLikelihood"/>
         </distribution>
 
-        <operator id="treeScaler" scaleFactor="0.5" weight="1" tree="@tree" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
+        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" tree="@tree"/>
 
-        <operator spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" weight="5" size="1.0" tree="@tree"/>
+        <operator spec='SubtreeSlide' weight="5" gaussian="true" size="1.0" tree="@tree"/>
 
-        <operator weight="10" tree="@tree" spec="beast.base.evolution.operator.Uniform"/>
-        <operator id="narrow" spec="Exchange" isNarrow="true" weight="1" tree="@tree"/>
-        <operator id="wide" spec="Exchange" isNarrow="false" weight="1" tree="@tree"/>
-        <operator spec="WilsonBalding" weight="1" tree="@tree"/>
+        <operator spec='Uniform' weight="10" tree="@tree"/>
+        <operator id='narrow' spec='Exchange' isNarrow='true' weight="1" tree="@tree"/>
+        <operator id='wide' spec='Exchange' isNarrow='false' weight="1" tree="@tree"/>
+        <operator spec='WilsonBalding' weight="1" tree="@tree"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
-            <model idref="likelihood"/>
+            <model idref='likelihood'/>
             <log idref="likelihood"/>
-            <log spec="beast.base.evolution.tree.TreeStatLogger" tree="@tree"/>
+            <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree'/>
         </logger>
         <logger logEvery="1000" fileName="test.$(seed).trees">
             <log idref="tree"/>
         </logger>
         <logger logEvery="20000">
-            <model idref="likelihood"/>
+            <model idref='likelihood'/>
             <log idref="likelihood"/>
-            <ESS spec="beast.base.spec.inference.util.ESS" name="log" arg="@likelihood"/>
+            <ESS spec='ESS' name='log' arg="@likelihood"/>
         </logger>
     </run>
 
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShortUncertain2MLE.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testJukesCantorShortUncertain2MLE.xml
similarity index 62%
rename from beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShortUncertain2MLE.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/testJukesCantorShortUncertain2MLE.xml
index 53849976..117f3115 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShortUncertain2MLE.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/testJukesCantorShortUncertain2MLE.xml
@@ -1,6 +1,6 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<beast version="2.8"
-       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt">
+<beast version='2.0'
+       namespace='beast.base.evolution.alignment:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
+
 
     <!-- The sequence alignment from testJukesCantorShortUncertain2.xml, after 
     reconstructing the MLE for the sequences from the noisy simulated read data.
@@ -29,58 +29,58 @@
     </data>
 
     <!-- The Jukes-Cantor substitution model (Jukes & Cantor, 1969)             -->
-    <input spec="beast.base.spec.evolution.substitutionmodel.JukesCantor" id="jc69"/>
+    <input spec='JukesCantor' id='jc69'/>
 
     <!-- site model                                                              -->
-    <input spec="beast.base.spec.evolution.sitemodel.SiteModel" id="siteModel" gammaCategoryCount="1">
-        <substModel idref="jc69"/>
+    <input spec='SiteModel' id="siteModel" gammaCategoryCount='1'>
+        <substModel idref='jc69'/>
     </input>
 
-    <input spec="beast.base.spec.evolution.likelihood.TreeLikelihood" id="treeLikelihood">
+    <input spec='TreeLikelihood' id="treeLikelihood">
         <data idref="alignment"/>
         <tree idref="tree"/>
         <siteModel idref="siteModel"/>
     </input>
 
-    <tree id="tree"/>
+    <tree id='tree'/>
 
-    <tree spec="beast.base.spec.evolution.tree.ClusterTree" id="upgmatree" clusterType="upgma" initial="@tree">
-        <taxa idref="alignment"/>
+    <tree spec='beast.base.evolution.tree.ClusterTree' id='upgmatree' clusterType='upgma' initial='@tree'>
+        <taxa idref='alignment'/>
     </tree>
-    <tree spec="beast.base.spec.evolution.tree.coalescent.RandomTree" id="coalescentSimulator" initial="@tree" taxa="@alignment">
-        <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
-            <popSize value="0.05" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+    <tree spec='beast.base.evolution.tree.coalescent.RandomTree' id='coalescentSimulator' initial='@tree' taxa='@alignment'>
+        <populationModel spec='ConstantPopulation'>
+            <popSize spec='parameter.RealParameter' value='0.05'/>
         </populationModel>
     </tree>
 
     <run spec="MCMC" id="mcmc" chainLength="5000000" preBurnin="50000">
 
-        <init idref="coalescentSimulator"/>
-        <distribution spec="CompoundDistribution" id="posterior">
-            <distribution id="likelihood" idref="treeLikelihood"/>
+        <init idref='coalescentSimulator'/>
+        <distribution spec='CompoundDistribution' id='posterior'>
+            <distribution id='likelihood' idref="treeLikelihood"/>
         </distribution>
 
-        <operator id="treeScaler" scaleFactor="0.5" weight="1" tree="@tree" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
+        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" tree="@tree"/>
 
-        <operator spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" weight="5" size="1.0" tree="@tree"/>
+        <operator spec='SubtreeSlide' weight="5" gaussian="true" size="1.0" tree="@tree"/>
 
-        <operator weight="10" tree="@tree" spec="beast.base.evolution.operator.Uniform"/>
-        <operator id="narrow" spec="Exchange" isNarrow="true" weight="1" tree="@tree"/>
-        <operator id="wide" spec="Exchange" isNarrow="false" weight="1" tree="@tree"/>
-        <operator spec="WilsonBalding" weight="1" tree="@tree"/>
+        <operator spec='Uniform' weight="10" tree="@tree"/>
+        <operator id='narrow' spec='Exchange' isNarrow='true' weight="1" tree="@tree"/>
+        <operator id='wide' spec='Exchange' isNarrow='false' weight="1" tree="@tree"/>
+        <operator spec='WilsonBalding' weight="1" tree="@tree"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
-            <model idref="likelihood"/>
+            <model idref='likelihood'/>
             <log idref="likelihood"/>
-            <log spec="beast.base.evolution.tree.TreeStatLogger" tree="@tree"/>
+            <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree'/>
         </logger>
         <logger logEvery="1000" fileName="test.$(seed).trees">
             <log idref="tree"/>
         </logger>
         <logger logEvery="20000">
-            <model idref="likelihood"/>
+            <model idref='likelihood'/>
             <log idref="likelihood"/>
-            <ESS spec="beast.base.spec.inference.util.ESS" name="log" arg="@likelihood"/>
+            <ESS spec='ESS' name='log' arg="@likelihood"/>
         </logger>
     </run>
 
diff --git a/beast-base/src/test/resources/beast.base/examples/testMultipleAlignments_randomTaxaOrder.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testMultipleAlignments_randomTaxaOrder.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/testMultipleAlignments_randomTaxaOrder.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/testMultipleAlignments_randomTaxaOrder.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/testOpSubSchedule.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testOpSubSchedule.xml
similarity index 67%
rename from beast-base/src/test/resources/beast.base/examples/spec/testOpSubSchedule.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/testOpSubSchedule.xml
index f828101e..e49dfc59 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/testOpSubSchedule.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/testOpSubSchedule.xml
@@ -1,6 +1,6 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<beast version="2.8"
-       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt">
+<beast version='2.0'
+       namespace='beast.base.evolution.alignment:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
+
 
     <!-- The sequence alignment                                                  -->
     <!-- ntax=6 nchar=768                                                        -->
@@ -27,47 +27,50 @@
     </data>
 
     <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
-    <input spec="beast.base.spec.evolution.substitutionmodel.HKY" id="hky">
-        <kappa idref="hky.kappa"/>
-        <frequencies id="freqs" spec="beast.base.spec.evolution.substitutionmodel.Frequencies">
-            <data idref="alignment"/>
+    <input spec='HKY' id='hky'>
+        <kappa idref='hky.kappa'/>
+        <frequencies id='freqs' spec='Frequencies'>
+            <data idref='alignment'/>
         </frequencies>
     </input>
 
     <!-- site model                                                              -->
-    <input spec="beast.base.spec.evolution.sitemodel.SiteModel" id="siteModel" gammaCategoryCount="1">
+    <input spec='SiteModel' id="siteModel" gammaCategoryCount='1'>
         <!--
             <parameter name='shape' id='shape' value='0.5'/>
             <parameter name='proportionInvariant' id='propInvar' value='0.2'/>
         -->
-        <substModel idref="hky"/>
+        <substModel idref='hky'/>
     </input>
 
-    <input spec="beast.base.spec.evolution.likelihood.TreeLikelihood" id="treeLikelihood">
+    <input spec='TreeLikelihood' id="treeLikelihood">
         <data idref="alignment"/>
         <tree idref="tree"/>
         <siteModel idref="siteModel"/>
     </input>
 
-    <parameter id="hky.kappa" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+    <parameter id="hky.kappa" value="1.0" lower="0.0"/>
 
-    <tree id="tree"/>
+    <tree id='tree'/>
 
-    <tree spec="beast.base.spec.evolution.tree.ClusterTree" id="upgmatree" clusterType="upgma" initial="@tree">
-        <taxa idref="alignment"/>
+    <tree spec='beast.base.evolution.tree.ClusterTree' id='upgmatree' clusterType='upgma' initial='@tree'>
+        <taxa idref='alignment'/>
     </tree>
-    <tree spec="beast.base.spec.evolution.tree.coalescent.RandomTree" id="coalescentSimulator" initial="@tree" taxa="@alignment">
-        <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
-            <popSize value="1" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+    <tree spec='beast.base.evolution.tree.coalescent.RandomTree' id='coalescentSimulator' initial='@tree' taxa='@alignment'>
+        <populationModel spec='ConstantPopulation'>
+            <popSize spec='parameter.RealParameter' value='1'/>
         </populationModel>
     </tree>
 
+
     <run spec="MCMC" id="mcmc" chainLength="1000000" preBurnin="50000">
 
-        <init idref="coalescentSimulator"/>
-        <distribution spec="CompoundDistribution" id="posterior">
-            <distribution spec="beast.base.spec.inference.distribution.LogNormal" param="@hky.kappa"><M spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real" value="1.0"/><S spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal" value="0.5"/></distribution>
-            <distribution id="likelihood" idref="treeLikelihood"/>
+        <init idref='coalescentSimulator'/>
+        <distribution spec='CompoundDistribution' id='posterior'>
+            <distribution spec='beast.base.inference.distribution.Prior' x='@hky.kappa'>
+                <distr spec='beast.base.inference.distribution.OneOnX'/>
+            </distribution>
+            <distribution id='likelihood' idref="treeLikelihood"/>
         </distribution>
 
          <operatorschedule id="operatorSchedule" spec="OperatorSchedule">
@@ -75,31 +78,31 @@
             <subschedule id="operatorTrees" spec="OperatorSchedule" weight="50" weightIsPercentage="true" operatorPattern="^.*tree.*"/>
          </operatorschedule>
 
-        <operator id="kappaScaler" scaleFactor="0.5" weight="1" parameter="@hky.kappa" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-        <operator id="treeScaler" scaleFactor="0.5" weight="1" tree="@tree" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
+        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" parameter="@hky.kappa"/>
+        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" tree="@tree"/>
 
-        <operator id="subtreeSlide" spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" weight="5" size="1.0" tree="@tree"/>
+        <operator id='subtreeSlide' spec='SubtreeSlide' weight="5" gaussian="true" size="1.0" tree="@tree"/>
 
-        <operator id="uniform" weight="10" tree="@tree" spec="beast.base.evolution.operator.Uniform"/>
-        <operator id="narrow" spec="Exchange" isNarrow="true" weight="1" tree="@tree"/>
-        <operator id="wide" spec="Exchange" isNarrow="false" weight="1" tree="@tree"/>
-        <operator id="wilsonBalding" spec="WilsonBalding" weight="1" tree="@tree"/>
+        <operator id='uniform' spec='Uniform' weight="10" tree="@tree"/>
+        <operator id='narrow' spec='Exchange' isNarrow='true' weight="1" tree="@tree"/>
+        <operator id='wide' spec='Exchange' isNarrow='false' weight="1" tree="@tree"/>
+        <operator id='wilsonBalding' spec='WilsonBalding' weight="1" tree="@tree"/>
 
         <logger logEvery="10000" fileName="test.$(seed).log">
-            <model idref="likelihood"/>
+            <model idref='likelihood'/>
             <log idref="likelihood"/>
-            <log idref="hky.kappa"/>
-            <log spec="beast.base.evolution.tree.TreeStatLogger" tree="@tree"/>
+            <log idref='hky.kappa'/>
+            <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree'/>
         </logger>
         <logger logEvery="10000" fileName="test.$(seed).trees">
             <log idref="tree"/>
         </logger>
         <logger logEvery="10000">
-            <model idref="likelihood"/>
+            <model idref='likelihood'/>
             <log idref="likelihood"/>
-            <ESS spec="beast.base.spec.inference.util.ESS" name="log" arg="@likelihood"/>
-            <log idref="hky.kappa"/>
-            <ESS spec="beast.base.spec.inference.util.ESS" name="log" arg="@hky.kappa"/>
+            <ESS spec='ESS' name='log' arg="@likelihood"/>
+            <log idref='hky.kappa'/>
+            <ESS spec='ESS' name='log' arg="@hky.kappa"/>
         </logger>
     </run>
 
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/testPlates.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testPlates.xml
similarity index 71%
rename from beast-base/src/test/resources/beast.base/examples/spec/testPlates.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/testPlates.xml
index b5a0da18..12a2e919 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/testPlates.xml
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/testPlates.xml
@@ -1,6 +1,6 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<beast version="2.8"
-       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt">
+<beast version='2.0'
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
+
 
     <!-- The sequence alignment                                                  -->
     <!-- ntax=6 nchar=768                                                        -->
@@ -57,64 +57,69 @@
         </sequence>
     </data>
 
-    <plate spec="util.Plate" var="n" range=".p1,.p2,.p3">
+    <plate spec='util.Plate' var='n' range='.p1,.p2,.p3'>
         <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
-        <input spec="beast.base.spec.evolution.substitutionmodel.HKY" id="hky$(n)" kappa="@hky.kappa$(n)">
-            <frequencies id="freqs$(n)" spec="beast.base.spec.evolution.substitutionmodel.Frequencies" data="@alignment$(n)"/>
+        <input spec='HKY' id='hky$(n)' kappa='@hky.kappa$(n)'>
+            <frequencies id='freqs$(n)' spec='Frequencies' data='@alignment$(n)'/>
         </input>
 
         <!-- site model                                                              -->
-        <input spec="beast.base.spec.evolution.sitemodel.SiteModel" id="siteModel$(n)" substModel="@hky$(n)"/>
+        <input spec='SiteModel' id="siteModel$(n)" substModel='@hky$(n)'/>
 
-        <input spec="beast.base.spec.evolution.likelihood.TreeLikelihood" id="treeLikelihood$(n)" data="@alignment$(n)" tree="@tree" siteModel="@siteModel$(n)"/>
+        <input spec='TreeLikelihood' id="treeLikelihood$(n)"
+            data="@alignment$(n)"
+            tree="@tree"
+            siteModel="@siteModel$(n)"
+        />
 
-        <parameter id="hky.kappa$(n)" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+        <parameter id="hky.kappa$(n)" value="1.0" lower="0.0"/>
     </plate>
 
-    <tree spec="beast.base.spec.evolution.tree.ClusterTree" id="tree" clusterType="upgma" taxa="@alignment.p1"/>
+    <tree spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma' taxa='@alignment.p1'/>
+
 
     <run spec="MCMC" id="mcmc" chainLength="10000000">
-        <state storeEvery="100000">
+        <state storeEvery='100000'>
             <stateNode idref="hky.kappa.p1"/>
             <stateNode idref="hky.kappa.p2"/>
             <stateNode idref="hky.kappa.p3"/>
             <stateNode idref="tree"/>
         </state>
 
-        <distribution spec="CompoundDistribution" id="likelihood">
-            <plate var="n" range=".p1,.p2,.p3">
-                <distribution id="likelihood$(n)" idref="treeLikelihood$(n)"/>
+        <distribution spec='CompoundDistribution' id='likelihood'>
+            <plate var='n' range='.p1,.p2,.p3'>
+                <distribution id='likelihood$(n)' idref="treeLikelihood$(n)"/>
             </plate>
         </distribution>
     
-        <plate var="n" range=".p1,.p2,.p3">
-            <operator id="kappaScaler$(n)" scaleFactor="0.5" weight="1" parameter="@hky.kappa$(n)" spec="beast.base.spec.inference.operator.ScaleOperator"/>
+        <plate var='n' range='.p1,.p2,.p3'>
+            <operator id='kappaScaler$(n)' spec='ScaleOperator' scaleFactor="0.5" weight="1" parameter="@hky.kappa$(n)"/>
         </plate>
-        <operator id="treeScaler" scaleFactor="0.5" weight="1" tree="@tree" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
-        <operator weight="10" tree="@tree" spec="beast.base.evolution.operator.Uniform"/>
-        <operator spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" weight="5" size="1.0" tree="@tree"/>
-        <operator id="narrow" spec="Exchange" isNarrow="true" weight="1" tree="@tree"/>
-        <operator id="wide" spec="Exchange" isNarrow="false" weight="1" tree="@tree"/>
-        <operator spec="WilsonBalding" weight="1" tree="@tree"/>
+        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" tree="@tree"/>
+        <operator spec='Uniform' weight="10" tree="@tree"/>
+        <operator spec='SubtreeSlide' weight="5" gaussian="true" size="1.0" tree="@tree"/>
+        <operator id='narrow' spec='Exchange' isNarrow='true' weight="1" tree="@tree"/>
+        <operator id='wide' spec='Exchange' isNarrow='false' weight="1" tree="@tree"/>
+        <operator spec='WilsonBalding' weight="1" tree="@tree"/>
 
         <logger logEvery="10000" fileName="test.$(seed).log">
-	        <model idref="likelihood"/>
+	        <model idref='likelihood'/>
             <log idref="likelihood"/>
-            <plate var="n" range=".p1,.p2,.p3">
-                <log idref="hky.kappa$(n)"/>
+            <plate var='n' range='.p1,.p2,.p3'>
+                <log idref='hky.kappa$(n)'/>
             </plate>
-            <log spec="beast.base.evolution.tree.TreeStatLogger"><tree idref="tree"/></log>
+            <log spec='beast.base.evolution.tree.TreeStatLogger'><tree idref='tree'/></log>
         </logger>
         <logger logEvery="10000" fileName="test.$(seed).trees">
             <log idref="tree"/>
         </logger>
         <logger logEvery="10000">
-	        <model idref="likelihood"/>
+	        <model idref='likelihood'/>
             <log idref="likelihood"/>
-    	    <ESS spec="beast.base.spec.inference.util.ESS" name="log" arg="@likelihood"/>
-            <plate var="n" range=".p1,.p2,.p3">
-                <log idref="hky.kappa$(n)"/>
-        	    <ESS spec="beast.base.spec.inference.util.ESS" name="log" arg="@hky.kappa$(n)"/>
+    	    <ESS spec='ESS' name='log' arg="@likelihood"/>
+            <plate var='n' range='.p1,.p2,.p3'>
+                <log idref='hky.kappa$(n)'/>
+        	    <ESS spec='ESS' name='log' arg="@hky.kappa$(n)"/>
             </plate>
         </logger>
 
diff --git a/beast-base/src/test/resources/beast.base/examples/legacy/testRNA.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testRNA.xml
new file mode 100644
index 00000000..041817ff
--- /dev/null
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/testRNA.xml
@@ -0,0 +1,212 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<beast beautitemplate='Standard' beautistatus=''
+       namespace="beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.alignment:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood"
+       version="2.0">
+
+<!-- A fake RNA alignment.  Should give exactly the same result as testGTR.xml. -->
+
+    <data id="primate-mtDNA">
+        <sequence id="seq_Lemur_catta" taxon="Lemur_catta" totalcount="4"
+                  value="AAGCUUCAUAGGAGCAACCAUUCUAAUAAUCGCACAUGGCCUUACAUCAUCCAUAUUAUUCUGUCUAGCCAACUCUAACUACGAACGAAUCCAUAGCCGUACAAUACUACUAGCACGAGGGAUCCAAACCAUUCUCCCUCUUAUAGCCACCUGAUGACUACUCGCCAGCCUAACUAACCUAGCCCUACCCACCUCUAUCAAUUUAAUUGGCGAACUAUUCGUCACUAUAGCAUCCUUCUCAUGAUCAAACAUUACAAUUAUCUUAAUAGGCUUAAAUAUGCUCAUCACCGCUCUCUAUUCCCUCUAUAUAUUAACUACUACACAACGAGGAAAACUCACAUAUCAUUCGCACAACCUAAACCCAUCCUUUACACGAGAAAACACCCUUAUAUCCAUACACAUACUCCCCCUUCUCCUAUUUACCUUAAACCCCAAAAUUAUUCUAGGACCCACGUACUGUAAAUAUAGUUUAAA-AAAACACUAGAUUGUGAAUCCAGAAAUAGAAGCUCAAAC-CUUCUUAUUUACCGAGAAAGUAAUGUAUGAACUGCUAACUCUGCACUCCGUAUAUAAAAAUACGGCUAUCUCAACUUUUAAAGGAUAGAAGUAAUCCAUUGGCCUUAGGAGCCAAAAA-AUUGGUGCAACUCCAAAUAAAAGUAAUAAAUCUAUUAUCCUCUUUCACCCUUGUCACACUGAUUAUCCUAACUUUACCUAUCAUUAUAAACGUUACAAACAUAUACAAAAACUACCCCUAUGCACCAUACGUAAAAUCUUCUAUUGCAUGUGCCUUCAUCACUAGCCUCAUCCCAACUAUAUUAUUUAUCUCCUCAGGACAAGAAACAAUCAUUUCCAACUGACAUUGAAUAACAAUCCAAACCCUAAAACUAUCUAUUAGCUU"/>
+        <sequence id="seq_Homo_sapiens" taxon="Homo_sapiens" totalcount="4"
+                  value="AAGCUUCACCGGCGCAGUCAUUCUCAUAAUCGCCCACGGGCUUACAUCCUCAUUACUAUUCUGCCUAGCAAACUCAAACUACGAACGCACUCACAGUCGCAUCAUAAUCCUCUCUCAAGGACUUCAAACUCUACUCCCACUAAUAGCUUUUUGAUGACUUCUAGCAAGCCUCGCUAACCUCGCCUUACCCCCCACUAUUAACCUACUGGGAGAACUCUCUGUGCUAGUAACCACGUUCUCCUGAUCAAAUAUCACUCUCCUACUUACAGGACUCAACAUACUAGUCACAGCCCUAUACUCCCUCUACAUAUUUACCACAACACAAUGGGGCUCACUCACCCACCACAUUAACAACAUAAAACCCUCAUUCACACGAGAAAACACCCUCAUGUUCAUACACCUAUCCCCCAUUCUCCUCCUAUCCCUCAACCCCGACAUCAUUACCGGGUUUUCCUCUUGUAAAUAUAGUUUAACCAAAACAUCAGAUUGUGAAUCUGACAACAGAGGCUUA-CGACCCCUUAUUUACCGAGAAAGCU-CACAAGAACUGCUAACUCAUGCCCCCAUGUCUAACAACAUGGCUUUCUCAACUUUUAAAGGAUAACAGCUAUCCAUUGGUCUUAGGCCCCAAAAAUUUUGGUGCAACUCCAAAUAAAAGUAAUAACCAUGCACACUACUAUAACCACCCUAACCCUGACUUCCCUAAUUCCCCCCAUCCUUACCACCCUCGUUAACCCUAACAAAAAAAACUCAUACCCCCAUUAUGUAAAAUCCAUUGUCGCAUCCACCUUUAUUAUCAGUCUCUUCCCCACAACAAUAUUCAUGUGCCUAGACCAAGAAGUUAUUAUCUCGAACUGACACUGAGCCACAACCCAAACAACCCAGCUCUCCCUAAGCUU"/>
+        <sequence id="seq_Pan" taxon="Pan" totalcount="4"
+                  value="AAGCUUCACCGGCGCAAUUAUCCUCAUAAUCGCCCACGGACUUACAUCCUCAUUAUUAUUCUGCCUAGCAAACUCAAAUUAUGAACGCACCCACAGUCGCAUCAUAAUUCUCUCCCAAGGACUUCAAACUCUACUCCCACUAAUAGCCUUUUGAUGACUCCUAGCAAGCCUCGCUAACCUCGCCCUACCCCCUACCAUUAAUCUCCUAGGGGAACUCUCCGUGCUAGUAACCUCAUUCUCCUGAUCAAAUACCACUCUCCUACUCACAGGAUUCAACAUACUAAUCACAGCCCUGUACUCCCUCUACAUGUUUACCACAACACAAUGAGGCUCACUCACCCACCACAUUAAUAACAUAAAGCCCUCAUUCACACGAGAAAAUACUCUCAUAUUUUUACACCUAUCCCCCAUCCUCCUUCUAUCCCUCAAUCCUGAUAUCAUCACUGGAUUCACCUCCUGUAAAUAUAGUUUAACCAAAACAUCAGAUUGUGAAUCUGACAACAGAGGCUCA-CGACCCCUUAUUUACCGAGAAAGCU-UAUAAGAACUGCUAAUUCAUAUCCCCAUGCCUGACAACAUGGCUUUCUCAACUUUUAAAGGAUAACAGCCAUCCGUUGGUCUUAGGCCCCAAAAAUUUUGGUGCAACUCCAAAUAAAAGUAAUAACCAUGUAUACUACCAUAACCACCUUAACCCUAACUCCCUUAAUUCUCCCCAUCCUCACCACCCUCAUUAACCCUAACAAAAAAAACUCAUAUCCCCAUUAUGUGAAAUCCAUUAUCGCGUCCACCUUUAUCAUUAGCCUUUUCCCCACAACAAUAUUCAUAUGCCUAGACCAAGAAGCUAUUAUCUCAAACUGGCACUGAGCAACAACCCAAACAACCCAGCUCUCCCUAAGCUU"/>
+        <sequence id="seq_Gorilla" taxon="Gorilla" totalcount="4"
+                  value="AAGCUUCACCGGCGCAGUUGUUCUUAUAAUUGCCCACGGACUUACAUCAUCAUUAUUAUUCUGCCUAGCAAACUCAAACUACGAACGAACCCACAGCCGCAUCAUAAUUCUCUCUCAAGGACUCCAAACCCUACUCCCACUAAUAGCCCUUUGAUGACUUCUGGCAAGCCUCGCCAACCUCGCCUUACCCCCCACCAUUAACCUACUAGGAGAGCUCUCCGUACUAGUAACCACAUUCUCCUGAUCAAACACCACCCUUUUACUUACAGGAUCUAACAUACUAAUUACAGCCCUGUACUCCCUUUAUAUAUUUACCACAACACAAUGAGGCCCACUCACACACCACAUCACCAACAUAAAACCCUCAUUUACACGAGAAAACAUCCUCAUAUUCAUGCACCUAUCCCCCAUCCUCCUCCUAUCCCUCAACCCCGAUAUUAUCACCGGGUUCACCUCCUGUAAAUAUAGUUUAACCAAAACAUCAGAUUGUGAAUCUGAUAACAGAGGCUCA-CAACCCCUUAUUUACCGAGAAAGCU-CGUAAGAGCUGCUAACUCAUACCCCCGUGCUUGACAACAUGGCUUUCUCAACUUUUAAAGGAUAACAGCUAUCCAUUGGUCUUAGGACCCAAAAAUUUUGGUGCAACUCCAAAUAAAAGUAAUAACUAUGUACGCUACCAUAACCACCUUAGCCCUAACUUCCUUAAUUCCCCCUAUCCUUACCACCUUCAUCAAUCCUAACAAAAAAAGCUCAUACCCCCAUUACGUAAAAUCUAUCGUCGCAUCCACCUUUAUCAUCAGCCUCUUCCCCACAACAAUAUUUCUAUGCCUAGACCAAGAAGCUAUUAUCUCAAGCUGACACUGAGCAACAACCCAAACAAUUCAACUCUCCCUAAGCUU"/>
+        <sequence id="seq_Pongo" taxon="Pongo" totalcount="4"
+                  value="AAGCUUCACCGGCGCAACCACCCUCAUGAUUGCCCAUGGACUCACAUCCUCCCUACUGUUCUGCCUAGCAAACUCAAACUACGAACGAACCCACAGCCGCAUCAUAAUCCUCUCUCAAGGCCUUCAAACUCUACUCCCCCUAAUAGCCCUCUGAUGACUUCUAGCAAGCCUCACUAACCUUGCCCUACCACCCACCAUCAACCUUCUAGGAGAACUCUCCGUACUAAUAGCCAUAUUCUCUUGAUCUAACAUCACCAUCCUACUAACAGGACUCAACAUACUAAUCACAACCCUAUACUCUCUCUAUAUAUUCACCACAACACAACGAGGUACACCCACACACCACAUCAACAACAUAAAACCUUCUUUCACACGCGAAAAUACCCUCAUGCUCAUACACCUAUCCCCCAUCCUCCUCUUAUCCCUCAACCCCAGCAUCAUCGCUGGGUUCGCCUACUGUAAAUAUAGUUUAACCAAAACAUUAGAUUGUGAAUCUAAUAAUAGGGCCCCA-CAACCCCUUAUUUACCGAGAAAGCU-CACAAGAACUGCUAACUCUCACU-CCAUGUGUGACAACAUGGCUUUCUCAGCUUUUAAAGGAUAACAGCUAUCCCUUGGUCUUAGGAUCCAAAAAUUUUGGUGCAACUCCAAAUAAAAGUAACAGCCAUGUUUACCACCAUAACUGCCCUCACCUUAACUUCCCUAAUCCCCCCCAUUACCGCUACCCUCAUUAACCCCAACAAAAAAAACCCAUACCCCCACUAUGUAAAAACGGCCAUCGCAUCCGCCUUUACUAUCAGCCUUAUCCCAACAACAAUAUUUAUCUGCCUAGGACAAGAAACCAUCGUCACAAACUGAUGCUGAACAACCACCCAGACACUACAACUCUCACUAAGCUU"/>
+        <sequence id="seq_Hylobates" taxon="Hylobates" totalcount="4"
+                  value="AAGCUUUACAGGUGCAACCGUCCUCAUAAUCGCCCACGGACUAACCUCUUCCCUGCUAUUCUGCCUUGCAAACUCAAACUACGAACGAACUCACAGCCGCAUCAUAAUCCUAUCUCGAGGGCUCCAAGCCUUACUCCCACUGAUAGCCUUCUGAUGACUCGCAGCAAGCCUCGCUAACCUCGCCCUACCCCCCACUAUUAACCUCCUAGGUGAACUCUUCGUACUAAUGGCCUCCUUCUCCUGGGCAAACACUACUAUUACACUCACCGGGCUCAACGUACUAAUCACGGCCCUAUACUCCCUUUACAUAUUUAUCAUAACACAACGAGGCACACUUACACACCACAUUAAAAACAUAAAACCCUCACUCACACGAGAAAACAUAUUAAUACUUAUGCACCUCUUCCCCCUCCUCCUCCUAACCCUCAACCCUAACAUCAUUACUGGCUUUACUCCCUGUAAACAUAGUUUAAUCAAAACAUUAGAUUGUGAAUCUAACAAUAGAGGCUCG-AAACCUCUUGCUUACCGAGAAAGCC-CACAAGAACUGCUAACUCACUAUCCCAUGUAUGACAACAUGGCUUUCUCAACUUUUAAAGGAUAACAGCUAUCCAUUGGUCUUAGGACCCAAAAAUUUUGGUGCAACUCCAAAUAAAAGUAAUAGCAAUGUACACCACCAUAGCCAUUCUAACGCUAACCUCCCUAAUUCCCCCCAUUACAGCCACCCUUAUUAACCCCAAUAAAAAGAACUUAUACCCGCACUACGUAAAAAUGACCAUUGCCUCUACCUUUAUAAUCAGCCUAUUUCCCACAAUAAUAUUCAUGUGCACAGACCAAGAAACCAUUAUUUCAAACUGACACUGAACUGCAACCCAAACGCUAGAACUCUCCCUAAGCUU"/>
+        <sequence id="seq_Macaca_fuscata" taxon="Macaca_fuscata" totalcount="4"
+                  value="AAGCUUUUCCGGCGCAACCAUCCUUAUGAUCGCUCACGGACUCACCUCUUCCAUAUAUUUCUGCCUAGCCAAUUCAAACUAUGAACGCACUCACAACCGUACCAUACUACUGUCCCGAGGACUUCAAAUCCUACUUCCACUAACAGCCUUUUGAUGAUUAACAGCAAGCCUUACUAACCUUGCCCUACCCCCCACUAUCAAUCUACUAGGUGAACUCUUUGUAAUCGCAACCUCAUUCUCCUGAUCCCAUAUCACCAUUAUGCUAACAGGACUUAACAUAUUAAUUACGGCCCUCUACUCUCUCCACAUAUUCACUACAACACAACGAGGAACACUCACACAUCACAUAAUCAACAUAAAGCCCCCCUUCACACGAGAAAACACAUUAAUAUUCAUACACCUCGCUCCAAUUAUCCUUCUAUCCCUCAACCCCAACAUCAUCCUGGGGUUUACCUCCUGUAGAUAUAGUUUAACUAAAACACUAGAUUGUGAAUCUAACCAUAGAGACUCA-CCACCUCUUAUUUACCGAGAAAACU-CGCAAGGACUGCUAACCCAUGUACCCGUACCUAAAAUUACGGUUUUCUCAACUUUUAAAGGAUAACAGCUAUCCAUUGACCUUAGGAGUCAAAAACAUUGGUGCAACUCCAAAUAAAAGUAAUAAUCAUGCACACCCCCAUCAUUAUAACAACCCUUAUCUCCCUAACUCUCCCAAUUUUUGCCACCCUCAUCAACCCUUACAAAAAACGUCCAUACCCAGAUUACGUAAAAACAACCGUAAUAUAUGCUUUCAUCAUCAGCCUCCCCUCAACAACUUUAUUCAUCUUCUCAAACCAAGAAACAACCAUUUGGAGCUGACAUUGAAUAAUGACCCAAACACUAGACCUAACGCUAAGCUU"/>
+        <sequence id="seq_M._mulatta" taxon="M._mulatta" totalcount="4"
+                  value="AAGCUUUUCUGGCGCAACCAUCCUCAUGAUUGCUCACGGACUCACCUCUUCCAUAUAUUUCUGCCUAGCCAAUUCAAACUAUGAACGCACUCACAACCGUACCAUACUACUGUCCCGGGGACUUCAAAUCCUACUUCCACUAACAGCUUUCUGAUGAUUAACAGCAAGCCUUACUAACCUUGCCCUACCCCCCACUAUCAACCUACUAGGUGAACUCUUUGUAAUCGCGACCUCAUUCUCCUGGUCCCAUAUCACCAUUAUAUUAACAGGAUUUAACAUACUAAUUACGGCCCUCUACUCCCUCCACAUAUUCACCACAACACAACGAGGAGCACUCACACAUCACAUAAUCAACAUAAAACCCCCCUUCACACGAGAAAACAUAUUAAUAUUCAUACACCUCGCUCCAAUCAUCCUCCUAUCUCUCAACCCCAACAUCAUCCUGGGGUUUACUUCCUGUAGAUAUAGUUUAACUAAAACAUUAGAUUGUGAAUCUAACCAUAGAGACUUA-CCACCUCUUAUUUACCGAGAAAACU-CGCGAGGACUGCUAACCCAUGUAUCCGUACCUAAAAUUACGGUUUUCUCAACUUUUAAAGGAUAACAGCUAUCCAUUGACCUUAGGAGUCAAAAAUAUUGGUGCAACUCCAAAUAAAAGUAAUAAUCAUGCACACCCCUAUCAUAAUAACAACCCUUAUCUCCCUAACUCUCCCAAUUUUUGCCACCCUCAUCAACCCUUACAAAAAACGUCCAUACCCAGAUUACGUAAAAACAACCGUAAUAUAUGCUUUCAUCAUCAGCCUCCCCUCAACAACUUUAUUCAUCUUCUCAAACCAAGAAACAACCAUUUGAAGCUGACAUUGAAUAAUAACCCAAACACUAGACCUAACACUAAGCUU"/>
+        <sequence id="seq_M._fascicularis" taxon="M._fascicularis" totalcount="4"
+                  value="AAGCUUCUCCGGCGCAACCACCCUUAUAAUCGCCCACGGGCUCACCUCUUCCAUGUAUUUCUGCUUGGCCAAUUCAAACUAUGAGCGCACUCAUAACCGUACCAUACUACUAUCCCGAGGACUUCAAAUUCUACUUCCAUUGACAGCCUUCUGAUGACUCACAGCAAGCCUUACUAACCUUGCCCUACCCCCCACUAUUAAUCUACUAGGCGAACUCUUUGUAAUCACAACUUCAUUUUCCUGAUCCCAUAUCACCAUUGUGUUAACGGGCCUUAAUAUACUAAUCACAGCCCUCUACUCUCUCCACAUGUUCAUUACAGUACAACGAGGAACACUCACACACCACAUAAUCAAUAUAAAACCCCCCUUCACACGAGAAAACAUAUUAAUAUUCAUACACCUCGCUCCAAUUAUCCUUCUAUCUCUCAACCCCAACAUCAUCCUGGGGUUUACCUCCUGUAAAUAUAGUUUAACUAAAACAUUAGAUUGUGAAUCUAACUAUAGAGGCCUA-CCACUUCUUAUUUACCGAGAAAACU-CGCAAGGACUGCUAAUCCAUGCCUCCGUACUUAAAACUACGGUUUCCUCAACUUUUAAAGGAUAACAGCUAUCCAUUGACCUUAGGAGUCAAAAACAUUGGUGCAACUCCAAAUAAAAGUAAUAAUCAUGCACACCCCCAUCAUAAUAACAACCCUCAUCUCCCUGACCCUUCCAAUUUUUGCCACCCUCACCAACCCCUAUAAAAAACGUUCAUACCCAGACUACGUAAAAACAACCGUAAUAUAUGCUUUUAUUACCAGUCUCCCCUCAACAACCCUAUUCAUCCUCUCAAACCAAGAAACAACCAUUUGGAGUUGACAUUGAAUAACAACCCAAACAUUAGACCUAACACUAAGCUU"/>
+        <sequence id="seq_M._sylvanus" taxon="M._sylvanus" totalcount="4"
+                  value="AAGCUUCUCCGGUGCAACUAUCCUUAUAGUUGCCCAUGGACUCACCUCUUCCAUAUACUUCUGCUUGGCCAACUCAAACUACGAACGCACCCACAGCCGCAUCAUACUACUAUCCCGAGGACUCCAAAUCCUACUCCCACUAACAGCCUUCUGAUGAUUCACAGCAAGCCUUACUAAUCUUGCUCUACCCUCCACUAUUAAUCUACUGGGCGAACUCUUCGUAAUCGCAACCUCAUUUUCCUGAUCCCACAUCACCAUCAUACUAACAGGACUGAACAUACUAAUUACAGCCCUCUACUCUCUUCACAUAUUCACCACAACACAACGAGGAGCGCUCACACACCACAUAAUUAACAUAAAACCACCUUUCACACGAGAAAACAUAUUAAUACUCAUACACCUCGCUCCAAUUAUUCUUCUAUCUCUUAACCCCAACAUCAUUCUAGGAUUUACUUCCUGUAAAUAUAGUUUAAUUAAAACAUUAGACUGUGAAUCUAACUAUAGAAGCUUA-CCACUUCUUAUUUACCGAGAAAACU-UGCAAGGACCGCUAAUCCACACCUCCGUACUUAAAACUACGGUUUUCUCAACUUUUAAAGGAUAACAGCUAUCCAUUGGCCUUAGGAGUCAAAAAUAUUGGUGCAACUCCAAAUAAAAGUAAUAAUCAUGUAUACCCCCAUCAUAAUAACAACUCUCAUCUCCCUAACUCUUCCAAUUUUCGCUACCCUUAUCAACCCCAACAAAAAACACCUAUAUCCAAACUACGUAAAAACAGCCGUAAUAUAUGCUUUCAUUACCAGCCUCUCUUCAACAACUUUAUAUAUAUUCUUAAACCAAGAAACAAUCAUCUGAAGCUGGCACUGAAUAAUAACCCAAACACUAAGCCUAACAUUAAGCUU"/>
+        <sequence id="seq_Saimiri_sciureus" taxon="Saimiri_sciureus" totalcount="4"
+                  value="AAGCUUCACCGGCGCAAUGAUCCUAAUAAUCGCUCACGGGUUUACUUCGUCUAUGCUAUUCUGCCUAGCAAACUCAAAUUACGAACGAAUUCACAGCCGAACAAUAACAUUUACUCGAGGGCUCCAAACACUAUUCCCGCUUAUAGGCCUCUGAUGACUCCUAGCAAAUCUCGCUAACCUCGCCCUACCCACAGCUAUUAAUCUAGUAGGAGAAUUACUCACAAUCGUAUCUUCCUUCUCUUGAUCCAACUUUACUAUUAUAUUCACAGGACUUAAUAUACUAAUUACAGCACUCUACUCACUUCAUAUGUAUGCCUCUACACAGCGAGGUCCACUUACAUACAGCACCAGCAAUAUAAAACCAAUAUUUACACGAGAAAAUACGCUAAUAUUUAUACAUAUAACACCAAUCCUCCUCCUUACCUUGAGCCCCAAGGUAAUUAUAGGACCCUCACCUUGUAAUUAUAGUUUAGCUAAAACAUUAGAUUGUGAAUCUAAUAAUAGAAGAAUA-UAACUUCUUAAUUACCGAGAAAGUG-CGCAAGAACUGCUAAUUCAUGCUCCCAAGACUAACAACUUGGCUUCCUCAACUUUUAAAGGAUAGUAGUUAUCCAUUGGUCUUAGGAGCCAAAAACAUUGGUGCAACUCCAAAUAAAAGUAAUA---AUACACUUCUCCAUCACUCUAAUAACACUAAUUAGCCUACUAGCGCCAAUCCUAGCUACCCUCAUUAACCCUAACAAAAGCACACUAUACCCGUACUACGUAAAACUAGCCAUCAUCUACGCCCUCAUUACCAGUACCUUAUCUAUAAUAUUCUUUAUCCUUACAGGCCAAGAAUCAAUAAUUUCAAACUGACACUGAAUAACUAUCCAAACCAUCAAACUAUCCCUAAGCUU"/>
+        <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4"
+                  value="AAGUUUCAUUGGAGCCACCACUCUUAUAAUUGCCCAUGGCCUCACCUCCUCCCUAUUAUUUUGCCUAGCAAAUACAAACUACGAACGAGUCCACAGUCGAACAAUAGCACUAGCCCGUGGCCUUCAAACCCUAUUACCUCUUGCAGCAACAUGAUGACUCCUCGCCAGCUUAACCAACCUGGCCCUUCCCCCAACAAUUAAUUUAAUCGGUGAACUGUCCGUAAUAAUAGCAGCAUUUUCAUGGUCACACCUAACUAUUAUCUUAGUAGGCCUUAACACCCUUAUCACCGCCCUAUAUUCCCUAUAUAUACUAAUCAUAACUCAACGAGGAAAAUACACAUAUCAUAUCAACAAUAUCAUGCCCCCUUUCACCCGAGAAAAUACAUUAAUAAUCAUACACCUAUUUCCCUUAAUCCUACUAUCUACCAACCCCAAAGUAAUUAUAGGAACCAUGUACUGUAAAUAUAGUUUAAACAAAACAUUAGAUUGUGAGUCUAAUAAUAGAAGCCCAAAGAUUUCUUAUUUACCAAGAAAGUA-UGCAAGAACUGCUAACUCAUGCCUCCAUAUAUAACAAUGUGGCUUUCUU-ACUUUUAAAGGAUAGAAGUAAUCCAUCGGUCUUAGGAACCGAAAA-AUUGGUGCAACUCCAAAUAAAAGUAAUAAAUUUAUUUUCAUCCUCCAUUUUACUAUCACUUACACUCUUAAUUACCCCAUUUAUUAUUACAACAACUAAAAAAUAUGAAACACAUGCAUACCCUUACUACGUAAAAAACUCUAUCGCCUGCGCAUUUAUAACAAGCCUAGUCCCAAUGCUCAUAUUUCUAUACACAAAUCAAGAAAUAAUCAUUUCCAACUGACAUUGAAUAACGAUUCAUACUAUCAAAUUAUGCCUAAGCUU"/>
+    </data>
+
+
+    <map name="Beta">beast.base.inference.distribution.Beta</map>
+    <map name="Exponential">beast.base.inference.distribution.Exponential</map>
+    <map name="InverseGamma">beast.base.inference.distribution.InverseGamma</map>
+    <map name="LogNormal">beast.base.inference.distribution.LogNormalDistributionModel</map>
+    <map name="Gamma">beast.base.inference.distribution.Gamma</map>
+    <map name="Uniform">beast.base.inference.distribution.Uniform</map>
+    <map name="prior">beast.base.inference.distribution.Prior</map>
+    <map name="LaplaceDistribution">beast.base.inference.distribution.LaplaceDistribution</map>
+    <map name="OneOnX">beast.base.inference.distribution.OneOnX</map>
+    <map name="Normal">beast.base.inference.distribution.Normal</map>
+
+
+    <run chainLength="5000000" id="mcmc" spec="MCMC">
+        <state id="state" storeEvery="5000">
+            <tree id="Tree.t:primate" name="stateNode">
+                <taxonset id="TaxonSet.coding" spec="TaxonSet">
+                    <alignment filter="2-457,660-896" id="coding" spec="FilteredAlignment">
+                        <data idref="primate-mtDNA"/>
+                    </alignment>
+                </taxonset>
+            </tree>
+            <parameter id="birthRate.t:primate" name="stateNode" value="1.0"/>
+            <parameter id="rateAC.s:primate" lower="0.0" name="stateNode" value="1.0"/>
+            <parameter id="rateAG.s:primate" lower="0.0" name="stateNode" value="1.0"/>
+            <parameter id="rateAT.s:primate" lower="0.0" name="stateNode" value="1.0"/>
+            <parameter id="rateCG.s:primate" lower="0.0" name="stateNode" value="1.0"/>
+            <parameter id="rateGT.s:primate" lower="0.0" name="stateNode" value="1.0"/>
+            <parameter dimension="4" id="freqParameter.s:primate" lower="0.0" name="stateNode" upper="1.0"
+                       value="0.25"/>
+        </state>
+
+        <init estimate="false" id="RandomTree.t:primate" initial="@Tree.t:primate"
+              spec="beast.base.evolution.tree.coalescent.RandomTree" taxa="@coding">
+            <populationModel id="ConstantPopulation0.t:primate" spec="ConstantPopulation">
+                <parameter id="randomPopSize.t:primate" name="popSize" value="1"/>
+            </populationModel>
+        </init>
+
+        <distribution id="posterior" spec="CompoundDistribution">
+            <distribution id="prior" spec="CompoundDistribution">
+                <distribution birthDiffRate="@birthRate.t:primate" id="YuleModel.t:primate"
+                              spec="beast.base.evolution.speciation.YuleModel" tree="@Tree.t:primate"/>
+                <prior id="YuleBirthRatePrior.t:primate" name="distribution" x="@birthRate.t:primate">
+                    <Uniform id="Uniform.0" name="distr" upper="Infinity"/>
+                </prior>
+                <prior id="RateACPrior.s:primate" name="distribution" x="@rateAC.s:primate">
+                    <LogNormal id="LogNormalDistributionModel.0" name="distr">
+                        <parameter estimate="false" id="RealParameter.0" name="M" value="0"/>
+                        <parameter estimate="false" id="RealParameter.01" lower="0.0" name="S" upper="5.0"
+                                   value="1.25"/>
+                    </LogNormal>
+                </prior>
+                <prior id="RateAGPrior.s:primate" name="distribution" x="@rateAG.s:primate">
+                    <LogNormal id="LogNormalDistributionModel.01" name="distr">
+                        <parameter estimate="false" id="RealParameter.02" name="M" value="0"/>
+                        <parameter estimate="false" id="RealParameter.03" lower="0.0" name="S" upper="5.0"
+                                   value="1.25"/>
+                    </LogNormal>
+                </prior>
+                <prior id="RateATPrior.s:primate" name="distribution" x="@rateAT.s:primate">
+                    <LogNormal id="LogNormalDistributionModel.02" name="distr">
+                        <parameter estimate="false" id="RealParameter.04" name="M" value="0"/>
+                        <parameter estimate="false" id="RealParameter.05" lower="0.0" name="S" upper="5.0"
+                                   value="1.25"/>
+                    </LogNormal>
+                </prior>
+                <prior id="RateCGPrior.s:primate" name="distribution" x="@rateCG.s:primate">
+                    <LogNormal id="LogNormalDistributionModel.03" name="distr">
+                        <parameter estimate="false" id="RealParameter.06" name="M" value="0"/>
+                        <parameter estimate="false" id="RealParameter.07" lower="0.0" name="S" upper="5.0"
+                                   value="1.25"/>
+                    </LogNormal>
+                </prior>
+                <prior id="RateGTPrior.s:primate" name="distribution" x="@rateGT.s:primate">
+                    <LogNormal id="LogNormalDistributionModel.04" name="distr">
+                        <parameter estimate="false" id="RealParameter.08" name="M" value="0"/>
+                        <parameter estimate="false" id="RealParameter.09" lower="0.0" name="S" upper="5.0"
+                                   value="1.25"/>
+                    </LogNormal>
+                </prior>
+            </distribution>
+            <distribution id="likelihood" spec="CompoundDistribution">
+                <distribution data="@coding" id="treeLikelihood.coding" spec="TreeLikelihood" tree="@Tree.t:primate">
+                    <siteModel id="SiteModel.s:primate" spec="SiteModel">
+                        <parameter estimate="false" id="mutationRate.s:primate" name="mutationRate" value="1.0"/>
+                        <parameter estimate="false" id="gammaShape.s:primate" name="shape" value="1.0"/>
+                        <parameter estimate="false" id="proportionInvariant.s:primate" lower="0.0"
+                                   name="proportionInvariant" upper="1.0" value="0.0"/>
+                        <substModel id="gtr.s:primate" rateAC="@rateAC.s:primate" rateAG="@rateAG.s:primate"
+                                    rateAT="@rateAT.s:primate" rateCG="@rateCG.s:primate" rateGT="@rateGT.s:primate"
+                                    spec="GTR">
+                            <parameter estimate="false" id="rateCT.s:primate" lower="0.0" name="rateCT" value="1.0"/>
+                            <frequencies frequencies="@freqParameter.s:primate" id="estimatedFreqs.s:primate"
+                                         spec="Frequencies"/>
+                        </substModel>
+                    </siteModel>
+                    <branchRateModel id="StrictClock.c:primate" spec="beast.base.evolution.branchratemodel.StrictClockModel">
+                        <parameter estimate="false" id="clockRate.c:primate" name="clock.rate" value="1.0"/>
+                    </branchRateModel>
+                </distribution>
+                <distribution branchRateModel="@StrictClock.c:primate" id="treeLikelihood.noncoding"
+                              siteModel="@SiteModel.s:primate" spec="TreeLikelihood" tree="@Tree.t:primate">
+                    <data data="@primate-mtDNA" filter="1,458-659,897-898" id="noncoding" spec="FilteredAlignment"/>
+                </distribution>
+            </distribution>
+        </distribution>
+
+        <operator id="YuleBirthRateScaler.t:primate" parameter="@birthRate.t:primate" scaleFactor="0.75"
+                  spec="ScaleOperator" weight="3.0"/>
+
+        <operator id="treeScaler.t:primate" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:primate" weight="3.0"/>
+
+        <operator id="treeRootScaler.t:primate" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator"
+                  tree="@Tree.t:primate" weight="3.0"/>
+
+        <operator id="UniformOperator.t:primate" spec="Uniform" tree="@Tree.t:primate" weight="30.0"/>
+
+        <operator id="SubtreeSlide.t:primate" spec="SubtreeSlide" tree="@Tree.t:primate" weight="15.0"/>
+
+        <operator id="narrow.t:primate" spec="Exchange" tree="@Tree.t:primate" weight="15.0"/>
+
+        <operator id="wide.t:primate" isNarrow="false" spec="Exchange" tree="@Tree.t:primate" weight="3.0"/>
+
+        <operator id="WilsonBalding.t:primate" spec="WilsonBalding" tree="@Tree.t:primate" weight="3.0"/>
+
+        <operator id="RateACScaler.s:primate" parameter="@rateAC.s:primate" scaleFactor="0.5" spec="ScaleOperator"
+                  weight="0.1"/>
+
+        <operator id="RateAGScaler.s:primate" parameter="@rateAG.s:primate" scaleFactor="0.5" spec="ScaleOperator"
+                  weight="0.1"/>
+
+        <operator id="RateATScaler.s:primate" parameter="@rateAT.s:primate" scaleFactor="0.5" spec="ScaleOperator"
+                  weight="0.1"/>
+
+        <operator id="RateCGScaler.s:primate" parameter="@rateCG.s:primate" scaleFactor="0.5" spec="ScaleOperator"
+                  weight="0.1"/>
+
+        <operator id="RateGTScaler.s:primate" parameter="@rateGT.s:primate" scaleFactor="0.5" spec="ScaleOperator"
+                  weight="0.1"/>
+
+        <operator delta="0.01" id="FrequenciesExchanger.s:primate" spec="DeltaExchangeOperator" weight="0.1">
+            <parameter idref="freqParameter.s:primate"/>
+        </operator>
+
+        <logger fileName="testRNA.log" id="tracelog" logEvery="5000" model="@posterior" sanitiseHeaders="true"
+                sort="smart">
+            <log idref="posterior"/>
+            <log idref="likelihood"/>
+            <log idref="prior"/>
+            <log idref="treeLikelihood.noncoding"/>
+            <log idref="treeLikelihood.coding"/>
+            <log id="TreeHeight.t:primate" spec="beast.base.evolution.tree.TreeStatLogger" tree="@Tree.t:primate"/>
+            <log idref="YuleModel.t:primate"/>
+            <parameter idref="birthRate.t:primate" name="log"/>
+            <parameter idref="rateAC.s:primate" name="log"/>
+            <parameter idref="rateAG.s:primate" name="log"/>
+            <parameter idref="rateAT.s:primate" name="log"/>
+            <parameter idref="rateCG.s:primate" name="log"/>
+            <parameter idref="rateGT.s:primate" name="log"/>
+            <parameter idref="freqParameter.s:primate" name="log"/>
+        </logger>
+
+        <logger id="screenlog" logEvery="5000">
+            <log idref="posterior"/>
+            <log arg="@posterior" id="ESS.0" spec="util.ESS"/>
+            <log idref="likelihood"/>
+            <log idref="prior"/>
+        </logger>
+
+        <logger fileName="testRNA.trees" id="treelog.t:primate" logEvery="5000" mode="tree">
+            <log id="TreeWithMetaDataLogger.t:primate" spec="beast.base.evolution.TreeWithMetaDataLogger"
+                 tree="@Tree.t:primate"/>
+        </logger>
+
+    </run>
+
+</beast>
diff --git a/beast-base/src/test/resources/beast.base/examples/testRandomLocalClock.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testRandomLocalClock.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/testRandomLocalClock.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/testRandomLocalClock.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/testRelaxedClock.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testRelaxedClock.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/testRelaxedClock.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/testRelaxedClock.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/legacy/testRestrictedGTR.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testRestrictedGTR.xml
new file mode 100644
index 00000000..d5734fa6
--- /dev/null
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/testRestrictedGTR.xml
@@ -0,0 +1,179 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<beast beautitemplate='Standard' beautistatus=''
+       namespace="beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.alignment:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood"
+       version="2.0">
+
+
+    <data id="primate-mtDNA">
+        <sequence id="seq_Lemur_catta" taxon="Lemur_catta" totalcount="4"
+                  value="AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATTCTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGGGATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCTAGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTCATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTCCCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAACCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATTTACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAACACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATGTATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGATAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTATAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTGCATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAACAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT"/>
+        <sequence id="seq_Homo_sapiens" taxon="Homo_sapiens" totalcount="4"
+                  value="AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
+        <sequence id="seq_Pan" taxon="Pan" totalcount="4"
+                  value="AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATTCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCTCGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAAGCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TATAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCACCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCGCGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAGCTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
+        <sequence id="seq_Gorilla" taxon="Gorilla" totalcount="4"
+                  value="AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGGACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCTCGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTCCTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTCCCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAAACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCTATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CGTAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTACCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCGCATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAGCTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT"/>
+        <sequence id="seq_Pongo" taxon="Pongo" totalcount="4"
+                  value="AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGGCCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCTTGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTCTTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTCTCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAAACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTTATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAACATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGATAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAACAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCGCTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCGCATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAACCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT"/>
+        <sequence id="seq_Hylobates" taxon="Hylobates" totalcount="4"
+                  value="AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATTCTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGGGCTCCAAGCCTTACTCCCACTGATAGCCTTCTGATGACTCGCAGCAAGCCTCGCTAACCTCGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTCCTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTCCCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAAACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCTAACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAACATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CACAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAGCCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTGCCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAACCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT"/>
+        <sequence id="seq_Macaca_fuscata" taxon="Macaca_fuscata" totalcount="4"
+                  value="AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGGACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTCCTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTCTCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAAGCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAACACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT"/>
+        <sequence id="seq_M._mulatta" taxon="M._mulatta" totalcount="4"
+                  value="AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGGACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTCCTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTCCCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCTATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAACATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CGCGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT"/>
+        <sequence id="seq_M._fascicularis" taxon="M._fascicularis" totalcount="4"
+                  value="AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTTCTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGTACCATACTACTATCCCGAGGACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTCCTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTCTCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAACATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTGCCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAATATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAACAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT"/>
+        <sequence id="seq_M._sylvanus" taxon="M._sylvanus" totalcount="4"
+                  value="AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTTCTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGCATCATACTACTATCCCGAGGACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCTTGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTCCTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTCTCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAAACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCTATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAACATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TGCAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCGCTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAATATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAACAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT"/>
+        <sequence id="seq_Saimiri_sciureus" taxon="Saimiri_sciureus" totalcount="4"
+                  value="AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTCTATGCTATTCTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAATAACATTTACTCGAGGGCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCTCGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTCTTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTCACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAAACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCTTACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAACATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CGCAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGATAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAATA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAGCTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCATCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAATCAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT"/>
+        <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4"
+                  value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
+    </data>
+
+
+    <map name="Beta">beast.base.inference.distribution.Beta</map>
+    <map name="Exponential">beast.base.inference.distribution.Exponential</map>
+    <map name="InverseGamma">beast.base.inference.distribution.InverseGamma</map>
+    <map name="LogNormal">beast.base.inference.distribution.LogNormalDistributionModel</map>
+    <map name="Gamma">beast.base.inference.distribution.Gamma</map>
+    <map name="Uniform">beast.base.inference.distribution.Uniform</map>
+    <map name="prior">beast.base.inference.distribution.Prior</map>
+    <map name="LaplaceDistribution">beast.base.inference.distribution.LaplaceDistribution</map>
+    <map name="OneOnX">beast.base.inference.distribution.OneOnX</map>
+    <map name="Normal">beast.base.inference.distribution.Normal</map>
+
+
+    <run chainLength="5000000" id="mcmc" spec="MCMC">
+        <state id="state" storeEvery="5000">
+            <tree id="Tree.t:primate" name="stateNode">
+                <taxonset id="TaxonSet.coding" spec="TaxonSet">
+                    <alignment filter="2-457,660-896" id="coding" spec="FilteredAlignment">
+                        <data idref="primate-mtDNA"/>
+                    </alignment>
+                </taxonset>
+            </tree>
+            <parameter id="birthRate.t:primate" name="stateNode" value="1.0"/>
+            <parameter id="rateTransversion.s:primate" lower="0.0" name="stateNode" value="1.0"/>
+            <parameter id="rateAG.s:primate" lower="0.0" name="stateNode" value="1.0"/>
+            <parameter dimension="4" id="freqParameter.s:primate" lower="0.0" name="stateNode" upper="1.0"
+                       value="0.25"/>
+        </state>
+
+        <init estimate="false" id="RandomTree.t:primate" initial="@Tree.t:primate"
+              spec="beast.base.evolution.tree.coalescent.RandomTree" taxa="@coding">
+            <populationModel id="ConstantPopulation0.t:primate" spec="ConstantPopulation">
+                <parameter id="randomPopSize.t:primate" name="popSize" value="1"/>
+            </populationModel>
+        </init>
+
+        <distribution id="posterior" spec="CompoundDistribution">
+            <distribution id="prior" spec="CompoundDistribution">
+                <distribution birthDiffRate="@birthRate.t:primate" id="YuleModel.t:primate"
+                              spec="beast.base.evolution.speciation.YuleModel" tree="@Tree.t:primate"/>
+                <prior id="YuleBirthRatePrior.t:primate" name="distribution" x="@birthRate.t:primate">
+                    <Uniform id="Uniform.0" name="distr" upper="Infinity"/>
+                </prior>
+                <prior id="RateTransversionPrior.s:primate" name="distribution" x="@rateTransversion.s:primate">
+                    <LogNormal id="LogNormalDistributionModel.0" name="distr">
+                        <parameter estimate="false" id="RealParameter.0" name="M" value="0"/>
+                        <parameter estimate="false" id="RealParameter.01" lower="0.0" name="S" upper="5.0"
+                                   value="1.25"/>
+                    </LogNormal>
+                </prior>
+                <prior id="RateAGPrior.s:primate" name="distribution" x="@rateAG.s:primate">
+                    <LogNormal id="LogNormalDistributionModel.01" name="distr">
+                        <parameter estimate="false" id="RealParameter.02" name="M" value="0"/>
+                        <parameter estimate="false" id="RealParameter.03" lower="0.0" name="S" upper="5.0"
+                                   value="1.25"/>
+                    </LogNormal>
+                </prior>
+            </distribution>
+            <distribution id="likelihood" spec="CompoundDistribution">
+                <distribution data="@coding" id="treeLikelihood.coding" spec="TreeLikelihood" tree="@Tree.t:primate">
+                    <siteModel id="SiteModel.s:primate" spec="SiteModel">
+                        <parameter estimate="false" id="mutationRate.s:primate" name="mutationRate" value="1.0"/>
+                        <parameter estimate="false" id="gammaShape.s:primate" name="shape" value="1.0"/>
+                        <parameter estimate="false" id="proportionInvariant.s:primate" lower="0.0"
+                                   name="proportionInvariant" upper="1.0" value="0.0"/>
+                        <substModel id="gtr.s:primate"
+                                    rateAC="@rateTransversion.s:primate"
+                                    rateAG="@rateAG.s:primate"
+                                    rateAT="@rateTransversion.s:primate"
+                                    rateCG="@rateTransversion.s:primate"
+                                    rateGT="@rateTransversion.s:primate"
+                                    spec="GTR">
+                            <parameter estimate="false" id="rateCT.s:primate" lower="0.0" name="rateCT" value="1.0"/>
+                            <frequencies frequencies="@freqParameter.s:primate" id="estimatedFreqs.s:primate"
+                                         spec="Frequencies"/>
+                        </substModel>
+                    </siteModel>
+                    <branchRateModel id="StrictClock.c:primate" spec="beast.base.evolution.branchratemodel.StrictClockModel">
+                        <parameter estimate="false" id="clockRate.c:primate" name="clock.rate" value="1.0"/>
+                    </branchRateModel>
+                </distribution>
+                <distribution branchRateModel="@StrictClock.c:primate" id="treeLikelihood.noncoding"
+                              siteModel="@SiteModel.s:primate" spec="TreeLikelihood" tree="@Tree.t:primate">
+                    <data data="@primate-mtDNA" filter="1,458-659,897-898" id="noncoding" spec="FilteredAlignment"/>
+                </distribution>
+            </distribution>
+        </distribution>
+
+        <operator id="YuleBirthRateScaler.t:primate" parameter="@birthRate.t:primate" scaleFactor="0.75"
+                  spec="ScaleOperator" weight="3.0"/>
+
+        <operator id="treeScaler.t:primate" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:primate" weight="3.0"/>
+
+        <operator id="treeRootScaler.t:primate" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator"
+                  tree="@Tree.t:primate" weight="3.0"/>
+
+        <operator id="UniformOperator.t:primate" spec="Uniform" tree="@Tree.t:primate" weight="30.0"/>
+
+        <operator id="SubtreeSlide.t:primate" spec="SubtreeSlide" tree="@Tree.t:primate" weight="15.0"/>
+
+        <operator id="narrow.t:primate" spec="Exchange" tree="@Tree.t:primate" weight="15.0"/>
+
+        <operator id="wide.t:primate" isNarrow="false" spec="Exchange" tree="@Tree.t:primate" weight="3.0"/>
+
+        <operator id="WilsonBalding.t:primate" spec="WilsonBalding" tree="@Tree.t:primate" weight="3.0"/>
+
+        <operator id="RateTransversionScaler.s:primate" parameter="@rateTransversion.s:primate" scaleFactor="0.5"
+                  spec="ScaleOperator"
+                  weight="0.1"/>
+
+        <operator id="RateAGScaler.s:primate" parameter="@rateAG.s:primate" scaleFactor="0.5" spec="ScaleOperator"
+                  weight="0.1"/>
+
+        <operator delta="0.01" id="FrequenciesExchanger.s:primate" spec="DeltaExchangeOperator" weight="0.1">
+            <parameter idref="freqParameter.s:primate"/>
+        </operator>
+
+        <logger fileName="primate-mtDNA-restrictedGTR.log" id="tracelog" logEvery="5000" model="@posterior"
+                sanitiseHeaders="true"
+                sort="smart">
+            <log idref="posterior"/>
+            <log idref="likelihood"/>
+            <log idref="prior"/>
+            <log idref="treeLikelihood.noncoding"/>
+            <log idref="treeLikelihood.coding"/>
+            <log id="TreeHeight.t:primate" spec="beast.base.evolution.tree.TreeStatLogger" tree="@Tree.t:primate"/>
+            <log idref="YuleModel.t:primate"/>
+            <parameter idref="birthRate.t:primate" name="log"/>
+            <parameter idref="rateTransversion.s:primate" name="log"/>
+            <parameter idref="rateAG.s:primate" name="log"/>
+            <parameter idref="freqParameter.s:primate" name="log"/>
+        </logger>
+
+        <logger id="screenlog" logEvery="5000">
+            <log idref="posterior"/>
+            <log arg="@posterior" id="ESS.0" spec="util.ESS"/>
+            <log idref="likelihood"/>
+            <log idref="prior"/>
+        </logger>
+
+        <logger fileName="primate-mtDNA-restrictedGTR-$(tree).trees" id="treelog.t:primate" logEvery="5000" mode="tree">
+            <log id="TreeWithMetaDataLogger.t:primate" spec="beast.base.evolution.TreeWithMetaDataLogger"
+                 tree="@Tree.t:primate"/>
+        </logger>
+    </run>
+</beast>
diff --git a/beast-base/src/test/resources/beast.base/examples/testSRD06.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testSRD06.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/testSRD06.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/testSRD06.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/legacy/testSYM.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testSYM.xml
new file mode 100644
index 00000000..9b9c012d
--- /dev/null
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/testSYM.xml
@@ -0,0 +1,207 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<beast beautitemplate='Standard' beautistatus=''
+       namespace="beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.alignment:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood"
+       version="2.0">
+
+
+    <data id="primate-mtDNA">
+        <sequence id="seq_Lemur_catta" taxon="Lemur_catta" totalcount="4"
+                  value="AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATTCTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGGGATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCTAGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTCATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTCCCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAACCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATTTACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAACACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATGTATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGATAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTATAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTGCATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAACAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT"/>
+        <sequence id="seq_Homo_sapiens" taxon="Homo_sapiens" totalcount="4"
+                  value="AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
+        <sequence id="seq_Pan" taxon="Pan" totalcount="4"
+                  value="AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATTCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCTCGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAAGCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TATAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCACCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCGCGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAGCTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
+        <sequence id="seq_Gorilla" taxon="Gorilla" totalcount="4"
+                  value="AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGGACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCTCGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTCCTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTCCCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAAACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCTATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CGTAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTACCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCGCATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAGCTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT"/>
+        <sequence id="seq_Pongo" taxon="Pongo" totalcount="4"
+                  value="AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGGCCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCTTGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTCTTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTCTCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAAACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTTATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAACATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGATAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAACAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCGCTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCGCATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAACCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT"/>
+        <sequence id="seq_Hylobates" taxon="Hylobates" totalcount="4"
+                  value="AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATTCTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGGGCTCCAAGCCTTACTCCCACTGATAGCCTTCTGATGACTCGCAGCAAGCCTCGCTAACCTCGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTCCTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTCCCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAAACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCTAACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAACATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CACAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAGCCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTGCCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAACCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT"/>
+        <sequence id="seq_Macaca_fuscata" taxon="Macaca_fuscata" totalcount="4"
+                  value="AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGGACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTCCTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTCTCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAAGCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAACACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT"/>
+        <sequence id="seq_M._mulatta" taxon="M._mulatta" totalcount="4"
+                  value="AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGGACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTCCTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTCCCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCTATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAACATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CGCGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT"/>
+        <sequence id="seq_M._fascicularis" taxon="M._fascicularis" totalcount="4"
+                  value="AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTTCTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGTACCATACTACTATCCCGAGGACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTCCTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTCTCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAACATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTGCCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAATATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAACAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT"/>
+        <sequence id="seq_M._sylvanus" taxon="M._sylvanus" totalcount="4"
+                  value="AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTTCTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGCATCATACTACTATCCCGAGGACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCTTGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTCCTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTCTCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAAACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCTATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAACATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TGCAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCGCTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAATATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAACAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT"/>
+        <sequence id="seq_Saimiri_sciureus" taxon="Saimiri_sciureus" totalcount="4"
+                  value="AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTCTATGCTATTCTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAATAACATTTACTCGAGGGCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCTCGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTCTTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTCACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAAACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCTTACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAACATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CGCAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGATAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAATA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAGCTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCATCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAATCAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT"/>
+        <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4"
+                  value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
+    </data>
+
+
+    <map name="Beta">beast.base.inference.distribution.Beta</map>
+    <map name="Exponential">beast.base.inference.distribution.Exponential</map>
+    <map name="InverseGamma">beast.base.inference.distribution.InverseGamma</map>
+    <map name="LogNormal">beast.base.inference.distribution.LogNormalDistributionModel</map>
+    <map name="Gamma">beast.base.inference.distribution.Gamma</map>
+    <map name="Uniform">beast.base.inference.distribution.Uniform</map>
+    <map name="prior">beast.base.inference.distribution.Prior</map>
+    <map name="LaplaceDistribution">beast.base.inference.distribution.LaplaceDistribution</map>
+    <map name="OneOnX">beast.base.inference.distribution.OneOnX</map>
+    <map name="Normal">beast.base.inference.distribution.Normal</map>
+
+
+    <run chainLength="5000000" id="mcmc" spec="MCMC">
+        <state id="state" storeEvery="5000">
+            <tree id="Tree.t:primate" name="stateNode">
+                <taxonset id="TaxonSet.coding" spec="TaxonSet">
+                    <alignment filter="2-457,660-896" id="coding" spec="FilteredAlignment">
+                        <data idref="primate-mtDNA"/>
+                    </alignment>
+                </taxonset>
+            </tree>
+            <parameter id="birthRate.t:primate" name="stateNode" value="1.0"/>
+            <parameter id="rateAC.s:primate" lower="0.0" name="stateNode" value="1.0"/>
+            <parameter id="rateAG.s:primate" lower="0.0" name="stateNode" value="1.0"/>
+            <parameter id="rateAT.s:primate" lower="0.0" name="stateNode" value="1.0"/>
+            <parameter id="rateCG.s:primate" lower="0.0" name="stateNode" value="1.0"/>
+            <parameter id="rateGT.s:primate" lower="0.0" name="stateNode" value="1.0"/>
+            <parameter dimension="4" id="freqParameter.s:primate" lower="0.0" name="stateNode" upper="1.0"
+                       value="0.25"/>
+        </state>
+
+        <init estimate="false" id="RandomTree.t:primate" initial="@Tree.t:primate"
+              spec="beast.base.evolution.tree.coalescent.RandomTree" taxa="@coding">
+            <populationModel id="ConstantPopulation0.t:primate" spec="ConstantPopulation">
+                <parameter id="randomPopSize.t:primate" name="popSize" value="1"/>
+            </populationModel>
+        </init>
+
+        <distribution id="posterior" spec="CompoundDistribution">
+            <distribution id="prior" spec="CompoundDistribution">
+                <distribution birthDiffRate="@birthRate.t:primate" id="YuleModel.t:primate"
+                              spec="beast.base.evolution.speciation.YuleModel" tree="@Tree.t:primate"/>
+                <prior id="YuleBirthRatePrior.t:primate" name="distribution" x="@birthRate.t:primate">
+                    <Uniform id="Uniform.0" name="distr" upper="Infinity"/>
+                </prior>
+                <prior id="RateACPrior.s:primate" name="distribution" x="@rateAC.s:primate">
+                    <LogNormal id="LogNormalDistributionModel.0" name="distr">
+                        <parameter estimate="false" id="RealParameter.0" name="M" value="0"/>
+                        <parameter estimate="false" id="RealParameter.01" lower="0.0" name="S" upper="5.0"
+                                   value="1.25"/>
+                    </LogNormal>
+                </prior>
+                <prior id="RateAGPrior.s:primate" name="distribution" x="@rateAG.s:primate">
+                    <LogNormal id="LogNormalDistributionModel.01" name="distr">
+                        <parameter estimate="false" id="RealParameter.02" name="M" value="0"/>
+                        <parameter estimate="false" id="RealParameter.03" lower="0.0" name="S" upper="5.0"
+                                   value="1.25"/>
+                    </LogNormal>
+                </prior>
+                <prior id="RateATPrior.s:primate" name="distribution" x="@rateAT.s:primate">
+                    <LogNormal id="LogNormalDistributionModel.02" name="distr">
+                        <parameter estimate="false" id="RealParameter.04" name="M" value="0"/>
+                        <parameter estimate="false" id="RealParameter.05" lower="0.0" name="S" upper="5.0"
+                                   value="1.25"/>
+                    </LogNormal>
+                </prior>
+                <prior id="RateCGPrior.s:primate" name="distribution" x="@rateCG.s:primate">
+                    <LogNormal id="LogNormalDistributionModel.03" name="distr">
+                        <parameter estimate="false" id="RealParameter.06" name="M" value="0"/>
+                        <parameter estimate="false" id="RealParameter.07" lower="0.0" name="S" upper="5.0"
+                                   value="1.25"/>
+                    </LogNormal>
+                </prior>
+                <prior id="RateGTPrior.s:primate" name="distribution" x="@rateGT.s:primate">
+                    <LogNormal id="LogNormalDistributionModel.04" name="distr">
+                        <parameter estimate="false" id="RealParameter.08" name="M" value="0"/>
+                        <parameter estimate="false" id="RealParameter.09" lower="0.0" name="S" upper="5.0"
+                                   value="1.25"/>
+                    </LogNormal>
+                </prior>
+            </distribution>
+            <distribution id="likelihood" spec="CompoundDistribution">
+                <distribution data="@coding" id="treeLikelihood.coding" spec="TreeLikelihood" tree="@Tree.t:primate">
+                    <siteModel id="SiteModel.s:primate" spec="SiteModel">
+                        <parameter estimate="false" id="mutationRate.s:primate" name="mutationRate" value="1.0"/>
+                        <parameter estimate="false" id="gammaShape.s:primate" name="shape" value="1.0"/>
+                        <parameter estimate="false" id="proportionInvariant.s:primate" lower="0.0"
+                                   name="proportionInvariant" upper="1.0" value="0.0"/>
+                        <substModel id="gtr.s:primate" rateAC="@rateAC.s:primate" rateAG="@rateAG.s:primate"
+                                    rateAT="@rateAT.s:primate" rateCG="@rateCG.s:primate" rateGT="@rateGT.s:primate"
+                                    spec="GTR">
+                            <parameter estimate="false" id="rateCT.s:primate" lower="0.0" name="rateCT" value="1.0"/>
+                            <frequencies frequencies="@freqParameter.s:primate" id="estimatedFreqs.s:primate"
+                                         spec="Frequencies"/>
+                        </substModel>
+                    </siteModel>
+                    <branchRateModel id="StrictClock.c:primate" spec="beast.base.evolution.branchratemodel.StrictClockModel">
+                        <parameter estimate="false" id="clockRate.c:primate" name="clock.rate" value="1.0"/>
+                    </branchRateModel>
+                </distribution>
+                <distribution branchRateModel="@StrictClock.c:primate" id="treeLikelihood.noncoding"
+                              siteModel="@SiteModel.s:primate" spec="TreeLikelihood" tree="@Tree.t:primate">
+                    <data data="@primate-mtDNA" filter="1,458-659,897-898" id="noncoding" spec="FilteredAlignment"/>
+                </distribution>
+            </distribution>
+        </distribution>
+
+        <operator id="YuleBirthRateScaler.t:primate" parameter="@birthRate.t:primate" scaleFactor="0.75"
+                  spec="ScaleOperator" weight="3.0"/>
+
+        <operator id="treeScaler.t:primate" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:primate" weight="3.0"/>
+
+        <operator id="treeRootScaler.t:primate" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator"
+                  tree="@Tree.t:primate" weight="3.0"/>
+
+        <operator id="UniformOperator.t:primate" spec="Uniform" tree="@Tree.t:primate" weight="30.0"/>
+
+        <operator id="SubtreeSlide.t:primate" spec="SubtreeSlide" tree="@Tree.t:primate" weight="15.0"/>
+
+        <operator id="narrow.t:primate" spec="Exchange" tree="@Tree.t:primate" weight="15.0"/>
+
+        <operator id="wide.t:primate" isNarrow="false" spec="Exchange" tree="@Tree.t:primate" weight="3.0"/>
+
+        <operator id="WilsonBalding.t:primate" spec="WilsonBalding" tree="@Tree.t:primate" weight="3.0"/>
+
+        <operator id="RateACScaler.s:primate" parameter="@rateAC.s:primate" scaleFactor="0.5" spec="ScaleOperator"
+                  weight="0.1"/>
+
+        <operator id="RateAGScaler.s:primate" parameter="@rateAG.s:primate" scaleFactor="0.5" spec="ScaleOperator"
+                  weight="0.1"/>
+
+        <operator id="RateATScaler.s:primate" parameter="@rateAT.s:primate" scaleFactor="0.5" spec="ScaleOperator"
+                  weight="0.1"/>
+
+        <operator id="RateCGScaler.s:primate" parameter="@rateCG.s:primate" scaleFactor="0.5" spec="ScaleOperator"
+                  weight="0.1"/>
+
+        <operator id="RateGTScaler.s:primate" parameter="@rateGT.s:primate" scaleFactor="0.5" spec="ScaleOperator"
+                  weight="0.1"/>
+
+        <logger fileName="primate-mtDNA-SYM.log" id="tracelog" logEvery="5000" model="@posterior" sanitiseHeaders="true"
+                sort="smart">
+            <log idref="posterior"/>
+            <log idref="likelihood"/>
+            <log idref="prior"/>
+            <log idref="treeLikelihood.noncoding"/>
+            <log idref="treeLikelihood.coding"/>
+            <log id="TreeHeight.t:primate" spec="beast.base.evolution.tree.TreeStatLogger" tree="@Tree.t:primate"/>
+            <log idref="YuleModel.t:primate"/>
+            <parameter idref="birthRate.t:primate" name="log"/>
+            <parameter idref="rateAC.s:primate" name="log"/>
+            <parameter idref="rateAG.s:primate" name="log"/>
+            <parameter idref="rateAT.s:primate" name="log"/>
+            <parameter idref="rateCG.s:primate" name="log"/>
+            <parameter idref="rateGT.s:primate" name="log"/>
+            <parameter idref="freqParameter.s:primate" name="log"/>
+        </logger>
+
+        <logger id="screenlog" logEvery="5000">
+            <log idref="posterior"/>
+            <log arg="@posterior" id="ESS.0" spec="util.ESS"/>
+            <log idref="likelihood"/>
+            <log idref="prior"/>
+        </logger>
+
+        <logger fileName="$(tree).trees" id="treelog.t:primate" logEvery="5000" mode="tree">
+            <log id="TreeWithMetaDataLogger.t:primate" spec="beast.base.evolution.TreeWithMetaDataLogger"
+                 tree="@Tree.t:primate"/>
+        </logger>
+
+    </run>
+
+</beast>
diff --git a/beast-base/src/test/resources/beast.base/examples/testSeqGen.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testSeqGen.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/testSeqGen.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/testSeqGen.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/testSimulatedAlignment.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testSimulatedAlignment.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/testSimulatedAlignment.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/testSimulatedAlignment.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/testStarBeast.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testStarBeast.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/testStarBeast.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/testStarBeast.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/testStarBeastFBD.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testStarBeastFBD.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/testStarBeastFBD.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/testStarBeastFBD.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/legacy/testTIM.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testTIM.xml
new file mode 100644
index 00000000..e8b380b8
--- /dev/null
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/testTIM.xml
@@ -0,0 +1,188 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<beast beautitemplate='Standard' beautistatus=''
+       namespace="beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.alignment:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood"
+       version="2.0">
+
+
+    <data id="primate-mtDNA">
+        <sequence id="seq_Lemur_catta" taxon="Lemur_catta" totalcount="4"
+                  value="AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATTCTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGGGATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCTAGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTCATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTCCCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAACCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATTTACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAACACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATGTATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGATAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTATAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTGCATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAACAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT"/>
+        <sequence id="seq_Homo_sapiens" taxon="Homo_sapiens" totalcount="4"
+                  value="AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
+        <sequence id="seq_Pan" taxon="Pan" totalcount="4"
+                  value="AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATTCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCTCGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAAGCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TATAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCACCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCGCGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAGCTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
+        <sequence id="seq_Gorilla" taxon="Gorilla" totalcount="4"
+                  value="AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGGACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCTCGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTCCTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTCCCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAAACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCTATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CGTAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTACCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCGCATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAGCTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT"/>
+        <sequence id="seq_Pongo" taxon="Pongo" totalcount="4"
+                  value="AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGGCCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCTTGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTCTTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTCTCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAAACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTTATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAACATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGATAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAACAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCGCTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCGCATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAACCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT"/>
+        <sequence id="seq_Hylobates" taxon="Hylobates" totalcount="4"
+                  value="AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATTCTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGGGCTCCAAGCCTTACTCCCACTGATAGCCTTCTGATGACTCGCAGCAAGCCTCGCTAACCTCGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTCCTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTCCCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAAACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCTAACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAACATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CACAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAGCCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTGCCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAACCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT"/>
+        <sequence id="seq_Macaca_fuscata" taxon="Macaca_fuscata" totalcount="4"
+                  value="AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGGACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTCCTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTCTCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAAGCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAACACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT"/>
+        <sequence id="seq_M._mulatta" taxon="M._mulatta" totalcount="4"
+                  value="AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGGACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTCCTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTCCCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCTATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAACATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CGCGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT"/>
+        <sequence id="seq_M._fascicularis" taxon="M._fascicularis" totalcount="4"
+                  value="AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTTCTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGTACCATACTACTATCCCGAGGACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTCCTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTCTCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAACATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTGCCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAATATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAACAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT"/>
+        <sequence id="seq_M._sylvanus" taxon="M._sylvanus" totalcount="4"
+                  value="AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTTCTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGCATCATACTACTATCCCGAGGACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCTTGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTCCTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTCTCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAAACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCTATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAACATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TGCAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCGCTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAATATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAACAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT"/>
+        <sequence id="seq_Saimiri_sciureus" taxon="Saimiri_sciureus" totalcount="4"
+                  value="AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTCTATGCTATTCTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAATAACATTTACTCGAGGGCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCTCGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTCTTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTCACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAAACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCTTACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAACATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CGCAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGATAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAATA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAGCTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCATCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAATCAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT"/>
+        <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4"
+                  value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
+    </data>
+
+
+    <map name="Beta">beast.base.inference.distribution.Beta</map>
+    <map name="Exponential">beast.base.inference.distribution.Exponential</map>
+    <map name="InverseGamma">beast.base.inference.distribution.InverseGamma</map>
+    <map name="LogNormal">beast.base.inference.distribution.LogNormalDistributionModel</map>
+    <map name="Gamma">beast.base.inference.distribution.Gamma</map>
+    <map name="Uniform">beast.base.inference.distribution.Uniform</map>
+    <map name="prior">beast.base.inference.distribution.Prior</map>
+    <map name="LaplaceDistribution">beast.base.inference.distribution.LaplaceDistribution</map>
+    <map name="OneOnX">beast.base.inference.distribution.OneOnX</map>
+    <map name="Normal">beast.base.inference.distribution.Normal</map>
+
+
+    <run chainLength="5000000" id="mcmc" spec="MCMC">
+        <state id="state" storeEvery="5000">
+            <tree id="Tree.t:primate" name="stateNode">
+                <taxonset id="TaxonSet.coding" spec="TaxonSet">
+                    <alignment filter="2-457,660-896" id="coding" spec="FilteredAlignment">
+                        <data idref="primate-mtDNA"/>
+                    </alignment>
+                </taxonset>
+            </tree>
+            <parameter id="birthRate.t:primate" name="stateNode" value="1.0"/>
+            <parameter id="rateAG.s:primate" lower="0.0" name="stateNode" value="1.0"/>
+            <parameter id="rateTransversions1.s:primate" lower="0.0" name="stateNode" value="1.0"/>
+            <parameter id="rateTransversions2.s:primate" lower="0.0" name="stateNode" value="1.0"/>
+            <parameter dimension="4" id="freqParameter.s:primate" lower="0.0" name="stateNode" upper="1.0"
+                       value="0.25"/>
+        </state>
+
+        <init estimate="false" id="RandomTree.t:primate" initial="@Tree.t:primate"
+              spec="beast.base.evolution.tree.coalescent.RandomTree" taxa="@coding">
+            <populationModel id="ConstantPopulation0.t:primate" spec="ConstantPopulation">
+                <parameter id="randomPopSize.t:primate" name="popSize" value="1"/>
+            </populationModel>
+        </init>
+
+        <distribution id="posterior" spec="CompoundDistribution">
+            <distribution id="prior" spec="CompoundDistribution">
+                <distribution birthDiffRate="@birthRate.t:primate" id="YuleModel.t:primate"
+                              spec="beast.base.evolution.speciation.YuleModel" tree="@Tree.t:primate"/>
+                <prior id="YuleBirthRatePrior.t:primate" name="distribution" x="@birthRate.t:primate">
+                    <Uniform id="Uniform.0" name="distr" upper="Infinity"/>
+                </prior>
+                <prior id="RateAGPrior.s:primate" name="distribution" x="@rateAG.s:primate">
+                    <LogNormal id="LogNormalDistributionModel.0" name="distr">
+                        <parameter estimate="false" id="RealParameter.0" name="M" value="0"/>
+                        <parameter estimate="false" id="RealParameter.01" lower="0.0" name="S" upper="5.0"
+                                   value="1.25"/>
+                    </LogNormal>
+                </prior>
+                <prior id="RateTransversions1Prior.s:primate" name="distribution" x="@rateTransversions1.s:primate">
+                    <LogNormal id="LogNormalDistributionModel.01" name="distr">
+                        <parameter estimate="false" id="RealParameter.02" name="M" value="0"/>
+                        <parameter estimate="false" id="RealParameter.03" lower="0.0" name="S" upper="5.0"
+                                   value="1.25"/>
+                    </LogNormal>
+                </prior>
+                <prior id="RateTransversions2Prior.s:primate" name="distribution" x="@rateTransversions2.s:primate">
+                    <LogNormal id="LogNormalDistributionModel.02" name="distr">
+                        <parameter estimate="false" id="RealParameter.04" name="M" value="0"/>
+                        <parameter estimate="false" id="RealParameter.05" lower="0.0" name="S" upper="5.0"
+                                   value="1.25"/>
+                    </LogNormal>
+                </prior>
+            </distribution>
+            <distribution id="likelihood" spec="CompoundDistribution">
+                <distribution data="@coding" id="treeLikelihood.coding" spec="TreeLikelihood" tree="@Tree.t:primate">
+                    <siteModel id="SiteModel.s:primate" spec="SiteModel">
+                        <parameter estimate="false" id="mutationRate.s:primate" name="mutationRate" value="1.0"/>
+                        <parameter estimate="false" id="gammaShape.s:primate" name="shape" value="1.0"/>
+                        <parameter estimate="false" id="proportionInvariant.s:primate" lower="0.0"
+                                   name="proportionInvariant" upper="1.0" value="0.0"/>
+                        <substModel id="tim.s:primate" rateAG="@rateAG.s:primate"
+                                    rateTransversions1="@rateTransversions1.s:primate"
+                                    rateTransversions2="@rateTransversions2.s:primate"
+                                    spec="TIM">
+                            <parameter estimate="false" id="rateCT.s:primate" lower="0.0" name="rateCT" value="1.0"/>
+                            <frequencies frequencies="@freqParameter.s:primate" id="estimatedFreqs.s:primate"
+                                         spec="Frequencies"/>
+                        </substModel>
+                    </siteModel>
+                    <branchRateModel id="StrictClock.c:primate" spec="beast.base.evolution.branchratemodel.StrictClockModel">
+                        <parameter estimate="false" id="clockRate.c:primate" name="clock.rate" value="1.0"/>
+                    </branchRateModel>
+                </distribution>
+                <distribution branchRateModel="@StrictClock.c:primate" id="treeLikelihood.noncoding"
+                              siteModel="@SiteModel.s:primate" spec="TreeLikelihood" tree="@Tree.t:primate">
+                    <data data="@primate-mtDNA" filter="1,458-659,897-898" id="noncoding" spec="FilteredAlignment"/>
+                </distribution>
+            </distribution>
+        </distribution>
+
+        <operator id="YuleBirthRateScaler.t:primate" parameter="@birthRate.t:primate" scaleFactor="0.75"
+                  spec="ScaleOperator" weight="3.0"/>
+
+        <operator id="treeScaler.t:primate" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:primate" weight="3.0"/>
+
+        <operator id="treeRootScaler.t:primate" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator"
+                  tree="@Tree.t:primate" weight="3.0"/>
+
+        <operator id="UniformOperator.t:primate" spec="Uniform" tree="@Tree.t:primate" weight="30.0"/>
+
+        <operator id="SubtreeSlide.t:primate" spec="SubtreeSlide" tree="@Tree.t:primate" weight="15.0"/>
+
+        <operator id="narrow.t:primate" spec="Exchange" tree="@Tree.t:primate" weight="15.0"/>
+
+        <operator id="wide.t:primate" isNarrow="false" spec="Exchange" tree="@Tree.t:primate" weight="3.0"/>
+
+        <operator id="WilsonBalding.t:primate" spec="WilsonBalding" tree="@Tree.t:primate" weight="3.0"/>
+
+        <operator id="RateAGScaler.s:primate" parameter="@rateAG.s:primate" scaleFactor="0.5" spec="ScaleOperator"
+                  weight="0.1"/>
+
+        <operator id="RateTransversions1Scaler.s:primate" parameter="@rateTransversions1.s:primate" scaleFactor="0.5"
+                  spec="ScaleOperator" weight="0.1"/>
+
+        <operator id="RateTransversions2Scaler.s:primate" parameter="@rateTransversions2.s:primate" scaleFactor="0.5"
+                  spec="ScaleOperator" weight="0.1"/>
+
+        <operator delta="0.01" id="FrequenciesExchanger.s:primate" spec="DeltaExchangeOperator" weight="0.1">
+            <parameter idref="freqParameter.s:primate"/>
+        </operator>
+
+        <logger fileName="primate-mtDNA-TIM.log" id="tracelog" logEvery="5000" model="@posterior" sanitiseHeaders="true"
+                sort="smart">
+            <log idref="posterior"/>
+            <log idref="likelihood"/>
+            <log idref="prior"/>
+            <log idref="treeLikelihood.noncoding"/>
+            <log idref="treeLikelihood.coding"/>
+            <log id="TreeHeight.t:primate" spec="beast.base.evolution.tree.TreeStatLogger" tree="@Tree.t:primate"/>
+            <log idref="YuleModel.t:primate"/>
+            <parameter idref="birthRate.t:primate" name="log"/>
+            <parameter idref="rateAG.s:primate" name="log"/>
+            <parameter idref="rateTransversions1.s:primate" name="log"/>
+            <parameter idref="rateTransversions2.s:primate" name="log"/>
+            <parameter idref="freqParameter.s:primate" name="log"/>
+        </logger>
+
+        <logger id="screenlog" logEvery="5000">
+            <log idref="posterior"/>
+            <log arg="@posterior" id="ESS.0" spec="util.ESS"/>
+            <log idref="likelihood"/>
+            <log idref="prior"/>
+        </logger>
+
+        <logger fileName="$(tree).trees" id="treelog.t:primate" logEvery="5000" mode="tree">
+            <log id="TreeWithMetaDataLogger.t:primate" spec="beast.base.evolution.TreeWithMetaDataLogger"
+                 tree="@Tree.t:primate"/>
+        </logger>
+
+    </run>
+
+</beast>
diff --git a/beast-base/src/test/resources/beast.base/examples/legacy/testTN93.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testTN93.xml
new file mode 100644
index 00000000..9e5a5af4
--- /dev/null
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/testTN93.xml
@@ -0,0 +1,161 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<beast beautitemplate='Standard' beautistatus=''
+       namespace="beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.alignment:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood"
+       version="2.0">
+
+
+    <data id="primate-mtDNA">
+        <sequence id="seq_Lemur_catta" taxon="Lemur_catta" totalcount="4"
+                  value="AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATTCTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGGGATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCTAGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTCATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTCCCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAACCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATTTACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAACACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATGTATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGATAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTATAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTGCATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAACAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT"/>
+        <sequence id="seq_Homo_sapiens" taxon="Homo_sapiens" totalcount="4"
+                  value="AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
+        <sequence id="seq_Pan" taxon="Pan" totalcount="4"
+                  value="AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATTCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCTCGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAAGCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TATAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCACCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCGCGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAGCTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
+        <sequence id="seq_Gorilla" taxon="Gorilla" totalcount="4"
+                  value="AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGGACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCTCGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTCCTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTCCCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAAACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCTATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CGTAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTACCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCGCATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAGCTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT"/>
+        <sequence id="seq_Pongo" taxon="Pongo" totalcount="4"
+                  value="AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGGCCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCTTGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTCTTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTCTCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAAACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTTATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAACATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGATAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAACAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCGCTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCGCATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAACCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT"/>
+        <sequence id="seq_Hylobates" taxon="Hylobates" totalcount="4"
+                  value="AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATTCTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGGGCTCCAAGCCTTACTCCCACTGATAGCCTTCTGATGACTCGCAGCAAGCCTCGCTAACCTCGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTCCTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTCCCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAAACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCTAACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAACATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CACAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAGCCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTGCCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAACCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT"/>
+        <sequence id="seq_Macaca_fuscata" taxon="Macaca_fuscata" totalcount="4"
+                  value="AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGGACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTCCTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTCTCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAAGCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAACACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT"/>
+        <sequence id="seq_M._mulatta" taxon="M._mulatta" totalcount="4"
+                  value="AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGGACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTCCTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTCCCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCTATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAACATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CGCGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT"/>
+        <sequence id="seq_M._fascicularis" taxon="M._fascicularis" totalcount="4"
+                  value="AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTTCTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGTACCATACTACTATCCCGAGGACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTCCTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTCTCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAACATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTGCCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAATATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAACAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT"/>
+        <sequence id="seq_M._sylvanus" taxon="M._sylvanus" totalcount="4"
+                  value="AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTTCTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGCATCATACTACTATCCCGAGGACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCTTGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTCCTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTCTCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAAACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCTATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAACATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TGCAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCGCTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAATATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAACAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT"/>
+        <sequence id="seq_Saimiri_sciureus" taxon="Saimiri_sciureus" totalcount="4"
+                  value="AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTCTATGCTATTCTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAATAACATTTACTCGAGGGCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCTCGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTCTTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTCACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAAACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCTTACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAACATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CGCAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGATAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAATA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAGCTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCATCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAATCAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT"/>
+        <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4"
+                  value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
+    </data>
+
+
+    <map name="Beta">beast.base.inference.distribution.Beta</map>
+    <map name="Exponential">beast.base.inference.distribution.Exponential</map>
+    <map name="InverseGamma">beast.base.inference.distribution.InverseGamma</map>
+    <map name="LogNormal">beast.base.inference.distribution.LogNormalDistributionModel</map>
+    <map name="Gamma">beast.base.inference.distribution.Gamma</map>
+    <map name="Uniform">beast.base.inference.distribution.Uniform</map>
+    <map name="prior">beast.base.inference.distribution.Prior</map>
+    <map name="LaplaceDistribution">beast.base.inference.distribution.LaplaceDistribution</map>
+    <map name="OneOnX">beast.base.inference.distribution.OneOnX</map>
+    <map name="Normal">beast.base.inference.distribution.Normal</map>
+
+
+    <run chainLength="5000000" id="mcmc" spec="MCMC">
+        <state id="state" storeEvery="5000">
+            <tree id="Tree.t:primate" name="stateNode">
+                <taxonset id="TaxonSet.coding" spec="TaxonSet">
+                    <alignment filter="2-457,660-896" id="coding" spec="FilteredAlignment">
+                        <data idref="primate-mtDNA"/>
+                    </alignment>
+                </taxonset>
+            </tree>
+            <parameter id="birthRate.t:primate" name="stateNode" value="1.0"/>
+            <parameter id="rateAG.s:primate" lower="0.0" name="stateNode" value="2.0"/>
+            <parameter id="rateCT.s:primate" lower="0.0" name="stateNode" value="2.0"/>
+            <parameter dimension="4" id="freqParameter.s:primate" lower="0.0" name="stateNode" upper="1.0"
+                       value="0.25"/>
+        </state>
+
+        <init estimate="false" id="RandomTree.t:primate" initial="@Tree.t:primate"
+              spec="beast.base.evolution.tree.coalescent.RandomTree" taxa="@coding">
+            <populationModel id="ConstantPopulation0.t:primate" spec="ConstantPopulation">
+                <parameter id="randomPopSize.t:primate" name="popSize" value="1"/>
+            </populationModel>
+        </init>
+
+        <distribution id="posterior" spec="CompoundDistribution">
+            <distribution id="prior" spec="CompoundDistribution">
+                <distribution birthDiffRate="@birthRate.t:primate" id="YuleModel.t:primate"
+                              spec="beast.base.evolution.speciation.YuleModel" tree="@Tree.t:primate"/>
+                <prior id="YuleBirthRatePrior.t:primate" name="distribution" x="@birthRate.t:primate">
+                    <Uniform id="Uniform.0" name="distr" upper="Infinity"/>
+                </prior>
+            </distribution>
+            <distribution id="likelihood" spec="CompoundDistribution">
+                <distribution data="@coding" id="treeLikelihood.coding" spec="TreeLikelihood" tree="@Tree.t:primate">
+                    <siteModel id="SiteModel.s:primate" spec="SiteModel">
+                        <parameter estimate="false" id="mutationRate.s:primate" name="mutationRate" value="1.0"/>
+                        <parameter estimate="false" id="gammaShape.s:primate" name="shape" value="1.0"/>
+                        <parameter estimate="false" id="proportionInvariant.s:primate" lower="0.0"
+                                   name="proportionInvariant" upper="1.0" value="0.0"/>
+                        <substModel id="tn93.s:primate" kappa1="@rateAG.s:primate" kappa2="@rateCT.s:primate"
+                                    spec="TN93">
+                            <frequencies frequencies="@freqParameter.s:primate" id="estimatedFreqs.s:primate"
+                                         spec="Frequencies"/>
+                        </substModel>
+                    </siteModel>
+                    <branchRateModel id="StrictClock.c:primate" spec="beast.base.evolution.branchratemodel.StrictClockModel">
+                        <parameter estimate="false" id="clockRate.c:primate" name="clock.rate" value="1.0"/>
+                    </branchRateModel>
+                </distribution>
+                <distribution branchRateModel="@StrictClock.c:primate" id="treeLikelihood.noncoding"
+                              siteModel="@SiteModel.s:primate" spec="TreeLikelihood" tree="@Tree.t:primate">
+                    <data data="@primate-mtDNA" filter="1,458-659,897-898" id="noncoding" spec="FilteredAlignment"/>
+                </distribution>
+            </distribution>
+        </distribution>
+
+        <operator id="YuleBirthRateScaler.t:primate" parameter="@birthRate.t:primate" scaleFactor="0.75"
+                  spec="ScaleOperator" weight="3.0"/>
+
+        <operator id="treeScaler.t:primate" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:primate" weight="3.0"/>
+
+        <operator id="treeRootScaler.t:primate" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator"
+                  tree="@Tree.t:primate" weight="3.0"/>
+
+        <operator id="UniformOperator.t:primate" spec="Uniform" tree="@Tree.t:primate" weight="30.0"/>
+
+        <operator id="SubtreeSlide.t:primate" spec="SubtreeSlide" tree="@Tree.t:primate" weight="15.0"/>
+
+        <operator id="narrow.t:primate" spec="Exchange" tree="@Tree.t:primate" weight="15.0"/>
+
+        <operator id="wide.t:primate" isNarrow="false" spec="Exchange" tree="@Tree.t:primate" weight="3.0"/>
+
+        <operator id="WilsonBalding.t:primate" spec="WilsonBalding" tree="@Tree.t:primate" weight="3.0"/>
+
+        <operator id="RateAGScaler.s:primate" parameter="@rateAG.s:primate" scaleFactor="0.5" spec="ScaleOperator"
+                  weight="0.1"/>
+
+        <operator id="RateCTScaler.s:primate" parameter="@rateCT.s:primate" scaleFactor="0.5" spec="ScaleOperator"
+                  weight="0.1"/>
+
+        <operator delta="0.01" id="FrequenciesExchanger.s:primate" spec="DeltaExchangeOperator" weight="0.1">
+            <parameter idref="freqParameter.s:primate"/>
+        </operator>
+
+        <logger fileName="primate-mtDNA-tn93.log" id="tracelog" logEvery="5000" model="@posterior"
+                sanitiseHeaders="true" sort="smart">
+            <log idref="posterior"/>
+            <log idref="likelihood"/>
+            <log idref="prior"/>
+            <log idref="treeLikelihood.coding"/>
+            <log id="TreeHeight.t:primate" spec="beast.base.evolution.tree.TreeStatLogger" tree="@Tree.t:primate"/>
+            <log idref="YuleModel.t:primate"/>
+            <parameter idref="birthRate.t:primate" name="log"/>
+            <log idref="treeLikelihood.noncoding"/>
+            <parameter idref="rateAG.s:primate" name="log"/>
+            <parameter idref="rateCT.s:primate" name="log"/>
+            <parameter idref="freqParameter.s:primate" name="log"/>
+        </logger>
+
+        <logger id="screenlog" logEvery="5000">
+            <log idref="posterior"/>
+            <log arg="@posterior" id="ESS.0" spec="util.ESS"/>
+            <log idref="likelihood"/>
+            <log idref="prior"/>
+            <parameter idref="rateAG.s:primate" name="log"/>
+            <parameter idref="rateCT.s:primate" name="log"/>
+        </logger>
+
+        <logger fileName="primate-mtDNA-tn93.trees" id="treelog.t:primate" logEvery="5000" mode="tree">
+            <log id="TreeWithMetaDataLogger.t:primate" spec="beast.base.evolution.TreeWithMetaDataLogger"
+                 tree="@Tree.t:primate"/>
+        </logger>
+
+    </run>
+
+</beast>
diff --git a/beast-base/src/test/resources/beast.base/examples/legacy/testTVM.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testTVM.xml
new file mode 100644
index 00000000..56147dcc
--- /dev/null
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/testTVM.xml
@@ -0,0 +1,197 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<beast beautitemplate='Standard' beautistatus=''
+       namespace="beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.alignment:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood"
+       version="2.0">
+
+    <data id="primate-mtDNA">
+        <sequence id="seq_Lemur_catta" taxon="Lemur_catta" totalcount="4"
+                  value="AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATTCTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGGGATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCTAGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTCATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTCCCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAACCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATTTACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAACACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATGTATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGATAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTATAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTGCATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAACAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT"/>
+        <sequence id="seq_Homo_sapiens" taxon="Homo_sapiens" totalcount="4"
+                  value="AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
+        <sequence id="seq_Pan" taxon="Pan" totalcount="4"
+                  value="AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATTCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCTCGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAAGCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TATAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCACCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCGCGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAGCTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
+        <sequence id="seq_Gorilla" taxon="Gorilla" totalcount="4"
+                  value="AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGGACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCTCGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTCCTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTCCCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAAACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCTATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CGTAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTACCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCGCATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAGCTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT"/>
+        <sequence id="seq_Pongo" taxon="Pongo" totalcount="4"
+                  value="AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGGCCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCTTGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTCTTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTCTCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAAACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTTATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAACATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGATAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAACAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCGCTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCGCATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAACCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT"/>
+        <sequence id="seq_Hylobates" taxon="Hylobates" totalcount="4"
+                  value="AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATTCTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGGGCTCCAAGCCTTACTCCCACTGATAGCCTTCTGATGACTCGCAGCAAGCCTCGCTAACCTCGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTCCTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTCCCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAAACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCTAACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAACATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CACAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAGCCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTGCCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAACCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT"/>
+        <sequence id="seq_Macaca_fuscata" taxon="Macaca_fuscata" totalcount="4"
+                  value="AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGGACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTCCTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTCTCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAAGCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAACACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT"/>
+        <sequence id="seq_M._mulatta" taxon="M._mulatta" totalcount="4"
+                  value="AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGGACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTCCTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTCCCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCTATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAACATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CGCGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT"/>
+        <sequence id="seq_M._fascicularis" taxon="M._fascicularis" totalcount="4"
+                  value="AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTTCTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGTACCATACTACTATCCCGAGGACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTCCTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTCTCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAACATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTGCCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAATATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAACAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT"/>
+        <sequence id="seq_M._sylvanus" taxon="M._sylvanus" totalcount="4"
+                  value="AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTTCTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGCATCATACTACTATCCCGAGGACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCTTGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTCCTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTCTCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAAACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCTATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAACATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TGCAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCGCTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAATATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAACAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT"/>
+        <sequence id="seq_Saimiri_sciureus" taxon="Saimiri_sciureus" totalcount="4"
+                  value="AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTCTATGCTATTCTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAATAACATTTACTCGAGGGCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCTCGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTCTTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTCACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAAACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCTTACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAACATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CGCAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGATAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAATA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAGCTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCATCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAATCAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT"/>
+        <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4"
+                  value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
+    </data>
+
+
+    <map name="Beta">beast.base.inference.distribution.Beta</map>
+    <map name="Exponential">beast.base.inference.distribution.Exponential</map>
+    <map name="InverseGamma">beast.base.inference.distribution.InverseGamma</map>
+    <map name="LogNormal">beast.base.inference.distribution.LogNormalDistributionModel</map>
+    <map name="Gamma">beast.base.inference.distribution.Gamma</map>
+    <map name="Uniform">beast.base.inference.distribution.Uniform</map>
+    <map name="prior">beast.base.inference.distribution.Prior</map>
+    <map name="LaplaceDistribution">beast.base.inference.distribution.LaplaceDistribution</map>
+    <map name="OneOnX">beast.base.inference.distribution.OneOnX</map>
+    <map name="Normal">beast.base.inference.distribution.Normal</map>
+
+
+    <run chainLength="5000000" id="mcmc" spec="MCMC">
+        <state id="state" storeEvery="5000">
+            <tree id="Tree.t:primate" name="stateNode">
+                <taxonset id="TaxonSet.coding" spec="TaxonSet">
+                    <alignment filter="2-457,660-896" id="coding" spec="FilteredAlignment">
+                        <data idref="primate-mtDNA"/>
+                    </alignment>
+                </taxonset>
+            </tree>
+            <parameter id="birthRate.t:primate" name="stateNode" value="1.0"/>
+            <parameter id="rateGT.s:primate" lower="0.0" name="stateNode" value="1.0"/>
+            <parameter id="rateTransitions.s:primate" lower="0.0" name="stateNode" value="1.0"/>
+            <parameter id="rateAT.s:primate" lower="0.0" name="stateNode" value="1.0"/>
+            <parameter id="rateCG.s:primate" lower="0.0" name="stateNode" value="1.0"/>
+            <parameter dimension="4" id="freqParameter.s:primate" lower="0.0" name="stateNode" upper="1.0"
+                       value="0.25"/>
+        </state>
+
+        <init estimate="false" id="RandomTree.t:primate" initial="@Tree.t:primate"
+              spec="beast.base.evolution.tree.coalescent.RandomTree" taxa="@coding">
+            <populationModel id="ConstantPopulation0.t:primate" spec="ConstantPopulation">
+                <parameter id="randomPopSize.t:primate" name="popSize" value="1"/>
+            </populationModel>
+        </init>
+
+        <distribution id="posterior" spec="CompoundDistribution">
+            <distribution id="prior" spec="CompoundDistribution">
+                <distribution birthDiffRate="@birthRate.t:primate" id="YuleModel.t:primate"
+                              spec="beast.base.evolution.speciation.YuleModel" tree="@Tree.t:primate"/>
+                <prior id="YuleBirthRatePrior.t:primate" name="distribution" x="@birthRate.t:primate">
+                    <Uniform id="Uniform.0" name="distr" upper="Infinity"/>
+                </prior>
+                <prior id="RateGTPrior.s:primate" name="distribution" x="@rateGT.s:primate">
+                    <LogNormal id="LogNormalDistributionModel.0" name="distr">
+                        <parameter estimate="false" id="RealParameter.0" name="M" value="0"/>
+                        <parameter estimate="false" id="RealParameter.01" lower="0.0" name="S" upper="5.0"
+                                   value="1.25"/>
+                    </LogNormal>
+                </prior>
+                <prior id="RateTransitionsPrior.s:primate" name="distribution" x="@rateTransitions.s:primate">
+                    <LogNormal id="LogNormalDistributionModel.01" name="distr">
+                        <parameter estimate="false" id="RealParameter.02" name="M" value="0"/>
+                        <parameter estimate="false" id="RealParameter.03" lower="0.0" name="S" upper="5.0"
+                                   value="1.25"/>
+                    </LogNormal>
+                </prior>
+                <prior id="RateATPrior.s:primate" name="distribution" x="@rateAT.s:primate">
+                    <LogNormal id="LogNormalDistributionModel.02" name="distr">
+                        <parameter estimate="false" id="RealParameter.04" name="M" value="0"/>
+                        <parameter estimate="false" id="RealParameter.05" lower="0.0" name="S" upper="5.0"
+                                   value="1.25"/>
+                    </LogNormal>
+                </prior>
+                <prior id="RateCGPrior.s:primate" name="distribution" x="@rateCG.s:primate">
+                    <LogNormal id="LogNormalDistributionModel.03" name="distr">
+                        <parameter estimate="false" id="RealParameter.06" name="M" value="0"/>
+                        <parameter estimate="false" id="RealParameter.07" lower="0.0" name="S" upper="5.0"
+                                   value="1.25"/>
+                    </LogNormal>
+                </prior>
+            </distribution>
+
+            <distribution id="likelihood" spec="CompoundDistribution">
+                <distribution data="@coding" id="treeLikelihood.coding" spec="TreeLikelihood" tree="@Tree.t:primate">
+                    <siteModel id="SiteModel.s:primate" spec="SiteModel">
+                        <parameter estimate="false" id="mutationRate.s:primate" name="mutationRate" value="1.0"/>
+                        <parameter estimate="false" id="gammaShape.s:primate" name="shape" value="1.0"/>
+                        <parameter estimate="false" id="proportionInvariant.s:primate" lower="0.0"
+                                   name="proportionInvariant" upper="1.0" value="0.0"/>
+                        <substModel id="tvm.s:primate" rateGT="@rateGT.s:primate" rateTransitions="@rateTransitions.s:primate"
+                                    rateAT="@rateAT.s:primate" rateCG="@rateCG.s:primate" spec="TVM">
+                            <parameter estimate="false" id="rateAC.s:primate" lower="0.0" name="rateAC" value="1.0"/>
+                            <frequencies frequencies="@freqParameter.s:primate" id="estimatedFreqs.s:primate"
+                                         spec="Frequencies"/>
+                        </substModel>
+                    </siteModel>
+                    <branchRateModel id="StrictClock.c:primate" spec="beast.base.evolution.branchratemodel.StrictClockModel">
+                        <parameter estimate="false" id="clockRate.c:primate" name="clock.rate" value="1.0"/>
+                    </branchRateModel>
+                </distribution>
+                <distribution branchRateModel="@StrictClock.c:primate" id="treeLikelihood.noncoding"
+                              siteModel="@SiteModel.s:primate" spec="TreeLikelihood" tree="@Tree.t:primate">
+                    <data data="@primate-mtDNA" filter="1,458-659,897-898" id="noncoding" spec="FilteredAlignment"/>
+                </distribution>
+            </distribution>
+        </distribution>
+
+        <operator id="YuleBirthRateScaler.t:primate" parameter="@birthRate.t:primate" scaleFactor="0.75"
+                  spec="ScaleOperator" weight="3.0"/>
+
+        <operator id="treeScaler.t:primate" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:primate" weight="3.0"/>
+
+        <operator id="treeRootScaler.t:primate" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator"
+                  tree="@Tree.t:primate" weight="3.0"/>
+
+        <operator id="UniformOperator.t:primate" spec="Uniform" tree="@Tree.t:primate" weight="30.0"/>
+
+        <operator id="SubtreeSlide.t:primate" spec="SubtreeSlide" tree="@Tree.t:primate" weight="15.0"/>
+
+        <operator id="narrow.t:primate" spec="Exchange" tree="@Tree.t:primate" weight="15.0"/>
+
+        <operator id="wide.t:primate" isNarrow="false" spec="Exchange" tree="@Tree.t:primate" weight="3.0"/>
+
+        <operator id="WilsonBalding.t:primate" spec="WilsonBalding" tree="@Tree.t:primate" weight="3.0"/>
+
+        <operator id="RateGTScaler.s:primate" parameter="@rateGT.s:primate" scaleFactor="0.5" spec="ScaleOperator"
+                  weight="0.1"/>
+
+        <operator id="RateATScaler.s:primate" parameter="@rateAT.s:primate" scaleFactor="0.5" spec="ScaleOperator"
+                  weight="0.1"/>
+
+        <operator id="RateCGScaler.s:primate" parameter="@rateCG.s:primate" scaleFactor="0.5" spec="ScaleOperator"
+                  weight="0.1"/>
+
+        <operator id="RateTransitionsScaler.s:primate" parameter="@rateTransitions.s:primate" scaleFactor="0.5" spec="ScaleOperator"
+                  weight="0.1"/>
+
+        <operator delta="0.01" id="FrequenciesExchanger.s:primate" spec="DeltaExchangeOperator" weight="0.1">
+            <parameter idref="freqParameter.s:primate"/>
+        </operator>
+
+        <logger fileName="primate-mtDNA-TVM.log" id="tracelog" logEvery="5000" model="@posterior" sanitiseHeaders="true"
+                sort="smart">
+            <log idref="posterior"/>
+            <log idref="likelihood"/>
+            <log idref="prior"/>
+            <log idref="treeLikelihood.noncoding"/>
+            <log idref="treeLikelihood.coding"/>
+            <log id="TreeHeight.t:primate" spec="beast.base.evolution.tree.TreeStatLogger" tree="@Tree.t:primate"/>
+            <log idref="YuleModel.t:primate"/>
+            <parameter idref="birthRate.t:primate" name="log"/>
+            <parameter idref="rateGT.s:primate" name="log"/>
+            <parameter idref="rateTransitions.s:primate" name="log"/>
+            <parameter idref="rateAT.s:primate" name="log"/>
+            <parameter idref="rateCG.s:primate" name="log"/>
+            <parameter idref="freqParameter.s:primate" name="log"/>
+        </logger>
+
+        <logger id="screenlog" logEvery="5000">
+            <log idref="posterior"/>
+            <log arg="@posterior" id="ESS.0" spec="util.ESS"/>
+            <log idref="likelihood"/>
+            <log idref="prior"/>
+        </logger>
+
+        <logger fileName="$(tree).trees" id="treelog.t:primate" logEvery="5000" mode="tree">
+            <log id="TreeWithMetaDataLogger.t:primate" spec="beast.base.evolution.TreeWithMetaDataLogger"
+                 tree="@Tree.t:primate"/>
+        </logger>
+
+    </run>
+</beast>
diff --git a/beast-base/src/test/resources/beast.base/examples/testTipDates.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testTipDates.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/testTipDates.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/testTipDates.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/testTipDates2.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testTipDates2.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/testTipDates2.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/testTipDates2.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/testTwoCalibrationsPrior.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testTwoCalibrationsPrior.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/testTwoCalibrationsPrior.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/testTwoCalibrationsPrior.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/testUCLNclock.json b/beast-base/src/test/resources/beast.base/examples/legacy/testUCLNclock.json
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/testUCLNclock.json
rename to beast-base/src/test/resources/beast.base/examples/legacy/testUCLNclock.json
diff --git a/beast-base/src/test/resources/beast.base/examples/testYuleCalibrated.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testYuleCalibrated.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/testYuleCalibrated.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/testYuleCalibrated.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/legacy/testYuleOneSite.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testYuleOneSite.xml
new file mode 100644
index 00000000..465f1bcc
--- /dev/null
+++ b/beast-base/src/test/resources/beast.base/examples/legacy/testYuleOneSite.xml
@@ -0,0 +1,90 @@
+<?xml version="1.0" standalone="yes"?>
+<!-- test Yule birth model and Birth Death model per Gernhard 2008-->
+<beast version='2.0'
+       namespace='beast.base.evolution.speciation:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
+
+    <data id="alignment" dataType="nucleotide">
+        <sequence taxon="A">A</sequence>
+        <sequence taxon="B">A</sequence>
+        <sequence taxon="C">A</sequence>
+        <sequence taxon="D">A</sequence>
+    </data>
+    
+    <!-- A prior on the distribution node heights defined given                  -->
+    <!-- a Yule speciation process (a pure birth process).                       -->
+    <input spec='YuleModel' id="yule">
+        <parameter name='birthDiffRate' idref="birthRate"/>
+	<tree spec='beast.base.evolution.tree.TreeParser' id='tree' IsLabelledNewick='true' taxa='@alignment'
+	        newick='((A:1.0,B:1.0):1.0,(C:1.0,D:1.0):1.0);'/>
+    </input>
+
+    <input spec='BirthDeathGernhard08Model' id="yulelike" type='unscaled' tree='@tree'>
+        <parameter name='birthDiffRate' idref="birthRate"/>
+	    <parameter name='relativeDeathRate' idref='relativeDeathRate'/>
+    </input>
+
+    <!-- site model                                                              -->
+    <input spec='SiteModel' id="siteModel" gammaCategoryCount='1'>
+	<substModel spec='HKY' id='hky'>
+	    <kappa id='hky.kappa' spec='parameter.RealParameter' value='1.0'/>
+	    <frequencies id='freqs' spec='Frequencies'>
+	       <data idref='alignment'/>
+	    </frequencies>
+	</substModel>
+    </input>
+
+    <parameter id="birthRate" value="1.0" lower="0.0" upper="100.0"/>
+    <parameter id='relativeDeathRate' value='0'/>
+
+    <!-- initial yule prior = -6.0, yule-like prior = -2.8219461696520542 -->
+    <!-- expected yule prior = 1/(n.lambda)\sum_{k=1}^{n-1}k/(n-k) where lambda = birth rate, n = number of taxa
+	with lambda=1, n=-4 we expect 1/4(1/3+2/2+3/1)=1.155555555
+ -->
+    <run spec='MCMC' chainLength="10">
+	<state>
+	    <stateNode idref='tree'/>
+	    <stateNode idref='birthRate'/>
+	    <stateNode id='tree-test-single-child-parsing' IsLabelledNewick='true' spec='beast.base.evolution.tree.TreeParser' singlechild='true' newick='((A:1.0):2,C:3);' >
+			<taxonset spec='beast.base.evolution.alignment.TaxonSet'>
+				<taxon spec='beast.base.evolution.alignment.Taxon' id='A'/>
+				<taxon spec='beast.base.evolution.alignment.Taxon' id='C'/>
+			</taxonset>
+		</stateNode>
+	</state>
+
+	<distribution spec='CompoundDistribution'>
+	        <distribution id="yule.prior" idref='yule'/>
+<!--
+		<distribution spec='TreeLikelihood' id="treeLikelihood" data='@alignment' tree='@tree' siteModel='@siteModel'/>
+-->
+	        <distribution id="yulelike.prior" idref='yulelike'/>
+	</distribution>
+
+        <operator spec='SubtreeSlide' weight="5" gaussian="true" size="1.0" tree="@tree"/>
+<!--
+        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" tree="@tree"/>
+-->
+        <operator spec='Uniform' weight="10" tree="@tree"/>
+        <operator id='narrow' spec='Exchange' isNarrow='true' weight="1" tree="@tree"/>
+        <operator id='wide' spec='Exchange' isNarrow='false' weight="1" tree="@tree"/>
+        <operator spec='WilsonBalding' weight="1" tree="@tree"/>
+<!--
+        <operator spec='ScaleOperator' scaleFactor="0.75" weight="3">
+            <parameter idref="birthRate"/>
+        </operator>
+-->
+	<logger logEvery='100'>
+	    <log idref='yule.prior'/>
+	    <!--log idref='treeLikelihood'/-->
+	    <log idref='yulelike.prior'/>
+            <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree'/>
+	</logger>
+	<logger logEvery='100' fileName='$(seed).log'>
+	    <log idref='yule.prior'/>
+	    <!--log idref='treeLikelihood'/-->
+	    <!--log idref='yulelike.prior'/-->
+            <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree'/>
+	</logger>
+    </run>
+
+</beast>
diff --git a/beast-base/src/test/resources/beast.base/examples/testYuleUncalibrated.xml b/beast-base/src/test/resources/beast.base/examples/legacy/testYuleUncalibrated.xml
similarity index 100%
rename from beast-base/src/test/resources/beast.base/examples/testYuleUncalibrated.xml
rename to beast-base/src/test/resources/beast.base/examples/legacy/testYuleUncalibrated.xml
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testSRD06CP12_3.xml b/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testSRD06CP12_3.xml
deleted file mode 100644
index 6d340685..00000000
--- a/beast-base/src/test/resources/beast.base/examples/spec/beast2vs1/testSRD06CP12_3.xml
+++ /dev/null
@@ -1,193 +0,0 @@
-<!--<?xml version="1.0" encoding="UTF-8" standalone="no"?>-->
-<!--<beast version='2.0'-->
-<!--       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:-->
-<!--       beast.base.evolution.tree.coalescent:beast.evolution.nuc:beast.base.evolution.alignment:-->
-<!--       beast.base.evolution.operator:beast.base.spec.inference.operator:-->
-<!--       beast.base.spec.evolution.sitemodel:beast.base.spec.evolution.substitutionmodel:-->
-<!--       beast.base.spec.evolution.branchratemodel:beast.base.spec.inference.parameter:-->
-<!--       beast.base.spec.inference.distribution:beast.base.spec.inference.util:-->
-<!--       beast.base.spec.evolution.tree:beast.base.spec.evolution.likelihood'>-->
-
-<!--    &lt;!&ndash; SRD06 model: split sequences in first together with seconds and thirds of all sites &ndash;&gt;-->
-<!--    <data id="alignment" dataType="nucleotide">-->
-<!--        <sequence taxon="human">-->
-<!--            AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCCTTATTTCTACTAGGACTATGAGAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTG-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCGGAGCTTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGGCCTCCATGACTTTTTCAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAATTATAGGCT-AAATCCTATATATCTTA-CACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACACCTCTTTACAGTGA-->
-<!--        </sequence>-->
-<!--        <sequence taxon="chimp">-->
-<!--            AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTCAAATCCCCTTATTTCTACTAGGACTATAAGAATCGAACTCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTAAGCACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCTCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AACCCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCGACACCTCTTTACAGTGA-->
-<!--        </sequence>-->
-<!--        <sequence taxon="bonobo">-->
-<!--            AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTTAAATCCCCTTATTTCTACTAGGACTATGAGAGTCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCTCTCAGTAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAGC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTTGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCCCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCAACACCTCTTTACAGTGA-->
-<!--        </sequence>-->
-<!--        <sequence taxon="gorilla">-->
-<!--            AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGAGGTTTAAACCCCCTTATTTCTACTAGGACTATGAGAATTGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTGTCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTCACATCCTTCCCGTACTAAGAAATTTAGGTTAAACATAGACCAAGAGCCTTCAAAGCCCTTAGTAAGTTA-CAACACTTAATTTCTGTAAGGACTGCAAAACCCTACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCAATGGGACTCAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAT-TCACCTCGGAGCTTGGTAAAAAGAGGCCCAGCCTCTGTCTTTAGATTTACAGTCCAATGCCTTA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGACCTTCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAGGTTAAATTACGGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCGTTAACCTTTTAAGTTAAAGATTAAGAGTATCGGCACCTCTTTGCAGTGA-->
-<!--        </sequence>-->
-<!--        <sequence taxon="orangutan">-->
-<!--            AGAAATATGTCTGACAAAAGAGTTACTTTGATAGAGTAAAAAATAGAGGTCTAAATCCCCTTATTTCTACTAGGACTATGGGAATTGAACCCACCCCTGAGAATCCAAAATTCTCCGTGCCACCCATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTA&#45;&#45;CACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTCA-CAGCACTTAATTTCTGTAAGGACTGCAAAACCCCACTTTGCATCAACTGAGCGCAAATCAGCCACTTTAATTAAGCTAAGCCCTCCTAGACCGATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAT-TGGCTTCAGTCCAAAGCCCCGGCAGGCCTTAAAGCTGCTCCTTCGAATTTGCAATTCAACATGACAA-TCACCTCAGGGCTTGGTAAAAAGAGGTCTGACCCCTGTTCTTAGATTTACAGCCTAATGCCTTAACTCGGCCATTTTACCGCAAAAAAGGAAGGAATCGAACCTCCTAAAGCTGGTTTCAAGCCAACCCCATAACCCCCATGACTTTTTCAAAAGGTACTAGAAAAACCATTTCGTAACTTTGTCAAAGTTAAATTACAGGTC-AGACCCTGTGTATCTTA-CATTGCAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACCAGCCTCTCTTTGCAATGA-->
-<!--        </sequence>-->
-<!--        <sequence taxon="siamang">-->
-<!--            AGAAATACGTCTGACGAAAGAGTTACTTTGATAGAGTAAATAACAGGGGTTTAAATCCCCTTATTTCTACTAGAACCATAGGAGTCGAACCCATCCTTGAGAATCCAAAACTCTCCGTGCCACCCGTCGCACCCTGTTCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCATACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTAACAAAACTTAATTTCTGCAAGGGCTGCAAAACCCTACTTTGCATCAACCGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCGATGGGACTTAAACCCATAAAAATTTAGTTAACAGCTAAACACCCTAAACAACCTGGCTTCAATCTAAAGCCCCGGCAGA-GTTGAAGCTGCTTCTTTGAACTTGCAATTCAACGTGAAAAATCACTTCGGAGCTTGGCAAAAAGAGGTTTCACCTCTGTCCTTAGATTTACAGTCTAATGCTTTA-CTCAGCCACTTTACCACAAAAAAGGAAGGAATCGAACCCTCTAAAACCGGTTTCAAGCCAGCCCCATAACCTTTATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATCACAGGTCCAAACCCCGTATATCTTATCACTGTAGAGCTAGACCAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACTACCGCCTCTTTACAGTGA-->
-<!--        </sequence>-->
-<!--    </data>-->
-
-<!--    <data data="@alignment" dataType="nucleotide" filter="1::3,2::3" id="CP12" name="taxa"-->
-<!--          spec="beast.base.spec.evolution.alignment.FilteredAlignment"/>-->
-<!--    <data data="@alignment" dataType="nucleotide" filter="3::3" id="CP3" name="taxa"-->
-<!--          spec="beast.base.spec.evolution.alignment.FilteredAlignment"/>-->
-
-<!--    <siteModel gammaCategoryCount="4" id="CP12.siteModel" spec="beast.base.spec.evolution.sitemodel.SiteModel">-->
-<!--        <parameter id="CP12.mutationRate" name="mutationRate" spec="RealScalarParam" domain="PositiveReal" value="1.0"/>-->
-<!--        <parameter id="CP12.gammaShape" name="shape" spec="RealScalarParam" domain="PositiveReal" value="0.5"/>-->
-<!--        <substModel id="CP12.hky" kappa="@CP12.hky.kappa" spec="HKY">-->
-<!--            <frequencies frequencies="@CP12.frequencies" id="CP12.freqs" spec="Frequencies"/>-->
-<!--        </substModel>-->
-<!--    </siteModel>-->
-
-<!--    <siteModel gammaCategoryCount="4" id="CP3.siteModel" spec="beast.base.spec.evolution.sitemodel.SiteModel">-->
-<!--        <parameter id="CP3.mutationRate" name="mutationRate" spec="RealScalarParam" domain="PositiveReal" value="1.0"/>-->
-<!--        <parameter id="CP3.gammaShape" name="shape" spec="RealScalarParam" domain="PositiveReal" value="0.5"/>-->
-<!--        <substModel id="CP3.hky" kappa="@CP3.hky.kappa" spec="HKY">-->
-<!--            <frequencies frequencies="@CP3.frequencies" id="CP3.freqs" spec="Frequencies"/>-->
-<!--        </substModel>-->
-<!--    </siteModel>-->
-
-<!--    <input spec='beast.base.spec.evolution.branchratemodel.StrictClockModel' id="branchRates">-->
-<!--        <clock.rate id="clockRate" spec="RealScalarParam" domain="PositiveReal" value="1.0"/>-->
-<!--    </input>-->
-
-<!--    <input spec='beast.base.spec.evolution.tree.ClusterTree' id='tree' clusterType='upgma'>-->
-<!--        &lt;!&ndash;trait idref='rateCategories'/&ndash;&gt;-->
-<!--        <taxa idref='alignment'/>-->
-<!--    </input>-->
-
-<!--    <input spec='TreeLikelihood' id="CP12.treeLikelihood">-->
-<!--        <data idref="CP12"/>-->
-<!--        <tree idref="tree"/>-->
-<!--        <siteModel idref="CP12.siteModel"/>-->
-<!--        <branchRateModel idref="branchRates"/>-->
-<!--    </input>-->
-
-<!--    <input spec='TreeLikelihood' id="CP3.treeLikelihood">-->
-<!--        <data idref="CP3"/>-->
-<!--        <tree idref="tree"/>-->
-<!--        <siteModel idref="CP3.siteModel"/>-->
-<!--        <branchRateModel idref="branchRates"/>-->
-<!--    </input>-->
-
-<!--    <parameter id="CP12.hky.kappa" spec="RealScalarParam" domain="PositiveReal" value="2.0"/>-->
-<!--    <parameter id="CP3.hky.kappa" spec="RealScalarParam" domain="PositiveReal" value="2.0"/>-->
-<!--    <parameter dimension="4" id="CP12.frequencies" spec="SimplexParam" value="0.25"/>-->
-<!--    <parameter dimension="4" id="CP3.frequencies" spec="SimplexParam" value="0.25"/>-->
-<!--    <parameter id="popSize" spec="RealScalarParam" domain="PositiveReal" value="0.077"/>-->
-
-<!--    <run spec="MCMC" id="mcmc" chainLength="10000000"> &lt;!&ndash;autoOptimize="true"&ndash;&gt;-->
-
-<!--        <distribution spec="CompoundDistribution" id="posterior">-->
-<!--            <distribution spec="CompoundDistribution" id="prior">-->
-<!--                <distribution id="CP12.hky.kappa.prior" spec='LogNormal' param='@CP12.hky.kappa' >-->
-<!--                    &lt;!&ndash; M="1" S="1.25" />&ndash;&gt;-->
-<!--                    <M spec="RealScalarParam" domain="Real" value="1.0"/>-->
-<!--                    <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>-->
-<!--                </distribution>-->
-<!--                <distribution id="CP3.hky.kappa.prior" spec='LogNormal' param='@CP3.hky.kappa' >-->
-<!--                    <M spec="RealScalarParam" domain="Real" value="1.0"/>-->
-<!--                    <S spec="RealScalarParam" domain="PositiveReal" value="1.25"/>-->
-<!--                </distribution>-->
-
-<!--                &lt;!&ndash; cannot use TruncatedReal to OneOnX &ndash;&gt;-->
-<!--&lt;!&ndash;                <distribution id='CP12.gammaShape.prior' spec='beast.base.spec.inference.distribution.TruncatedReal'&ndash;&gt;-->
-<!--&lt;!&ndash;                              param='@CP12.gammaShape' >&ndash;&gt;-->
-<!--&lt;!&ndash;                    <lower spec="RealScalarParam" domain="Real" value="0.1" estimate="false"/>&ndash;&gt;-->
-<!--&lt;!&ndash;                    <upper spec="RealScalarParam" domain="Real" value="1000.0" estimate="false"/>&ndash;&gt;-->
-<!--&lt;!&ndash;                    <distribution spec='beast.base.spec.beast2vs1.OneOnX' />&ndash;&gt;-->
-<!--&lt;!&ndash;                </distribution>&ndash;&gt;-->
-<!--&lt;!&ndash;                <distribution id='CP3.gammaShape.prior' spec='beast.base.spec.inference.distribution.TruncatedReal'&ndash;&gt;-->
-<!--&lt;!&ndash;                              param='@CP3.gammaShape' >&ndash;&gt;-->
-<!--&lt;!&ndash;                    <lower spec="RealScalarParam" domain="Real" value="0.1" estimate="false"/>&ndash;&gt;-->
-<!--&lt;!&ndash;                    <upper spec="RealScalarParam" domain="Real" value="1000.0" estimate="false"/>&ndash;&gt;-->
-<!--&lt;!&ndash;                    <distribution spec='beast.base.spec.beast2vs1.OneOnX' />&ndash;&gt;-->
-<!--&lt;!&ndash;                </distribution>&ndash;&gt;-->
-
-<!--                <distribution id="popSize.prior" spec='beast.base.spec.beast2vs1.OneOnX'-->
-<!--                              param='@popSize' />-->
-
-<!--                <distribution id="coalescent" spec="Coalescent">-->
-<!--                    <treeIntervals spec='beast.base.evolution.tree.TreeIntervals' id='TreeIntervals'>-->
-<!--                        <tree idref="tree"/>-->
-<!--                    </treeIntervals>-->
-<!--                    <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">-->
-<!--                        <popSize idref="popSize"/>-->
-<!--                    </populationModel>-->
-<!--                </distribution>-->
-<!--            </distribution>-->
-<!--            <distribution spec="CompoundDistribution" id='likelihood'>-->
-<!--                <distribution idref="CP12.treeLikelihood"/>-->
-<!--                <distribution idref="CP3.treeLikelihood"/>-->
-<!--            </distribution>-->
-<!--        </distribution>-->
-
-<!--        <operator id='compMuDelta' spec='beast.base.spec.inference.operator.DeltaExchangeOperator'-->
-<!--                  delta="0.75" weight="2">-->
-<!--            <weightvector  spec='beast.base.spec.inference.parameter.IntVectorParam'-->
-<!--                       domain="PositiveInt" value="512 256"/>-->
-<!--            <parameter idref="CP12.mutationRate"/>-->
-<!--            <parameter idref="CP3.mutationRate"/>-->
-<!--        </operator>-->
-
-<!--        <operator id='CP12kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.75" weight="0.1"-->
-<!--                  parameter="@CP12.hky.kappa"/>-->
-<!--        <operator id='CP12frequenciesDelta' spec='beast.base.spec.inference.operator.DeltaExchangeOperator' delta="0.01" weight="0.1"-->
-<!--                  rvparameter="@CP12.frequencies"/>-->
-<!--        <operator id='CP3kappaScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.75" weight="0.1"-->
-<!--                  parameter="@CP3.hky.kappa"/>-->
-<!--        <operator id='CP3frequenciesDelta' spec='DeltaExchangeOperator' delta="0.01" weight="0.1"-->
-<!--                  rvparameter="@CP3.frequencies"/>-->
-<!--        <operator id='CP12alphaScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.75" weight="0.1"-->
-<!--                  parameter="@CP12.gammaShape"/>-->
-<!--        <operator id='CP3alphaScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.75" weight="0.1"-->
-<!--                  parameter="@CP3.gammaShape"/>-->
-<!--        <operator id='popSizeScaler' spec='beast.base.spec.inference.operator.ScaleOperator' scaleFactor="0.75" weight="3"-->
-<!--                  parameter="@popSize"/>-->
-<!--        <operator id='treeScaler' spec='beast.base.spec.evolution.operator.ScaleTreeOperator' scaleFactor="0.75" weight="3" tree="@tree"/>-->
-<!--        <operator spec='Uniform' weight="30" tree="@tree"/>-->
-<!--        <operator spec='SubtreeSlide' weight="15" gaussian="true" size="0.0077" tree="@tree"/>-->
-<!--        <operator id='narrow' spec='Exchange' isNarrow='true' weight="15" tree="@tree"/>-->
-<!--        <operator id='wide' spec='Exchange' isNarrow='false' weight="3" tree="@tree"/>-->
-<!--        <operator spec='WilsonBalding' weight="1" tree="@tree"/>-->
-<!--        <operator spec='beast.base.spec.evolution.operator.UpDownOperator' scaleFactor="0.75" weight="3" down="@tree"/>-->
-
-<!--        <logger logEvery="1000" fileName="test.$(seed).log">-->
-<!--            <model idref='posterior'/>-->
-<!--            <log idref="posterior"/>-->
-<!--            <log idref="prior"/>-->
-<!--            <log idref="likelihood"/>-->
-<!--            <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree'/>-->
-<!--            <log idref="popSize"/>-->
-<!--            <log idref="CP12.hky.kappa"/>-->
-<!--            <log idref="CP3.hky.kappa"/>-->
-<!--            <log idref="CP12.frequencies"/>-->
-<!--            <log idref="CP3.frequencies"/>-->
-<!--            <log idref="CP12.gammaShape"/>-->
-<!--            <log idref="CP3.gammaShape"/>-->
-<!--            <log idref="CP12.mutationRate"/>-->
-<!--            <log idref="CP3.mutationRate"/>-->
-<!--            <log idref="clockRate"/>-->
-<!--            <log idref="CP12.treeLikelihood"/>-->
-<!--            <log idref="CP3.treeLikelihood"/>-->
-<!--            <log idref="coalescent"/>-->
-<!--        </logger>-->
-<!--        &lt;!&ndash;         <logger logEvery="1000" fileName="test.$(seed).trees">-->
-<!--    <log idref="tree"/>-->
-<!--</logger>        &ndash;&gt;-->
-<!--        <logger logEvery="100000">-->
-<!--            <model idref='posterior'/>-->
-<!--            <log idref="posterior"/>-->
-<!--            <log idref="prior"/>-->
-<!--            <log idref="likelihood"/>-->
-<!--            <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree'/>-->
-<!--            <log idref="popSize"/>-->
-<!--            <log idref="coalescent"/>-->
-<!--        </logger>-->
-<!--    </run>-->
-
-<!--</beast>-->
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/bitflip.xml b/beast-base/src/test/resources/beast.base/examples/spec/bitflip.xml
deleted file mode 100644
index 383b77fb..00000000
--- a/beast-base/src/test/resources/beast.base/examples/spec/bitflip.xml
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<beast version="2.8"
-       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt">
-
-    <parameter name="indicators" id="indicators" dimension="5" value="false" spec="beast.base.spec.inference.parameter.BoolVectorParam"/>
-
-    <run spec="MCMC" id="mcmc" chainLength="100000"> <!--autoOptimize="true"-->
-        <state>
-            <input name="stateNode" idref="indicators"/>
-        </state>
-	
-	<distribution spec="CompoundDistribution" id="posterior"/>
-
-        <operator id="bitflip" spec="beast.base.spec.inference.operator.BitFlipOperator" weight="1">
-            <input name="parameter" idref="indicators"/>
-        </operator>
-
-        <logger logEvery="10" fileName="bitflip.log">
-            <log idref="indicators"/>
-        </logger>
-    </run>
-
-</beast>
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/testGTR.xml b/beast-base/src/test/resources/beast.base/examples/spec/testGTR.xml
deleted file mode 100644
index 50899ee6..00000000
--- a/beast-base/src/test/resources/beast.base/examples/spec/testGTR.xml
+++ /dev/null
@@ -1,152 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<beast version="2.8"
-       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt"
-       beautitemplate="Standard"
-       beautistatus="">
-
-    <data id="primate-mtDNA">
-        <sequence id="seq_Lemur_catta" taxon="Lemur_catta" totalcount="4" value="AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATTCTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGGGATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCTAGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTCATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTCCCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAACCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATTTACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAACACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATGTATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGATAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTATAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTGCATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAACAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT"/>
-        <sequence id="seq_Homo_sapiens" taxon="Homo_sapiens" totalcount="4" value="AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
-        <sequence id="seq_Pan" taxon="Pan" totalcount="4" value="AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATTCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCTCGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAAGCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TATAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCACCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCGCGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAGCTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
-        <sequence id="seq_Gorilla" taxon="Gorilla" totalcount="4" value="AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGGACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCTCGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTCCTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTCCCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAAACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCTATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CGTAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTACCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCGCATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAGCTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT"/>
-        <sequence id="seq_Pongo" taxon="Pongo" totalcount="4" value="AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGGCCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCTTGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTCTTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTCTCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAAACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTTATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAACATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGATAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAACAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCGCTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCGCATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAACCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT"/>
-        <sequence id="seq_Hylobates" taxon="Hylobates" totalcount="4" value="AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATTCTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGGGCTCCAAGCCTTACTCCCACTGATAGCCTTCTGATGACTCGCAGCAAGCCTCGCTAACCTCGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTCCTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTCCCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAAACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCTAACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAACATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CACAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAGCCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTGCCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAACCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT"/>
-        <sequence id="seq_Macaca_fuscata" taxon="Macaca_fuscata" totalcount="4" value="AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGGACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTCCTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTCTCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAAGCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAACACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT"/>
-        <sequence id="seq_M._mulatta" taxon="M._mulatta" totalcount="4" value="AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGGACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTCCTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTCCCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCTATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAACATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CGCGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT"/>
-        <sequence id="seq_M._fascicularis" taxon="M._fascicularis" totalcount="4" value="AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTTCTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGTACCATACTACTATCCCGAGGACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTCCTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTCTCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAACATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTGCCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAATATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAACAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT"/>
-        <sequence id="seq_M._sylvanus" taxon="M._sylvanus" totalcount="4" value="AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTTCTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGCATCATACTACTATCCCGAGGACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCTTGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTCCTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTCTCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAAACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCTATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAACATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TGCAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCGCTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAATATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAACAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT"/>
-        <sequence id="seq_Saimiri_sciureus" taxon="Saimiri_sciureus" totalcount="4" value="AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTCTATGCTATTCTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAATAACATTTACTCGAGGGCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCTCGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTCTTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTCACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAAACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCTTACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAACATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CGCAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGATAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAATA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAGCTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCATCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAATCAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT"/>
-        <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4" value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
-    </data>
-
-    <run chainLength="5000000" id="mcmc" spec="MCMC">
-        <state id="state" storeEvery="5000">
-            <tree id="Tree.t:primate" name="stateNode">
-                <taxonset id="TaxonSet.coding" spec="TaxonSet">
-                    <alignment filter="2-457,660-896" id="coding" spec="beast.base.spec.evolution.alignment.FilteredAlignment">
-                        <data idref="primate-mtDNA"/>
-                    </alignment>
-                </taxonset>
-            </tree>
-            <parameter id="birthRate.t:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-            <parameter id="rateAC.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-            <parameter id="rateAG.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-            <parameter id="rateAT.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-            <parameter id="rateCG.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-            <parameter id="rateGT.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-            <parameter dimension="4" id="freqParameter.s:primate" name="stateNode" value="0.25" spec="beast.base.spec.inference.parameter.SimplexParam"/>
-        </state>
-
-        <init estimate="false" id="RandomTree.t:primate" initial="@Tree.t:primate" spec="beast.base.spec.evolution.tree.coalescent.RandomTree" taxa="@coding">
-            <populationModel id="ConstantPopulation0.t:primate" spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
-                <parameter id="randomPopSize.t:primate" name="popSize" value="1" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-            </populationModel>
-        </init>
-
-        <distribution id="posterior" spec="CompoundDistribution">
-            <distribution id="prior" spec="CompoundDistribution">
-                <distribution birthDiffRate="@birthRate.t:primate" id="YuleModel.t:primate" spec="beast.base.spec.evolution.speciation.YuleModel" tree="@Tree.t:primate"/>
-                <distribution id="Uniform.0" spec="beast.base.spec.inference.distribution.Uniform" param="@birthRate.t:primate" upper="1.0E6"/>
-                <distribution id="LogNormalDistributionModel.0" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateAC.s:primate">
-                        <parameter estimate="false" id="RealParameter.0" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="RealParameter.01" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </distribution>
-                <distribution id="LogNormalDistributionModel.01" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateAG.s:primate">
-                        <parameter estimate="false" id="RealParameter.02" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="RealParameter.03" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </distribution>
-                <distribution id="LogNormalDistributionModel.02" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateAT.s:primate">
-                        <parameter estimate="false" id="RealParameter.04" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="RealParameter.05" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </distribution>
-                <distribution id="LogNormalDistributionModel.03" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateCG.s:primate">
-                        <parameter estimate="false" id="RealParameter.06" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="RealParameter.07" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </distribution>
-                <distribution id="LogNormalDistributionModel.04" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateGT.s:primate">
-                        <parameter estimate="false" id="RealParameter.08" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="RealParameter.09" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </distribution>
-            </distribution>
-            <distribution id="likelihood" spec="CompoundDistribution">
-                <distribution data="@coding" id="treeLikelihood.coding" spec="beast.base.spec.evolution.likelihood.TreeLikelihood" tree="@Tree.t:primate">
-                    <siteModel id="SiteModel.s:primate" spec="beast.base.spec.evolution.sitemodel.SiteModel">
-                        <parameter estimate="false" id="mutationRate.s:primate" name="mutationRate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="gammaShape.s:primate" name="shape" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="proportionInvariant.s:primate" name="proportionInvariant" value="0.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="UnitInterval"/>
-                        <substModel id="gtr.s:primate" rateAC="@rateAC.s:primate" rateAG="@rateAG.s:primate" rateAT="@rateAT.s:primate" rateCG="@rateCG.s:primate" rateGT="@rateGT.s:primate" spec="beast.base.spec.evolution.substitutionmodel.GTR">
-                            <parameter estimate="false" id="rateCT.s:primate" name="rateCT" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-                            <frequencies frequencies="@freqParameter.s:primate" id="estimatedFreqs.s:primate" spec="beast.base.spec.evolution.substitutionmodel.Frequencies"/>
-                        </substModel>
-                    </siteModel>
-                    <branchRateModel id="StrictClock.c:primate" spec="beast.base.spec.evolution.branchratemodel.StrictClockModel">
-                        <parameter estimate="false" id="clockRate.c:primate" name="clock.rate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </branchRateModel>
-                </distribution>
-                <distribution branchRateModel="@StrictClock.c:primate" id="treeLikelihood.noncoding" siteModel="@SiteModel.s:primate" spec="beast.base.spec.evolution.likelihood.TreeLikelihood" tree="@Tree.t:primate">
-                    <data data="@primate-mtDNA" filter="1,458-659,897-898" id="noncoding" spec="beast.base.spec.evolution.alignment.FilteredAlignment"/>
-                </distribution>
-            </distribution>
-        </distribution>
-
-        <operator id="YuleBirthRateScaler.t:primate" parameter="@birthRate.t:primate" scaleFactor="0.75" weight="3.0" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator id="treeScaler.t:primate" scaleFactor="0.5" tree="@Tree.t:primate" weight="3.0" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
-
-        <operator id="treeRootScaler.t:primate" rootOnly="true" scaleFactor="0.5" tree="@Tree.t:primate" weight="3.0" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
-
-        <operator id="UniformOperator.t:primate" tree="@Tree.t:primate" weight="30.0" spec="beast.base.evolution.operator.Uniform"/>
-
-        <operator id="SubtreeSlide.t:primate" spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" tree="@Tree.t:primate" weight="15.0"/>
-
-        <operator id="narrow.t:primate" spec="Exchange" tree="@Tree.t:primate" weight="15.0"/>
-
-        <operator id="wide.t:primate" isNarrow="false" spec="Exchange" tree="@Tree.t:primate" weight="3.0"/>
-
-        <operator id="WilsonBalding.t:primate" spec="WilsonBalding" tree="@Tree.t:primate" weight="3.0"/>
-
-        <operator id="RateACScaler.s:primate" parameter="@rateAC.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator id="RateAGScaler.s:primate" parameter="@rateAG.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator id="RateATScaler.s:primate" parameter="@rateAT.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator id="RateCGScaler.s:primate" parameter="@rateCG.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator id="RateGTScaler.s:primate" parameter="@rateGT.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator delta="0.01" id="FrequenciesExchanger.s:primate" spec="beast.base.spec.inference.operator.DeltaExchangeOperator" weight="0.1">
-            <parameter idref="freqParameter.s:primate"/>
-        </operator>
-
-        <logger fileName="primate-mtDNA.log" id="tracelog" logEvery="5000" model="@posterior" sanitiseHeaders="true" sort="smart">
-            <log idref="posterior"/>
-            <log idref="likelihood"/>
-            <log idref="prior"/>
-            <log idref="treeLikelihood.noncoding"/>
-            <log idref="treeLikelihood.coding"/>
-            <log id="TreeHeight.t:primate" spec="beast.base.evolution.tree.TreeStatLogger" tree="@Tree.t:primate"/>
-            <log idref="YuleModel.t:primate"/>
-            <parameter idref="birthRate.t:primate" name="log"/>
-            <parameter idref="rateAC.s:primate" name="log"/>
-            <parameter idref="rateAG.s:primate" name="log"/>
-            <parameter idref="rateAT.s:primate" name="log"/>
-            <parameter idref="rateCG.s:primate" name="log"/>
-            <parameter idref="rateGT.s:primate" name="log"/>
-            <parameter idref="freqParameter.s:primate" name="log"/>
-        </logger>
-
-        <logger id="screenlog" logEvery="5000">
-            <log idref="posterior"/>
-            <log arg="@posterior" id="ESS.0" spec="beast.base.spec.inference.util.ESS"/>
-            <log idref="likelihood"/>
-            <log idref="prior"/>
-        </logger>
-
-        <logger fileName="$(tree).trees" id="treelog.t:primate" logEvery="5000" mode="tree">
-            <log id="TreeWithMetaDataLogger.t:primate" spec="beast.base.spec.evolution.TreeWithMetaDataLogger" tree="@Tree.t:primate"/>
-        </logger>
-
-    </run>
-
-</beast>
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/testRNA.xml b/beast-base/src/test/resources/beast.base/examples/spec/testRNA.xml
deleted file mode 100644
index 9d7f7013..00000000
--- a/beast-base/src/test/resources/beast.base/examples/spec/testRNA.xml
+++ /dev/null
@@ -1,154 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<beast version="2.8"
-       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt"
-       beautitemplate="Standard"
-       beautistatus="">
-
-<!-- A fake RNA alignment.  Should give exactly the same result as testGTR.xml. -->
-
-    <data id="primate-mtDNA">
-        <sequence id="seq_Lemur_catta" taxon="Lemur_catta" totalcount="4" value="AAGCUUCAUAGGAGCAACCAUUCUAAUAAUCGCACAUGGCCUUACAUCAUCCAUAUUAUUCUGUCUAGCCAACUCUAACUACGAACGAAUCCAUAGCCGUACAAUACUACUAGCACGAGGGAUCCAAACCAUUCUCCCUCUUAUAGCCACCUGAUGACUACUCGCCAGCCUAACUAACCUAGCCCUACCCACCUCUAUCAAUUUAAUUGGCGAACUAUUCGUCACUAUAGCAUCCUUCUCAUGAUCAAACAUUACAAUUAUCUUAAUAGGCUUAAAUAUGCUCAUCACCGCUCUCUAUUCCCUCUAUAUAUUAACUACUACACAACGAGGAAAACUCACAUAUCAUUCGCACAACCUAAACCCAUCCUUUACACGAGAAAACACCCUUAUAUCCAUACACAUACUCCCCCUUCUCCUAUUUACCUUAAACCCCAAAAUUAUUCUAGGACCCACGUACUGUAAAUAUAGUUUAAA-AAAACACUAGAUUGUGAAUCCAGAAAUAGAAGCUCAAAC-CUUCUUAUUUACCGAGAAAGUAAUGUAUGAACUGCUAACUCUGCACUCCGUAUAUAAAAAUACGGCUAUCUCAACUUUUAAAGGAUAGAAGUAAUCCAUUGGCCUUAGGAGCCAAAAA-AUUGGUGCAACUCCAAAUAAAAGUAAUAAAUCUAUUAUCCUCUUUCACCCUUGUCACACUGAUUAUCCUAACUUUACCUAUCAUUAUAAACGUUACAAACAUAUACAAAAACUACCCCUAUGCACCAUACGUAAAAUCUUCUAUUGCAUGUGCCUUCAUCACUAGCCUCAUCCCAACUAUAUUAUUUAUCUCCUCAGGACAAGAAACAAUCAUUUCCAACUGACAUUGAAUAACAAUCCAAACCCUAAAACUAUCUAUUAGCUU"/>
-        <sequence id="seq_Homo_sapiens" taxon="Homo_sapiens" totalcount="4" value="AAGCUUCACCGGCGCAGUCAUUCUCAUAAUCGCCCACGGGCUUACAUCCUCAUUACUAUUCUGCCUAGCAAACUCAAACUACGAACGCACUCACAGUCGCAUCAUAAUCCUCUCUCAAGGACUUCAAACUCUACUCCCACUAAUAGCUUUUUGAUGACUUCUAGCAAGCCUCGCUAACCUCGCCUUACCCCCCACUAUUAACCUACUGGGAGAACUCUCUGUGCUAGUAACCACGUUCUCCUGAUCAAAUAUCACUCUCCUACUUACAGGACUCAACAUACUAGUCACAGCCCUAUACUCCCUCUACAUAUUUACCACAACACAAUGGGGCUCACUCACCCACCACAUUAACAACAUAAAACCCUCAUUCACACGAGAAAACACCCUCAUGUUCAUACACCUAUCCCCCAUUCUCCUCCUAUCCCUCAACCCCGACAUCAUUACCGGGUUUUCCUCUUGUAAAUAUAGUUUAACCAAAACAUCAGAUUGUGAAUCUGACAACAGAGGCUUA-CGACCCCUUAUUUACCGAGAAAGCU-CACAAGAACUGCUAACUCAUGCCCCCAUGUCUAACAACAUGGCUUUCUCAACUUUUAAAGGAUAACAGCUAUCCAUUGGUCUUAGGCCCCAAAAAUUUUGGUGCAACUCCAAAUAAAAGUAAUAACCAUGCACACUACUAUAACCACCCUAACCCUGACUUCCCUAAUUCCCCCCAUCCUUACCACCCUCGUUAACCCUAACAAAAAAAACUCAUACCCCCAUUAUGUAAAAUCCAUUGUCGCAUCCACCUUUAUUAUCAGUCUCUUCCCCACAACAAUAUUCAUGUGCCUAGACCAAGAAGUUAUUAUCUCGAACUGACACUGAGCCACAACCCAAACAACCCAGCUCUCCCUAAGCUU"/>
-        <sequence id="seq_Pan" taxon="Pan" totalcount="4" value="AAGCUUCACCGGCGCAAUUAUCCUCAUAAUCGCCCACGGACUUACAUCCUCAUUAUUAUUCUGCCUAGCAAACUCAAAUUAUGAACGCACCCACAGUCGCAUCAUAAUUCUCUCCCAAGGACUUCAAACUCUACUCCCACUAAUAGCCUUUUGAUGACUCCUAGCAAGCCUCGCUAACCUCGCCCUACCCCCUACCAUUAAUCUCCUAGGGGAACUCUCCGUGCUAGUAACCUCAUUCUCCUGAUCAAAUACCACUCUCCUACUCACAGGAUUCAACAUACUAAUCACAGCCCUGUACUCCCUCUACAUGUUUACCACAACACAAUGAGGCUCACUCACCCACCACAUUAAUAACAUAAAGCCCUCAUUCACACGAGAAAAUACUCUCAUAUUUUUACACCUAUCCCCCAUCCUCCUUCUAUCCCUCAAUCCUGAUAUCAUCACUGGAUUCACCUCCUGUAAAUAUAGUUUAACCAAAACAUCAGAUUGUGAAUCUGACAACAGAGGCUCA-CGACCCCUUAUUUACCGAGAAAGCU-UAUAAGAACUGCUAAUUCAUAUCCCCAUGCCUGACAACAUGGCUUUCUCAACUUUUAAAGGAUAACAGCCAUCCGUUGGUCUUAGGCCCCAAAAAUUUUGGUGCAACUCCAAAUAAAAGUAAUAACCAUGUAUACUACCAUAACCACCUUAACCCUAACUCCCUUAAUUCUCCCCAUCCUCACCACCCUCAUUAACCCUAACAAAAAAAACUCAUAUCCCCAUUAUGUGAAAUCCAUUAUCGCGUCCACCUUUAUCAUUAGCCUUUUCCCCACAACAAUAUUCAUAUGCCUAGACCAAGAAGCUAUUAUCUCAAACUGGCACUGAGCAACAACCCAAACAACCCAGCUCUCCCUAAGCUU"/>
-        <sequence id="seq_Gorilla" taxon="Gorilla" totalcount="4" value="AAGCUUCACCGGCGCAGUUGUUCUUAUAAUUGCCCACGGACUUACAUCAUCAUUAUUAUUCUGCCUAGCAAACUCAAACUACGAACGAACCCACAGCCGCAUCAUAAUUCUCUCUCAAGGACUCCAAACCCUACUCCCACUAAUAGCCCUUUGAUGACUUCUGGCAAGCCUCGCCAACCUCGCCUUACCCCCCACCAUUAACCUACUAGGAGAGCUCUCCGUACUAGUAACCACAUUCUCCUGAUCAAACACCACCCUUUUACUUACAGGAUCUAACAUACUAAUUACAGCCCUGUACUCCCUUUAUAUAUUUACCACAACACAAUGAGGCCCACUCACACACCACAUCACCAACAUAAAACCCUCAUUUACACGAGAAAACAUCCUCAUAUUCAUGCACCUAUCCCCCAUCCUCCUCCUAUCCCUCAACCCCGAUAUUAUCACCGGGUUCACCUCCUGUAAAUAUAGUUUAACCAAAACAUCAGAUUGUGAAUCUGAUAACAGAGGCUCA-CAACCCCUUAUUUACCGAGAAAGCU-CGUAAGAGCUGCUAACUCAUACCCCCGUGCUUGACAACAUGGCUUUCUCAACUUUUAAAGGAUAACAGCUAUCCAUUGGUCUUAGGACCCAAAAAUUUUGGUGCAACUCCAAAUAAAAGUAAUAACUAUGUACGCUACCAUAACCACCUUAGCCCUAACUUCCUUAAUUCCCCCUAUCCUUACCACCUUCAUCAAUCCUAACAAAAAAAGCUCAUACCCCCAUUACGUAAAAUCUAUCGUCGCAUCCACCUUUAUCAUCAGCCUCUUCCCCACAACAAUAUUUCUAUGCCUAGACCAAGAAGCUAUUAUCUCAAGCUGACACUGAGCAACAACCCAAACAAUUCAACUCUCCCUAAGCUU"/>
-        <sequence id="seq_Pongo" taxon="Pongo" totalcount="4" value="AAGCUUCACCGGCGCAACCACCCUCAUGAUUGCCCAUGGACUCACAUCCUCCCUACUGUUCUGCCUAGCAAACUCAAACUACGAACGAACCCACAGCCGCAUCAUAAUCCUCUCUCAAGGCCUUCAAACUCUACUCCCCCUAAUAGCCCUCUGAUGACUUCUAGCAAGCCUCACUAACCUUGCCCUACCACCCACCAUCAACCUUCUAGGAGAACUCUCCGUACUAAUAGCCAUAUUCUCUUGAUCUAACAUCACCAUCCUACUAACAGGACUCAACAUACUAAUCACAACCCUAUACUCUCUCUAUAUAUUCACCACAACACAACGAGGUACACCCACACACCACAUCAACAACAUAAAACCUUCUUUCACACGCGAAAAUACCCUCAUGCUCAUACACCUAUCCCCCAUCCUCCUCUUAUCCCUCAACCCCAGCAUCAUCGCUGGGUUCGCCUACUGUAAAUAUAGUUUAACCAAAACAUUAGAUUGUGAAUCUAAUAAUAGGGCCCCA-CAACCCCUUAUUUACCGAGAAAGCU-CACAAGAACUGCUAACUCUCACU-CCAUGUGUGACAACAUGGCUUUCUCAGCUUUUAAAGGAUAACAGCUAUCCCUUGGUCUUAGGAUCCAAAAAUUUUGGUGCAACUCCAAAUAAAAGUAACAGCCAUGUUUACCACCAUAACUGCCCUCACCUUAACUUCCCUAAUCCCCCCCAUUACCGCUACCCUCAUUAACCCCAACAAAAAAAACCCAUACCCCCACUAUGUAAAAACGGCCAUCGCAUCCGCCUUUACUAUCAGCCUUAUCCCAACAACAAUAUUUAUCUGCCUAGGACAAGAAACCAUCGUCACAAACUGAUGCUGAACAACCACCCAGACACUACAACUCUCACUAAGCUU"/>
-        <sequence id="seq_Hylobates" taxon="Hylobates" totalcount="4" value="AAGCUUUACAGGUGCAACCGUCCUCAUAAUCGCCCACGGACUAACCUCUUCCCUGCUAUUCUGCCUUGCAAACUCAAACUACGAACGAACUCACAGCCGCAUCAUAAUCCUAUCUCGAGGGCUCCAAGCCUUACUCCCACUGAUAGCCUUCUGAUGACUCGCAGCAAGCCUCGCUAACCUCGCCCUACCCCCCACUAUUAACCUCCUAGGUGAACUCUUCGUACUAAUGGCCUCCUUCUCCUGGGCAAACACUACUAUUACACUCACCGGGCUCAACGUACUAAUCACGGCCCUAUACUCCCUUUACAUAUUUAUCAUAACACAACGAGGCACACUUACACACCACAUUAAAAACAUAAAACCCUCACUCACACGAGAAAACAUAUUAAUACUUAUGCACCUCUUCCCCCUCCUCCUCCUAACCCUCAACCCUAACAUCAUUACUGGCUUUACUCCCUGUAAACAUAGUUUAAUCAAAACAUUAGAUUGUGAAUCUAACAAUAGAGGCUCG-AAACCUCUUGCUUACCGAGAAAGCC-CACAAGAACUGCUAACUCACUAUCCCAUGUAUGACAACAUGGCUUUCUCAACUUUUAAAGGAUAACAGCUAUCCAUUGGUCUUAGGACCCAAAAAUUUUGGUGCAACUCCAAAUAAAAGUAAUAGCAAUGUACACCACCAUAGCCAUUCUAACGCUAACCUCCCUAAUUCCCCCCAUUACAGCCACCCUUAUUAACCCCAAUAAAAAGAACUUAUACCCGCACUACGUAAAAAUGACCAUUGCCUCUACCUUUAUAAUCAGCCUAUUUCCCACAAUAAUAUUCAUGUGCACAGACCAAGAAACCAUUAUUUCAAACUGACACUGAACUGCAACCCAAACGCUAGAACUCUCCCUAAGCUU"/>
-        <sequence id="seq_Macaca_fuscata" taxon="Macaca_fuscata" totalcount="4" value="AAGCUUUUCCGGCGCAACCAUCCUUAUGAUCGCUCACGGACUCACCUCUUCCAUAUAUUUCUGCCUAGCCAAUUCAAACUAUGAACGCACUCACAACCGUACCAUACUACUGUCCCGAGGACUUCAAAUCCUACUUCCACUAACAGCCUUUUGAUGAUUAACAGCAAGCCUUACUAACCUUGCCCUACCCCCCACUAUCAAUCUACUAGGUGAACUCUUUGUAAUCGCAACCUCAUUCUCCUGAUCCCAUAUCACCAUUAUGCUAACAGGACUUAACAUAUUAAUUACGGCCCUCUACUCUCUCCACAUAUUCACUACAACACAACGAGGAACACUCACACAUCACAUAAUCAACAUAAAGCCCCCCUUCACACGAGAAAACACAUUAAUAUUCAUACACCUCGCUCCAAUUAUCCUUCUAUCCCUCAACCCCAACAUCAUCCUGGGGUUUACCUCCUGUAGAUAUAGUUUAACUAAAACACUAGAUUGUGAAUCUAACCAUAGAGACUCA-CCACCUCUUAUUUACCGAGAAAACU-CGCAAGGACUGCUAACCCAUGUACCCGUACCUAAAAUUACGGUUUUCUCAACUUUUAAAGGAUAACAGCUAUCCAUUGACCUUAGGAGUCAAAAACAUUGGUGCAACUCCAAAUAAAAGUAAUAAUCAUGCACACCCCCAUCAUUAUAACAACCCUUAUCUCCCUAACUCUCCCAAUUUUUGCCACCCUCAUCAACCCUUACAAAAAACGUCCAUACCCAGAUUACGUAAAAACAACCGUAAUAUAUGCUUUCAUCAUCAGCCUCCCCUCAACAACUUUAUUCAUCUUCUCAAACCAAGAAACAACCAUUUGGAGCUGACAUUGAAUAAUGACCCAAACACUAGACCUAACGCUAAGCUU"/>
-        <sequence id="seq_M._mulatta" taxon="M._mulatta" totalcount="4" value="AAGCUUUUCUGGCGCAACCAUCCUCAUGAUUGCUCACGGACUCACCUCUUCCAUAUAUUUCUGCCUAGCCAAUUCAAACUAUGAACGCACUCACAACCGUACCAUACUACUGUCCCGGGGACUUCAAAUCCUACUUCCACUAACAGCUUUCUGAUGAUUAACAGCAAGCCUUACUAACCUUGCCCUACCCCCCACUAUCAACCUACUAGGUGAACUCUUUGUAAUCGCGACCUCAUUCUCCUGGUCCCAUAUCACCAUUAUAUUAACAGGAUUUAACAUACUAAUUACGGCCCUCUACUCCCUCCACAUAUUCACCACAACACAACGAGGAGCACUCACACAUCACAUAAUCAACAUAAAACCCCCCUUCACACGAGAAAACAUAUUAAUAUUCAUACACCUCGCUCCAAUCAUCCUCCUAUCUCUCAACCCCAACAUCAUCCUGGGGUUUACUUCCUGUAGAUAUAGUUUAACUAAAACAUUAGAUUGUGAAUCUAACCAUAGAGACUUA-CCACCUCUUAUUUACCGAGAAAACU-CGCGAGGACUGCUAACCCAUGUAUCCGUACCUAAAAUUACGGUUUUCUCAACUUUUAAAGGAUAACAGCUAUCCAUUGACCUUAGGAGUCAAAAAUAUUGGUGCAACUCCAAAUAAAAGUAAUAAUCAUGCACACCCCUAUCAUAAUAACAACCCUUAUCUCCCUAACUCUCCCAAUUUUUGCCACCCUCAUCAACCCUUACAAAAAACGUCCAUACCCAGAUUACGUAAAAACAACCGUAAUAUAUGCUUUCAUCAUCAGCCUCCCCUCAACAACUUUAUUCAUCUUCUCAAACCAAGAAACAACCAUUUGAAGCUGACAUUGAAUAAUAACCCAAACACUAGACCUAACACUAAGCUU"/>
-        <sequence id="seq_M._fascicularis" taxon="M._fascicularis" totalcount="4" value="AAGCUUCUCCGGCGCAACCACCCUUAUAAUCGCCCACGGGCUCACCUCUUCCAUGUAUUUCUGCUUGGCCAAUUCAAACUAUGAGCGCACUCAUAACCGUACCAUACUACUAUCCCGAGGACUUCAAAUUCUACUUCCAUUGACAGCCUUCUGAUGACUCACAGCAAGCCUUACUAACCUUGCCCUACCCCCCACUAUUAAUCUACUAGGCGAACUCUUUGUAAUCACAACUUCAUUUUCCUGAUCCCAUAUCACCAUUGUGUUAACGGGCCUUAAUAUACUAAUCACAGCCCUCUACUCUCUCCACAUGUUCAUUACAGUACAACGAGGAACACUCACACACCACAUAAUCAAUAUAAAACCCCCCUUCACACGAGAAAACAUAUUAAUAUUCAUACACCUCGCUCCAAUUAUCCUUCUAUCUCUCAACCCCAACAUCAUCCUGGGGUUUACCUCCUGUAAAUAUAGUUUAACUAAAACAUUAGAUUGUGAAUCUAACUAUAGAGGCCUA-CCACUUCUUAUUUACCGAGAAAACU-CGCAAGGACUGCUAAUCCAUGCCUCCGUACUUAAAACUACGGUUUCCUCAACUUUUAAAGGAUAACAGCUAUCCAUUGACCUUAGGAGUCAAAAACAUUGGUGCAACUCCAAAUAAAAGUAAUAAUCAUGCACACCCCCAUCAUAAUAACAACCCUCAUCUCCCUGACCCUUCCAAUUUUUGCCACCCUCACCAACCCCUAUAAAAAACGUUCAUACCCAGACUACGUAAAAACAACCGUAAUAUAUGCUUUUAUUACCAGUCUCCCCUCAACAACCCUAUUCAUCCUCUCAAACCAAGAAACAACCAUUUGGAGUUGACAUUGAAUAACAACCCAAACAUUAGACCUAACACUAAGCUU"/>
-        <sequence id="seq_M._sylvanus" taxon="M._sylvanus" totalcount="4" value="AAGCUUCUCCGGUGCAACUAUCCUUAUAGUUGCCCAUGGACUCACCUCUUCCAUAUACUUCUGCUUGGCCAACUCAAACUACGAACGCACCCACAGCCGCAUCAUACUACUAUCCCGAGGACUCCAAAUCCUACUCCCACUAACAGCCUUCUGAUGAUUCACAGCAAGCCUUACUAAUCUUGCUCUACCCUCCACUAUUAAUCUACUGGGCGAACUCUUCGUAAUCGCAACCUCAUUUUCCUGAUCCCACAUCACCAUCAUACUAACAGGACUGAACAUACUAAUUACAGCCCUCUACUCUCUUCACAUAUUCACCACAACACAACGAGGAGCGCUCACACACCACAUAAUUAACAUAAAACCACCUUUCACACGAGAAAACAUAUUAAUACUCAUACACCUCGCUCCAAUUAUUCUUCUAUCUCUUAACCCCAACAUCAUUCUAGGAUUUACUUCCUGUAAAUAUAGUUUAAUUAAAACAUUAGACUGUGAAUCUAACUAUAGAAGCUUA-CCACUUCUUAUUUACCGAGAAAACU-UGCAAGGACCGCUAAUCCACACCUCCGUACUUAAAACUACGGUUUUCUCAACUUUUAAAGGAUAACAGCUAUCCAUUGGCCUUAGGAGUCAAAAAUAUUGGUGCAACUCCAAAUAAAAGUAAUAAUCAUGUAUACCCCCAUCAUAAUAACAACUCUCAUCUCCCUAACUCUUCCAAUUUUCGCUACCCUUAUCAACCCCAACAAAAAACACCUAUAUCCAAACUACGUAAAAACAGCCGUAAUAUAUGCUUUCAUUACCAGCCUCUCUUCAACAACUUUAUAUAUAUUCUUAAACCAAGAAACAAUCAUCUGAAGCUGGCACUGAAUAAUAACCCAAACACUAAGCCUAACAUUAAGCUU"/>
-        <sequence id="seq_Saimiri_sciureus" taxon="Saimiri_sciureus" totalcount="4" value="AAGCUUCACCGGCGCAAUGAUCCUAAUAAUCGCUCACGGGUUUACUUCGUCUAUGCUAUUCUGCCUAGCAAACUCAAAUUACGAACGAAUUCACAGCCGAACAAUAACAUUUACUCGAGGGCUCCAAACACUAUUCCCGCUUAUAGGCCUCUGAUGACUCCUAGCAAAUCUCGCUAACCUCGCCCUACCCACAGCUAUUAAUCUAGUAGGAGAAUUACUCACAAUCGUAUCUUCCUUCUCUUGAUCCAACUUUACUAUUAUAUUCACAGGACUUAAUAUACUAAUUACAGCACUCUACUCACUUCAUAUGUAUGCCUCUACACAGCGAGGUCCACUUACAUACAGCACCAGCAAUAUAAAACCAAUAUUUACACGAGAAAAUACGCUAAUAUUUAUACAUAUAACACCAAUCCUCCUCCUUACCUUGAGCCCCAAGGUAAUUAUAGGACCCUCACCUUGUAAUUAUAGUUUAGCUAAAACAUUAGAUUGUGAAUCUAAUAAUAGAAGAAUA-UAACUUCUUAAUUACCGAGAAAGUG-CGCAAGAACUGCUAAUUCAUGCUCCCAAGACUAACAACUUGGCUUCCUCAACUUUUAAAGGAUAGUAGUUAUCCAUUGGUCUUAGGAGCCAAAAACAUUGGUGCAACUCCAAAUAAAAGUAAUA---AUACACUUCUCCAUCACUCUAAUAACACUAAUUAGCCUACUAGCGCCAAUCCUAGCUACCCUCAUUAACCCUAACAAAAGCACACUAUACCCGUACUACGUAAAACUAGCCAUCAUCUACGCCCUCAUUACCAGUACCUUAUCUAUAAUAUUCUUUAUCCUUACAGGCCAAGAAUCAAUAAUUUCAAACUGACACUGAAUAACUAUCCAAACCAUCAAACUAUCCCUAAGCUU"/>
-        <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4" value="AAGUUUCAUUGGAGCCACCACUCUUAUAAUUGCCCAUGGCCUCACCUCCUCCCUAUUAUUUUGCCUAGCAAAUACAAACUACGAACGAGUCCACAGUCGAACAAUAGCACUAGCCCGUGGCCUUCAAACCCUAUUACCUCUUGCAGCAACAUGAUGACUCCUCGCCAGCUUAACCAACCUGGCCCUUCCCCCAACAAUUAAUUUAAUCGGUGAACUGUCCGUAAUAAUAGCAGCAUUUUCAUGGUCACACCUAACUAUUAUCUUAGUAGGCCUUAACACCCUUAUCACCGCCCUAUAUUCCCUAUAUAUACUAAUCAUAACUCAACGAGGAAAAUACACAUAUCAUAUCAACAAUAUCAUGCCCCCUUUCACCCGAGAAAAUACAUUAAUAAUCAUACACCUAUUUCCCUUAAUCCUACUAUCUACCAACCCCAAAGUAAUUAUAGGAACCAUGUACUGUAAAUAUAGUUUAAACAAAACAUUAGAUUGUGAGUCUAAUAAUAGAAGCCCAAAGAUUUCUUAUUUACCAAGAAAGUA-UGCAAGAACUGCUAACUCAUGCCUCCAUAUAUAACAAUGUGGCUUUCUU-ACUUUUAAAGGAUAGAAGUAAUCCAUCGGUCUUAGGAACCGAAAA-AUUGGUGCAACUCCAAAUAAAAGUAAUAAAUUUAUUUUCAUCCUCCAUUUUACUAUCACUUACACUCUUAAUUACCCCAUUUAUUAUUACAACAACUAAAAAAUAUGAAACACAUGCAUACCCUUACUACGUAAAAAACUCUAUCGCCUGCGCAUUUAUAACAAGCCUAGUCCCAAUGCUCAUAUUUCUAUACACAAAUCAAGAAAUAAUCAUUUCCAACUGACAUUGAAUAACGAUUCAUACUAUCAAAUUAUGCCUAAGCUU"/>
-    </data>
-
-    <run chainLength="5000000" id="mcmc" spec="MCMC">
-        <state id="state" storeEvery="5000">
-            <tree id="Tree.t:primate" name="stateNode">
-                <taxonset id="TaxonSet.coding" spec="TaxonSet">
-                    <alignment filter="2-457,660-896" id="coding" spec="beast.base.spec.evolution.alignment.FilteredAlignment">
-                        <data idref="primate-mtDNA"/>
-                    </alignment>
-                </taxonset>
-            </tree>
-            <parameter id="birthRate.t:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-            <parameter id="rateAC.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-            <parameter id="rateAG.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-            <parameter id="rateAT.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-            <parameter id="rateCG.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-            <parameter id="rateGT.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-            <parameter dimension="4" id="freqParameter.s:primate" name="stateNode" value="0.25" spec="beast.base.spec.inference.parameter.SimplexParam"/>
-        </state>
-
-        <init estimate="false" id="RandomTree.t:primate" initial="@Tree.t:primate" spec="beast.base.spec.evolution.tree.coalescent.RandomTree" taxa="@coding">
-            <populationModel id="ConstantPopulation0.t:primate" spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
-                <parameter id="randomPopSize.t:primate" name="popSize" value="1" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-            </populationModel>
-        </init>
-
-        <distribution id="posterior" spec="CompoundDistribution">
-            <distribution id="prior" spec="CompoundDistribution">
-                <distribution birthDiffRate="@birthRate.t:primate" id="YuleModel.t:primate" spec="beast.base.spec.evolution.speciation.YuleModel" tree="@Tree.t:primate"/>
-                <distribution id="Uniform.0" spec="beast.base.spec.inference.distribution.Uniform" param="@birthRate.t:primate" upper="1.0E6"/>
-                <distribution id="LogNormalDistributionModel.0" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateAC.s:primate">
-                        <parameter estimate="false" id="RealParameter.0" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="RealParameter.01" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </distribution>
-                <distribution id="LogNormalDistributionModel.01" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateAG.s:primate">
-                        <parameter estimate="false" id="RealParameter.02" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="RealParameter.03" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </distribution>
-                <distribution id="LogNormalDistributionModel.02" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateAT.s:primate">
-                        <parameter estimate="false" id="RealParameter.04" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="RealParameter.05" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </distribution>
-                <distribution id="LogNormalDistributionModel.03" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateCG.s:primate">
-                        <parameter estimate="false" id="RealParameter.06" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="RealParameter.07" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </distribution>
-                <distribution id="LogNormalDistributionModel.04" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateGT.s:primate">
-                        <parameter estimate="false" id="RealParameter.08" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="RealParameter.09" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </distribution>
-            </distribution>
-            <distribution id="likelihood" spec="CompoundDistribution">
-                <distribution data="@coding" id="treeLikelihood.coding" spec="beast.base.spec.evolution.likelihood.TreeLikelihood" tree="@Tree.t:primate">
-                    <siteModel id="SiteModel.s:primate" spec="beast.base.spec.evolution.sitemodel.SiteModel">
-                        <parameter estimate="false" id="mutationRate.s:primate" name="mutationRate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="gammaShape.s:primate" name="shape" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="proportionInvariant.s:primate" name="proportionInvariant" value="0.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="UnitInterval"/>
-                        <substModel id="gtr.s:primate" rateAC="@rateAC.s:primate" rateAG="@rateAG.s:primate" rateAT="@rateAT.s:primate" rateCG="@rateCG.s:primate" rateGT="@rateGT.s:primate" spec="beast.base.spec.evolution.substitutionmodel.GTR">
-                            <parameter estimate="false" id="rateCT.s:primate" name="rateCT" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-                            <frequencies frequencies="@freqParameter.s:primate" id="estimatedFreqs.s:primate" spec="beast.base.spec.evolution.substitutionmodel.Frequencies"/>
-                        </substModel>
-                    </siteModel>
-                    <branchRateModel id="StrictClock.c:primate" spec="beast.base.spec.evolution.branchratemodel.StrictClockModel">
-                        <parameter estimate="false" id="clockRate.c:primate" name="clock.rate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </branchRateModel>
-                </distribution>
-                <distribution branchRateModel="@StrictClock.c:primate" id="treeLikelihood.noncoding" siteModel="@SiteModel.s:primate" spec="beast.base.spec.evolution.likelihood.TreeLikelihood" tree="@Tree.t:primate">
-                    <data data="@primate-mtDNA" filter="1,458-659,897-898" id="noncoding" spec="beast.base.spec.evolution.alignment.FilteredAlignment"/>
-                </distribution>
-            </distribution>
-        </distribution>
-
-        <operator id="YuleBirthRateScaler.t:primate" parameter="@birthRate.t:primate" scaleFactor="0.75" weight="3.0" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator id="treeScaler.t:primate" scaleFactor="0.5" tree="@Tree.t:primate" weight="3.0" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
-
-        <operator id="treeRootScaler.t:primate" rootOnly="true" scaleFactor="0.5" tree="@Tree.t:primate" weight="3.0" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
-
-        <operator id="UniformOperator.t:primate" tree="@Tree.t:primate" weight="30.0" spec="beast.base.evolution.operator.Uniform"/>
-
-        <operator id="SubtreeSlide.t:primate" spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" tree="@Tree.t:primate" weight="15.0"/>
-
-        <operator id="narrow.t:primate" spec="Exchange" tree="@Tree.t:primate" weight="15.0"/>
-
-        <operator id="wide.t:primate" isNarrow="false" spec="Exchange" tree="@Tree.t:primate" weight="3.0"/>
-
-        <operator id="WilsonBalding.t:primate" spec="WilsonBalding" tree="@Tree.t:primate" weight="3.0"/>
-
-        <operator id="RateACScaler.s:primate" parameter="@rateAC.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator id="RateAGScaler.s:primate" parameter="@rateAG.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator id="RateATScaler.s:primate" parameter="@rateAT.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator id="RateCGScaler.s:primate" parameter="@rateCG.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator id="RateGTScaler.s:primate" parameter="@rateGT.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator delta="0.01" id="FrequenciesExchanger.s:primate" spec="beast.base.spec.inference.operator.DeltaExchangeOperator" weight="0.1">
-            <parameter idref="freqParameter.s:primate"/>
-        </operator>
-
-        <logger fileName="testRNA.log" id="tracelog" logEvery="5000" model="@posterior" sanitiseHeaders="true" sort="smart">
-            <log idref="posterior"/>
-            <log idref="likelihood"/>
-            <log idref="prior"/>
-            <log idref="treeLikelihood.noncoding"/>
-            <log idref="treeLikelihood.coding"/>
-            <log id="TreeHeight.t:primate" spec="beast.base.evolution.tree.TreeStatLogger" tree="@Tree.t:primate"/>
-            <log idref="YuleModel.t:primate"/>
-            <parameter idref="birthRate.t:primate" name="log"/>
-            <parameter idref="rateAC.s:primate" name="log"/>
-            <parameter idref="rateAG.s:primate" name="log"/>
-            <parameter idref="rateAT.s:primate" name="log"/>
-            <parameter idref="rateCG.s:primate" name="log"/>
-            <parameter idref="rateGT.s:primate" name="log"/>
-            <parameter idref="freqParameter.s:primate" name="log"/>
-        </logger>
-
-        <logger id="screenlog" logEvery="5000">
-            <log idref="posterior"/>
-            <log arg="@posterior" id="ESS.0" spec="beast.base.spec.inference.util.ESS"/>
-            <log idref="likelihood"/>
-            <log idref="prior"/>
-        </logger>
-
-        <logger fileName="testRNA.trees" id="treelog.t:primate" logEvery="5000" mode="tree">
-            <log id="TreeWithMetaDataLogger.t:primate" spec="beast.base.spec.evolution.TreeWithMetaDataLogger" tree="@Tree.t:primate"/>
-        </logger>
-
-    </run>
-
-</beast>
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/testRestrictedGTR.xml b/beast-base/src/test/resources/beast.base/examples/spec/testRestrictedGTR.xml
deleted file mode 100644
index f14f49d4..00000000
--- a/beast-base/src/test/resources/beast.base/examples/spec/testRestrictedGTR.xml
+++ /dev/null
@@ -1,126 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<beast version="2.8"
-       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt"
-       beautitemplate="Standard"
-       beautistatus="">
-
-    <data id="primate-mtDNA">
-        <sequence id="seq_Lemur_catta" taxon="Lemur_catta" totalcount="4" value="AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATTCTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGGGATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCTAGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTCATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTCCCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAACCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATTTACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAACACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATGTATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGATAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTATAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTGCATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAACAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT"/>
-        <sequence id="seq_Homo_sapiens" taxon="Homo_sapiens" totalcount="4" value="AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
-        <sequence id="seq_Pan" taxon="Pan" totalcount="4" value="AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATTCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCTCGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAAGCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TATAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCACCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCGCGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAGCTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
-        <sequence id="seq_Gorilla" taxon="Gorilla" totalcount="4" value="AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGGACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCTCGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTCCTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTCCCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAAACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCTATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CGTAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTACCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCGCATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAGCTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT"/>
-        <sequence id="seq_Pongo" taxon="Pongo" totalcount="4" value="AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGGCCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCTTGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTCTTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTCTCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAAACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTTATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAACATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGATAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAACAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCGCTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCGCATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAACCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT"/>
-        <sequence id="seq_Hylobates" taxon="Hylobates" totalcount="4" value="AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATTCTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGGGCTCCAAGCCTTACTCCCACTGATAGCCTTCTGATGACTCGCAGCAAGCCTCGCTAACCTCGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTCCTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTCCCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAAACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCTAACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAACATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CACAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAGCCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTGCCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAACCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT"/>
-        <sequence id="seq_Macaca_fuscata" taxon="Macaca_fuscata" totalcount="4" value="AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGGACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTCCTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTCTCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAAGCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAACACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT"/>
-        <sequence id="seq_M._mulatta" taxon="M._mulatta" totalcount="4" value="AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGGACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTCCTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTCCCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCTATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAACATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CGCGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT"/>
-        <sequence id="seq_M._fascicularis" taxon="M._fascicularis" totalcount="4" value="AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTTCTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGTACCATACTACTATCCCGAGGACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTCCTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTCTCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAACATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTGCCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAATATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAACAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT"/>
-        <sequence id="seq_M._sylvanus" taxon="M._sylvanus" totalcount="4" value="AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTTCTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGCATCATACTACTATCCCGAGGACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCTTGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTCCTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTCTCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAAACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCTATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAACATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TGCAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCGCTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAATATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAACAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT"/>
-        <sequence id="seq_Saimiri_sciureus" taxon="Saimiri_sciureus" totalcount="4" value="AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTCTATGCTATTCTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAATAACATTTACTCGAGGGCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCTCGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTCTTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTCACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAAACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCTTACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAACATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CGCAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGATAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAATA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAGCTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCATCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAATCAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT"/>
-        <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4" value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
-    </data>
-
-    <run chainLength="5000000" id="mcmc" spec="MCMC">
-        <state id="state" storeEvery="5000">
-            <tree id="Tree.t:primate" name="stateNode">
-                <taxonset id="TaxonSet.coding" spec="TaxonSet">
-                    <alignment filter="2-457,660-896" id="coding" spec="beast.base.spec.evolution.alignment.FilteredAlignment">
-                        <data idref="primate-mtDNA"/>
-                    </alignment>
-                </taxonset>
-            </tree>
-            <parameter id="birthRate.t:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-            <parameter id="rateTransversion.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-            <parameter id="rateAG.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-            <parameter dimension="4" id="freqParameter.s:primate" name="stateNode" value="0.25" spec="beast.base.spec.inference.parameter.SimplexParam"/>
-        </state>
-
-        <init estimate="false" id="RandomTree.t:primate" initial="@Tree.t:primate" spec="beast.base.spec.evolution.tree.coalescent.RandomTree" taxa="@coding">
-            <populationModel id="ConstantPopulation0.t:primate" spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
-                <parameter id="randomPopSize.t:primate" name="popSize" value="1" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-            </populationModel>
-        </init>
-
-        <distribution id="posterior" spec="CompoundDistribution">
-            <distribution id="prior" spec="CompoundDistribution">
-                <distribution birthDiffRate="@birthRate.t:primate" id="YuleModel.t:primate" spec="beast.base.spec.evolution.speciation.YuleModel" tree="@Tree.t:primate"/>
-                <distribution id="Uniform.0" spec="beast.base.spec.inference.distribution.Uniform" param="@birthRate.t:primate" upper="1.0E6"/>
-                <distribution id="LogNormalDistributionModel.0" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateTransversion.s:primate">
-                        <parameter estimate="false" id="RealParameter.0" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="RealParameter.01" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </distribution>
-                <distribution id="LogNormalDistributionModel.01" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateAG.s:primate">
-                        <parameter estimate="false" id="RealParameter.02" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="RealParameter.03" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </distribution>
-            </distribution>
-            <distribution id="likelihood" spec="CompoundDistribution">
-                <distribution data="@coding" id="treeLikelihood.coding" spec="beast.base.spec.evolution.likelihood.TreeLikelihood" tree="@Tree.t:primate">
-                    <siteModel id="SiteModel.s:primate" spec="beast.base.spec.evolution.sitemodel.SiteModel">
-                        <parameter estimate="false" id="mutationRate.s:primate" name="mutationRate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="gammaShape.s:primate" name="shape" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="proportionInvariant.s:primate" name="proportionInvariant" value="0.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="UnitInterval"/>
-                        <substModel id="gtr.s:primate" rateAC="@rateTransversion.s:primate" rateAG="@rateAG.s:primate" rateAT="@rateTransversion.s:primate" rateCG="@rateTransversion.s:primate" rateGT="@rateTransversion.s:primate" spec="beast.base.spec.evolution.substitutionmodel.GTR">
-                            <parameter estimate="false" id="rateCT.s:primate" name="rateCT" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-                            <frequencies frequencies="@freqParameter.s:primate" id="estimatedFreqs.s:primate" spec="beast.base.spec.evolution.substitutionmodel.Frequencies"/>
-                        </substModel>
-                    </siteModel>
-                    <branchRateModel id="StrictClock.c:primate" spec="beast.base.spec.evolution.branchratemodel.StrictClockModel">
-                        <parameter estimate="false" id="clockRate.c:primate" name="clock.rate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </branchRateModel>
-                </distribution>
-                <distribution branchRateModel="@StrictClock.c:primate" id="treeLikelihood.noncoding" siteModel="@SiteModel.s:primate" spec="beast.base.spec.evolution.likelihood.TreeLikelihood" tree="@Tree.t:primate">
-                    <data data="@primate-mtDNA" filter="1,458-659,897-898" id="noncoding" spec="beast.base.spec.evolution.alignment.FilteredAlignment"/>
-                </distribution>
-            </distribution>
-        </distribution>
-
-        <operator id="YuleBirthRateScaler.t:primate" parameter="@birthRate.t:primate" scaleFactor="0.75" weight="3.0" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator id="treeScaler.t:primate" scaleFactor="0.5" tree="@Tree.t:primate" weight="3.0" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
-
-        <operator id="treeRootScaler.t:primate" rootOnly="true" scaleFactor="0.5" tree="@Tree.t:primate" weight="3.0" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
-
-        <operator id="UniformOperator.t:primate" tree="@Tree.t:primate" weight="30.0" spec="beast.base.evolution.operator.Uniform"/>
-
-        <operator id="SubtreeSlide.t:primate" spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" tree="@Tree.t:primate" weight="15.0"/>
-
-        <operator id="narrow.t:primate" spec="Exchange" tree="@Tree.t:primate" weight="15.0"/>
-
-        <operator id="wide.t:primate" isNarrow="false" spec="Exchange" tree="@Tree.t:primate" weight="3.0"/>
-
-        <operator id="WilsonBalding.t:primate" spec="WilsonBalding" tree="@Tree.t:primate" weight="3.0"/>
-
-        <operator id="RateTransversionScaler.s:primate" parameter="@rateTransversion.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator id="RateAGScaler.s:primate" parameter="@rateAG.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator delta="0.01" id="FrequenciesExchanger.s:primate" spec="beast.base.spec.inference.operator.DeltaExchangeOperator" weight="0.1">
-            <parameter idref="freqParameter.s:primate"/>
-        </operator>
-
-        <logger fileName="primate-mtDNA-restrictedGTR.log" id="tracelog" logEvery="5000" model="@posterior" sanitiseHeaders="true" sort="smart">
-            <log idref="posterior"/>
-            <log idref="likelihood"/>
-            <log idref="prior"/>
-            <log idref="treeLikelihood.noncoding"/>
-            <log idref="treeLikelihood.coding"/>
-            <log id="TreeHeight.t:primate" spec="beast.base.evolution.tree.TreeStatLogger" tree="@Tree.t:primate"/>
-            <log idref="YuleModel.t:primate"/>
-            <parameter idref="birthRate.t:primate" name="log"/>
-            <parameter idref="rateTransversion.s:primate" name="log"/>
-            <parameter idref="rateAG.s:primate" name="log"/>
-            <parameter idref="freqParameter.s:primate" name="log"/>
-        </logger>
-
-        <logger id="screenlog" logEvery="5000">
-            <log idref="posterior"/>
-            <log arg="@posterior" id="ESS.0" spec="beast.base.spec.inference.util.ESS"/>
-            <log idref="likelihood"/>
-            <log idref="prior"/>
-        </logger>
-
-        <logger fileName="primate-mtDNA-restrictedGTR-$(tree).trees" id="treelog.t:primate" logEvery="5000" mode="tree">
-            <log id="TreeWithMetaDataLogger.t:primate" spec="beast.base.spec.evolution.TreeWithMetaDataLogger" tree="@Tree.t:primate"/>
-        </logger>
-    </run>
-</beast>
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/testSYM.xml b/beast-base/src/test/resources/beast.base/examples/spec/testSYM.xml
deleted file mode 100644
index 3198b41a..00000000
--- a/beast-base/src/test/resources/beast.base/examples/spec/testSYM.xml
+++ /dev/null
@@ -1,148 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<beast version="2.8"
-       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt"
-       beautitemplate="Standard"
-       beautistatus="">
-
-    <data id="primate-mtDNA">
-        <sequence id="seq_Lemur_catta" taxon="Lemur_catta" totalcount="4" value="AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATTCTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGGGATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCTAGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTCATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTCCCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAACCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATTTACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAACACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATGTATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGATAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTATAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTGCATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAACAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT"/>
-        <sequence id="seq_Homo_sapiens" taxon="Homo_sapiens" totalcount="4" value="AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
-        <sequence id="seq_Pan" taxon="Pan" totalcount="4" value="AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATTCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCTCGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAAGCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TATAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCACCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCGCGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAGCTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
-        <sequence id="seq_Gorilla" taxon="Gorilla" totalcount="4" value="AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGGACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCTCGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTCCTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTCCCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAAACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCTATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CGTAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTACCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCGCATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAGCTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT"/>
-        <sequence id="seq_Pongo" taxon="Pongo" totalcount="4" value="AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGGCCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCTTGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTCTTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTCTCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAAACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTTATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAACATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGATAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAACAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCGCTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCGCATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAACCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT"/>
-        <sequence id="seq_Hylobates" taxon="Hylobates" totalcount="4" value="AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATTCTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGGGCTCCAAGCCTTACTCCCACTGATAGCCTTCTGATGACTCGCAGCAAGCCTCGCTAACCTCGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTCCTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTCCCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAAACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCTAACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAACATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CACAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAGCCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTGCCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAACCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT"/>
-        <sequence id="seq_Macaca_fuscata" taxon="Macaca_fuscata" totalcount="4" value="AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGGACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTCCTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTCTCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAAGCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAACACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT"/>
-        <sequence id="seq_M._mulatta" taxon="M._mulatta" totalcount="4" value="AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGGACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTCCTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTCCCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCTATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAACATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CGCGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT"/>
-        <sequence id="seq_M._fascicularis" taxon="M._fascicularis" totalcount="4" value="AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTTCTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGTACCATACTACTATCCCGAGGACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTCCTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTCTCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAACATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTGCCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAATATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAACAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT"/>
-        <sequence id="seq_M._sylvanus" taxon="M._sylvanus" totalcount="4" value="AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTTCTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGCATCATACTACTATCCCGAGGACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCTTGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTCCTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTCTCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAAACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCTATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAACATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TGCAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCGCTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAATATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAACAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT"/>
-        <sequence id="seq_Saimiri_sciureus" taxon="Saimiri_sciureus" totalcount="4" value="AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTCTATGCTATTCTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAATAACATTTACTCGAGGGCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCTCGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTCTTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTCACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAAACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCTTACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAACATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CGCAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGATAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAATA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAGCTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCATCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAATCAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT"/>
-        <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4" value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
-    </data>
-
-    <run chainLength="5000000" id="mcmc" spec="MCMC">
-        <state id="state" storeEvery="5000">
-            <tree id="Tree.t:primate" name="stateNode">
-                <taxonset id="TaxonSet.coding" spec="TaxonSet">
-                    <alignment filter="2-457,660-896" id="coding" spec="beast.base.spec.evolution.alignment.FilteredAlignment">
-                        <data idref="primate-mtDNA"/>
-                    </alignment>
-                </taxonset>
-            </tree>
-            <parameter id="birthRate.t:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-            <parameter id="rateAC.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-            <parameter id="rateAG.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-            <parameter id="rateAT.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-            <parameter id="rateCG.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-            <parameter id="rateGT.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-            <parameter dimension="4" id="freqParameter.s:primate" name="stateNode" value="0.25" spec="beast.base.spec.inference.parameter.SimplexParam"/>
-        </state>
-
-        <init estimate="false" id="RandomTree.t:primate" initial="@Tree.t:primate" spec="beast.base.spec.evolution.tree.coalescent.RandomTree" taxa="@coding">
-            <populationModel id="ConstantPopulation0.t:primate" spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
-                <parameter id="randomPopSize.t:primate" name="popSize" value="1" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-            </populationModel>
-        </init>
-
-        <distribution id="posterior" spec="CompoundDistribution">
-            <distribution id="prior" spec="CompoundDistribution">
-                <distribution birthDiffRate="@birthRate.t:primate" id="YuleModel.t:primate" spec="beast.base.spec.evolution.speciation.YuleModel" tree="@Tree.t:primate"/>
-                <distribution id="Uniform.0" spec="beast.base.spec.inference.distribution.Uniform" param="@birthRate.t:primate" upper="1.0E6"/>
-                <distribution id="LogNormalDistributionModel.0" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateAC.s:primate">
-                        <parameter estimate="false" id="RealParameter.0" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="RealParameter.01" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </distribution>
-                <distribution id="LogNormalDistributionModel.01" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateAG.s:primate">
-                        <parameter estimate="false" id="RealParameter.02" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="RealParameter.03" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </distribution>
-                <distribution id="LogNormalDistributionModel.02" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateAT.s:primate">
-                        <parameter estimate="false" id="RealParameter.04" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="RealParameter.05" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </distribution>
-                <distribution id="LogNormalDistributionModel.03" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateCG.s:primate">
-                        <parameter estimate="false" id="RealParameter.06" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="RealParameter.07" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </distribution>
-                <distribution id="LogNormalDistributionModel.04" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateGT.s:primate">
-                        <parameter estimate="false" id="RealParameter.08" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="RealParameter.09" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </distribution>
-            </distribution>
-            <distribution id="likelihood" spec="CompoundDistribution">
-                <distribution data="@coding" id="treeLikelihood.coding" spec="beast.base.spec.evolution.likelihood.TreeLikelihood" tree="@Tree.t:primate">
-                    <siteModel id="SiteModel.s:primate" spec="beast.base.spec.evolution.sitemodel.SiteModel">
-                        <parameter estimate="false" id="mutationRate.s:primate" name="mutationRate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="gammaShape.s:primate" name="shape" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="proportionInvariant.s:primate" name="proportionInvariant" value="0.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="UnitInterval"/>
-                        <substModel id="gtr.s:primate" rateAC="@rateAC.s:primate" rateAG="@rateAG.s:primate" rateAT="@rateAT.s:primate" rateCG="@rateCG.s:primate" rateGT="@rateGT.s:primate" spec="beast.base.spec.evolution.substitutionmodel.GTR">
-                            <parameter estimate="false" id="rateCT.s:primate" name="rateCT" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-                            <frequencies frequencies="@freqParameter.s:primate" id="estimatedFreqs.s:primate" spec="beast.base.spec.evolution.substitutionmodel.Frequencies"/>
-                        </substModel>
-                    </siteModel>
-                    <branchRateModel id="StrictClock.c:primate" spec="beast.base.spec.evolution.branchratemodel.StrictClockModel">
-                        <parameter estimate="false" id="clockRate.c:primate" name="clock.rate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </branchRateModel>
-                </distribution>
-                <distribution branchRateModel="@StrictClock.c:primate" id="treeLikelihood.noncoding" siteModel="@SiteModel.s:primate" spec="beast.base.spec.evolution.likelihood.TreeLikelihood" tree="@Tree.t:primate">
-                    <data data="@primate-mtDNA" filter="1,458-659,897-898" id="noncoding" spec="beast.base.spec.evolution.alignment.FilteredAlignment"/>
-                </distribution>
-            </distribution>
-        </distribution>
-
-        <operator id="YuleBirthRateScaler.t:primate" parameter="@birthRate.t:primate" scaleFactor="0.75" weight="3.0" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator id="treeScaler.t:primate" scaleFactor="0.5" tree="@Tree.t:primate" weight="3.0" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
-
-        <operator id="treeRootScaler.t:primate" rootOnly="true" scaleFactor="0.5" tree="@Tree.t:primate" weight="3.0" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
-
-        <operator id="UniformOperator.t:primate" tree="@Tree.t:primate" weight="30.0" spec="beast.base.evolution.operator.Uniform"/>
-
-        <operator id="SubtreeSlide.t:primate" spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" tree="@Tree.t:primate" weight="15.0"/>
-
-        <operator id="narrow.t:primate" spec="Exchange" tree="@Tree.t:primate" weight="15.0"/>
-
-        <operator id="wide.t:primate" isNarrow="false" spec="Exchange" tree="@Tree.t:primate" weight="3.0"/>
-
-        <operator id="WilsonBalding.t:primate" spec="WilsonBalding" tree="@Tree.t:primate" weight="3.0"/>
-
-        <operator id="RateACScaler.s:primate" parameter="@rateAC.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator id="RateAGScaler.s:primate" parameter="@rateAG.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator id="RateATScaler.s:primate" parameter="@rateAT.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator id="RateCGScaler.s:primate" parameter="@rateCG.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator id="RateGTScaler.s:primate" parameter="@rateGT.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <logger fileName="primate-mtDNA-SYM.log" id="tracelog" logEvery="5000" model="@posterior" sanitiseHeaders="true" sort="smart">
-            <log idref="posterior"/>
-            <log idref="likelihood"/>
-            <log idref="prior"/>
-            <log idref="treeLikelihood.noncoding"/>
-            <log idref="treeLikelihood.coding"/>
-            <log id="TreeHeight.t:primate" spec="beast.base.evolution.tree.TreeStatLogger" tree="@Tree.t:primate"/>
-            <log idref="YuleModel.t:primate"/>
-            <parameter idref="birthRate.t:primate" name="log"/>
-            <parameter idref="rateAC.s:primate" name="log"/>
-            <parameter idref="rateAG.s:primate" name="log"/>
-            <parameter idref="rateAT.s:primate" name="log"/>
-            <parameter idref="rateCG.s:primate" name="log"/>
-            <parameter idref="rateGT.s:primate" name="log"/>
-            <parameter idref="freqParameter.s:primate" name="log"/>
-        </logger>
-
-        <logger id="screenlog" logEvery="5000">
-            <log idref="posterior"/>
-            <log arg="@posterior" id="ESS.0" spec="beast.base.spec.inference.util.ESS"/>
-            <log idref="likelihood"/>
-            <log idref="prior"/>
-        </logger>
-
-        <logger fileName="$(tree).trees" id="treelog.t:primate" logEvery="5000" mode="tree">
-            <log id="TreeWithMetaDataLogger.t:primate" spec="beast.base.spec.evolution.TreeWithMetaDataLogger" tree="@Tree.t:primate"/>
-        </logger>
-
-    </run>
-
-</beast>
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/testTIM.xml b/beast-base/src/test/resources/beast.base/examples/spec/testTIM.xml
deleted file mode 100644
index e9882e7b..00000000
--- a/beast-base/src/test/resources/beast.base/examples/spec/testTIM.xml
+++ /dev/null
@@ -1,136 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<beast version="2.8"
-       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt"
-       beautitemplate="Standard"
-       beautistatus="">
-
-    <data id="primate-mtDNA">
-        <sequence id="seq_Lemur_catta" taxon="Lemur_catta" totalcount="4" value="AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATTCTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGGGATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCTAGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTCATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTCCCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAACCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATTTACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAACACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATGTATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGATAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTATAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTGCATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAACAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT"/>
-        <sequence id="seq_Homo_sapiens" taxon="Homo_sapiens" totalcount="4" value="AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
-        <sequence id="seq_Pan" taxon="Pan" totalcount="4" value="AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATTCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCTCGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAAGCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TATAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCACCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCGCGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAGCTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
-        <sequence id="seq_Gorilla" taxon="Gorilla" totalcount="4" value="AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGGACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCTCGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTCCTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTCCCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAAACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCTATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CGTAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTACCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCGCATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAGCTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT"/>
-        <sequence id="seq_Pongo" taxon="Pongo" totalcount="4" value="AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGGCCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCTTGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTCTTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTCTCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAAACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTTATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAACATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGATAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAACAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCGCTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCGCATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAACCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT"/>
-        <sequence id="seq_Hylobates" taxon="Hylobates" totalcount="4" value="AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATTCTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGGGCTCCAAGCCTTACTCCCACTGATAGCCTTCTGATGACTCGCAGCAAGCCTCGCTAACCTCGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTCCTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTCCCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAAACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCTAACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAACATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CACAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAGCCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTGCCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAACCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT"/>
-        <sequence id="seq_Macaca_fuscata" taxon="Macaca_fuscata" totalcount="4" value="AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGGACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTCCTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTCTCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAAGCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAACACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT"/>
-        <sequence id="seq_M._mulatta" taxon="M._mulatta" totalcount="4" value="AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGGACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTCCTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTCCCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCTATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAACATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CGCGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT"/>
-        <sequence id="seq_M._fascicularis" taxon="M._fascicularis" totalcount="4" value="AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTTCTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGTACCATACTACTATCCCGAGGACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTCCTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTCTCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAACATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTGCCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAATATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAACAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT"/>
-        <sequence id="seq_M._sylvanus" taxon="M._sylvanus" totalcount="4" value="AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTTCTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGCATCATACTACTATCCCGAGGACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCTTGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTCCTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTCTCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAAACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCTATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAACATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TGCAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCGCTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAATATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAACAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT"/>
-        <sequence id="seq_Saimiri_sciureus" taxon="Saimiri_sciureus" totalcount="4" value="AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTCTATGCTATTCTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAATAACATTTACTCGAGGGCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCTCGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTCTTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTCACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAAACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCTTACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAACATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CGCAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGATAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAATA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAGCTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCATCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAATCAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT"/>
-        <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4" value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
-    </data>
-
-    <run chainLength="5000000" id="mcmc" spec="MCMC">
-        <state id="state" storeEvery="5000">
-            <tree id="Tree.t:primate" name="stateNode">
-                <taxonset id="TaxonSet.coding" spec="TaxonSet">
-                    <alignment filter="2-457,660-896" id="coding" spec="beast.base.spec.evolution.alignment.FilteredAlignment">
-                        <data idref="primate-mtDNA"/>
-                    </alignment>
-                </taxonset>
-            </tree>
-            <parameter id="birthRate.t:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-            <parameter id="rateAG.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-            <parameter id="rateTransversions1.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-            <parameter id="rateTransversions2.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-            <parameter dimension="4" id="freqParameter.s:primate" name="stateNode" value="0.25" spec="beast.base.spec.inference.parameter.SimplexParam"/>
-        </state>
-
-        <init estimate="false" id="RandomTree.t:primate" initial="@Tree.t:primate" spec="beast.base.spec.evolution.tree.coalescent.RandomTree" taxa="@coding">
-            <populationModel id="ConstantPopulation0.t:primate" spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
-                <parameter id="randomPopSize.t:primate" name="popSize" value="1" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-            </populationModel>
-        </init>
-
-        <distribution id="posterior" spec="CompoundDistribution">
-            <distribution id="prior" spec="CompoundDistribution">
-                <distribution birthDiffRate="@birthRate.t:primate" id="YuleModel.t:primate" spec="beast.base.spec.evolution.speciation.YuleModel" tree="@Tree.t:primate"/>
-                <distribution id="Uniform.0" spec="beast.base.spec.inference.distribution.Uniform" param="@birthRate.t:primate" upper="1.0E6"/>
-                <distribution id="LogNormalDistributionModel.0" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateAG.s:primate">
-                        <parameter estimate="false" id="RealParameter.0" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="RealParameter.01" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </distribution>
-                <distribution id="LogNormalDistributionModel.01" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateTransversions1.s:primate">
-                        <parameter estimate="false" id="RealParameter.02" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="RealParameter.03" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </distribution>
-                <distribution id="LogNormalDistributionModel.02" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateTransversions2.s:primate">
-                        <parameter estimate="false" id="RealParameter.04" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="RealParameter.05" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </distribution>
-            </distribution>
-            <distribution id="likelihood" spec="CompoundDistribution">
-                <distribution data="@coding" id="treeLikelihood.coding" spec="beast.base.spec.evolution.likelihood.TreeLikelihood" tree="@Tree.t:primate">
-                    <siteModel id="SiteModel.s:primate" spec="beast.base.spec.evolution.sitemodel.SiteModel">
-                        <parameter estimate="false" id="mutationRate.s:primate" name="mutationRate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="gammaShape.s:primate" name="shape" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="proportionInvariant.s:primate" name="proportionInvariant" value="0.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="UnitInterval"/>
-                        <substModel id="tim.s:primate" rateAG="@rateAG.s:primate" rateTransversions1="@rateTransversions1.s:primate" rateTransversions2="@rateTransversions2.s:primate" spec="beast.base.spec.evolution.substitutionmodel.TIM">
-                            <parameter estimate="false" id="rateCT.s:primate" name="rateCT" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-                            <frequencies frequencies="@freqParameter.s:primate" id="estimatedFreqs.s:primate" spec="beast.base.spec.evolution.substitutionmodel.Frequencies"/>
-                        </substModel>
-                    </siteModel>
-                    <branchRateModel id="StrictClock.c:primate" spec="beast.base.spec.evolution.branchratemodel.StrictClockModel">
-                        <parameter estimate="false" id="clockRate.c:primate" name="clock.rate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </branchRateModel>
-                </distribution>
-                <distribution branchRateModel="@StrictClock.c:primate" id="treeLikelihood.noncoding" siteModel="@SiteModel.s:primate" spec="beast.base.spec.evolution.likelihood.TreeLikelihood" tree="@Tree.t:primate">
-                    <data data="@primate-mtDNA" filter="1,458-659,897-898" id="noncoding" spec="beast.base.spec.evolution.alignment.FilteredAlignment"/>
-                </distribution>
-            </distribution>
-        </distribution>
-
-        <operator id="YuleBirthRateScaler.t:primate" parameter="@birthRate.t:primate" scaleFactor="0.75" weight="3.0" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator id="treeScaler.t:primate" scaleFactor="0.5" tree="@Tree.t:primate" weight="3.0" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
-
-        <operator id="treeRootScaler.t:primate" rootOnly="true" scaleFactor="0.5" tree="@Tree.t:primate" weight="3.0" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
-
-        <operator id="UniformOperator.t:primate" tree="@Tree.t:primate" weight="30.0" spec="beast.base.evolution.operator.Uniform"/>
-
-        <operator id="SubtreeSlide.t:primate" spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" tree="@Tree.t:primate" weight="15.0"/>
-
-        <operator id="narrow.t:primate" spec="Exchange" tree="@Tree.t:primate" weight="15.0"/>
-
-        <operator id="wide.t:primate" isNarrow="false" spec="Exchange" tree="@Tree.t:primate" weight="3.0"/>
-
-        <operator id="WilsonBalding.t:primate" spec="WilsonBalding" tree="@Tree.t:primate" weight="3.0"/>
-
-        <operator id="RateAGScaler.s:primate" parameter="@rateAG.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator id="RateTransversions1Scaler.s:primate" parameter="@rateTransversions1.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator id="RateTransversions2Scaler.s:primate" parameter="@rateTransversions2.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator delta="0.01" id="FrequenciesExchanger.s:primate" spec="beast.base.spec.inference.operator.DeltaExchangeOperator" weight="0.1">
-            <parameter idref="freqParameter.s:primate"/>
-        </operator>
-
-        <logger fileName="primate-mtDNA-TIM.log" id="tracelog" logEvery="5000" model="@posterior" sanitiseHeaders="true" sort="smart">
-            <log idref="posterior"/>
-            <log idref="likelihood"/>
-            <log idref="prior"/>
-            <log idref="treeLikelihood.noncoding"/>
-            <log idref="treeLikelihood.coding"/>
-            <log id="TreeHeight.t:primate" spec="beast.base.evolution.tree.TreeStatLogger" tree="@Tree.t:primate"/>
-            <log idref="YuleModel.t:primate"/>
-            <parameter idref="birthRate.t:primate" name="log"/>
-            <parameter idref="rateAG.s:primate" name="log"/>
-            <parameter idref="rateTransversions1.s:primate" name="log"/>
-            <parameter idref="rateTransversions2.s:primate" name="log"/>
-            <parameter idref="freqParameter.s:primate" name="log"/>
-        </logger>
-
-        <logger id="screenlog" logEvery="5000">
-            <log idref="posterior"/>
-            <log arg="@posterior" id="ESS.0" spec="beast.base.spec.inference.util.ESS"/>
-            <log idref="likelihood"/>
-            <log idref="prior"/>
-        </logger>
-
-        <logger fileName="$(tree).trees" id="treelog.t:primate" logEvery="5000" mode="tree">
-            <log id="TreeWithMetaDataLogger.t:primate" spec="beast.base.spec.evolution.TreeWithMetaDataLogger" tree="@Tree.t:primate"/>
-        </logger>
-
-    </run>
-
-</beast>
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/testTN93.xml b/beast-base/src/test/resources/beast.base/examples/spec/testTN93.xml
deleted file mode 100644
index 732ccf06..00000000
--- a/beast-base/src/test/resources/beast.base/examples/spec/testTN93.xml
+++ /dev/null
@@ -1,121 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<beast version="2.8"
-       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt"
-       beautitemplate="Standard"
-       beautistatus="">
-
-    <data id="primate-mtDNA">
-        <sequence id="seq_Lemur_catta" taxon="Lemur_catta" totalcount="4" value="AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATTCTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGGGATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCTAGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTCATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTCCCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAACCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATTTACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAACACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATGTATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGATAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTATAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTGCATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAACAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT"/>
-        <sequence id="seq_Homo_sapiens" taxon="Homo_sapiens" totalcount="4" value="AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
-        <sequence id="seq_Pan" taxon="Pan" totalcount="4" value="AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATTCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCTCGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAAGCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TATAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCACCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCGCGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAGCTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
-        <sequence id="seq_Gorilla" taxon="Gorilla" totalcount="4" value="AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGGACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCTCGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTCCTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTCCCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAAACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCTATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CGTAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTACCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCGCATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAGCTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT"/>
-        <sequence id="seq_Pongo" taxon="Pongo" totalcount="4" value="AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGGCCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCTTGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTCTTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTCTCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAAACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTTATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAACATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGATAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAACAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCGCTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCGCATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAACCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT"/>
-        <sequence id="seq_Hylobates" taxon="Hylobates" totalcount="4" value="AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATTCTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGGGCTCCAAGCCTTACTCCCACTGATAGCCTTCTGATGACTCGCAGCAAGCCTCGCTAACCTCGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTCCTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTCCCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAAACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCTAACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAACATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CACAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAGCCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTGCCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAACCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT"/>
-        <sequence id="seq_Macaca_fuscata" taxon="Macaca_fuscata" totalcount="4" value="AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGGACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTCCTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTCTCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAAGCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAACACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT"/>
-        <sequence id="seq_M._mulatta" taxon="M._mulatta" totalcount="4" value="AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGGACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTCCTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTCCCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCTATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAACATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CGCGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT"/>
-        <sequence id="seq_M._fascicularis" taxon="M._fascicularis" totalcount="4" value="AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTTCTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGTACCATACTACTATCCCGAGGACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTCCTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTCTCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAACATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTGCCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAATATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAACAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT"/>
-        <sequence id="seq_M._sylvanus" taxon="M._sylvanus" totalcount="4" value="AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTTCTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGCATCATACTACTATCCCGAGGACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCTTGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTCCTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTCTCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAAACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCTATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAACATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TGCAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCGCTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAATATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAACAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT"/>
-        <sequence id="seq_Saimiri_sciureus" taxon="Saimiri_sciureus" totalcount="4" value="AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTCTATGCTATTCTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAATAACATTTACTCGAGGGCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCTCGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTCTTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTCACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAAACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCTTACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAACATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CGCAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGATAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAATA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAGCTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCATCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAATCAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT"/>
-        <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4" value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
-    </data>
-
-    <run chainLength="5000000" id="mcmc" spec="MCMC">
-        <state id="state" storeEvery="5000">
-            <tree id="Tree.t:primate" name="stateNode">
-                <taxonset id="TaxonSet.coding" spec="TaxonSet">
-                    <alignment filter="2-457,660-896" id="coding" spec="beast.base.spec.evolution.alignment.FilteredAlignment">
-                        <data idref="primate-mtDNA"/>
-                    </alignment>
-                </taxonset>
-            </tree>
-            <parameter id="birthRate.t:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-            <parameter id="rateAG.s:primate" name="stateNode" value="2.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-            <parameter id="rateCT.s:primate" name="stateNode" value="2.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-            <parameter dimension="4" id="freqParameter.s:primate" name="stateNode" value="0.25" spec="beast.base.spec.inference.parameter.SimplexParam"/>
-        </state>
-
-        <init estimate="false" id="RandomTree.t:primate" initial="@Tree.t:primate" spec="beast.base.spec.evolution.tree.coalescent.RandomTree" taxa="@coding">
-            <populationModel id="ConstantPopulation0.t:primate" spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
-                <parameter id="randomPopSize.t:primate" name="popSize" value="1" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-            </populationModel>
-        </init>
-
-        <distribution id="posterior" spec="CompoundDistribution">
-            <distribution id="prior" spec="CompoundDistribution">
-                <distribution birthDiffRate="@birthRate.t:primate" id="YuleModel.t:primate" spec="beast.base.spec.evolution.speciation.YuleModel" tree="@Tree.t:primate"/>
-                <distribution id="Uniform.0" spec="beast.base.spec.inference.distribution.Uniform" param="@birthRate.t:primate" upper="1.0E6"/>
-            </distribution>
-            <distribution id="likelihood" spec="CompoundDistribution">
-                <distribution data="@coding" id="treeLikelihood.coding" spec="beast.base.spec.evolution.likelihood.TreeLikelihood" tree="@Tree.t:primate">
-                    <siteModel id="SiteModel.s:primate" spec="beast.base.spec.evolution.sitemodel.SiteModel">
-                        <parameter estimate="false" id="mutationRate.s:primate" name="mutationRate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="gammaShape.s:primate" name="shape" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="proportionInvariant.s:primate" name="proportionInvariant" value="0.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="UnitInterval"/>
-                        <substModel id="tn93.s:primate" kappa1="@rateAG.s:primate" kappa2="@rateCT.s:primate" spec="beast.base.spec.evolution.substitutionmodel.TN93">
-                            <frequencies frequencies="@freqParameter.s:primate" id="estimatedFreqs.s:primate" spec="beast.base.spec.evolution.substitutionmodel.Frequencies"/>
-                        </substModel>
-                    </siteModel>
-                    <branchRateModel id="StrictClock.c:primate" spec="beast.base.spec.evolution.branchratemodel.StrictClockModel">
-                        <parameter estimate="false" id="clockRate.c:primate" name="clock.rate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </branchRateModel>
-                </distribution>
-                <distribution branchRateModel="@StrictClock.c:primate" id="treeLikelihood.noncoding" siteModel="@SiteModel.s:primate" spec="beast.base.spec.evolution.likelihood.TreeLikelihood" tree="@Tree.t:primate">
-                    <data data="@primate-mtDNA" filter="1,458-659,897-898" id="noncoding" spec="beast.base.spec.evolution.alignment.FilteredAlignment"/>
-                </distribution>
-            </distribution>
-        </distribution>
-
-        <operator id="YuleBirthRateScaler.t:primate" parameter="@birthRate.t:primate" scaleFactor="0.75" weight="3.0" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator id="treeScaler.t:primate" scaleFactor="0.5" tree="@Tree.t:primate" weight="3.0" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
-
-        <operator id="treeRootScaler.t:primate" rootOnly="true" scaleFactor="0.5" tree="@Tree.t:primate" weight="3.0" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
-
-        <operator id="UniformOperator.t:primate" tree="@Tree.t:primate" weight="30.0" spec="beast.base.evolution.operator.Uniform"/>
-
-        <operator id="SubtreeSlide.t:primate" spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" tree="@Tree.t:primate" weight="15.0"/>
-
-        <operator id="narrow.t:primate" spec="Exchange" tree="@Tree.t:primate" weight="15.0"/>
-
-        <operator id="wide.t:primate" isNarrow="false" spec="Exchange" tree="@Tree.t:primate" weight="3.0"/>
-
-        <operator id="WilsonBalding.t:primate" spec="WilsonBalding" tree="@Tree.t:primate" weight="3.0"/>
-
-        <operator id="RateAGScaler.s:primate" parameter="@rateAG.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator id="RateCTScaler.s:primate" parameter="@rateCT.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator delta="0.01" id="FrequenciesExchanger.s:primate" spec="beast.base.spec.inference.operator.DeltaExchangeOperator" weight="0.1">
-            <parameter idref="freqParameter.s:primate"/>
-        </operator>
-
-        <logger fileName="primate-mtDNA-tn93.log" id="tracelog" logEvery="5000" model="@posterior" sanitiseHeaders="true" sort="smart">
-            <log idref="posterior"/>
-            <log idref="likelihood"/>
-            <log idref="prior"/>
-            <log idref="treeLikelihood.coding"/>
-            <log id="TreeHeight.t:primate" spec="beast.base.evolution.tree.TreeStatLogger" tree="@Tree.t:primate"/>
-            <log idref="YuleModel.t:primate"/>
-            <parameter idref="birthRate.t:primate" name="log"/>
-            <log idref="treeLikelihood.noncoding"/>
-            <parameter idref="rateAG.s:primate" name="log"/>
-            <parameter idref="rateCT.s:primate" name="log"/>
-            <parameter idref="freqParameter.s:primate" name="log"/>
-        </logger>
-
-        <logger id="screenlog" logEvery="5000">
-            <log idref="posterior"/>
-            <log arg="@posterior" id="ESS.0" spec="beast.base.spec.inference.util.ESS"/>
-            <log idref="likelihood"/>
-            <log idref="prior"/>
-            <parameter idref="rateAG.s:primate" name="log"/>
-            <parameter idref="rateCT.s:primate" name="log"/>
-        </logger>
-
-        <logger fileName="primate-mtDNA-tn93.trees" id="treelog.t:primate" logEvery="5000" mode="tree">
-            <log id="TreeWithMetaDataLogger.t:primate" spec="beast.base.spec.evolution.TreeWithMetaDataLogger" tree="@Tree.t:primate"/>
-        </logger>
-
-    </run>
-
-</beast>
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/testTVM.xml b/beast-base/src/test/resources/beast.base/examples/spec/testTVM.xml
deleted file mode 100644
index 07030e1b..00000000
--- a/beast-base/src/test/resources/beast.base/examples/spec/testTVM.xml
+++ /dev/null
@@ -1,144 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<beast version="2.8"
-       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt"
-       beautitemplate="Standard"
-       beautistatus="">
-
-    <data id="primate-mtDNA">
-        <sequence id="seq_Lemur_catta" taxon="Lemur_catta" totalcount="4" value="AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATTCTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGGGATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCTAGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTCATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTCCCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAACCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATTTACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAACACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATGTATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGATAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTATAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTGCATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAACAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT"/>
-        <sequence id="seq_Homo_sapiens" taxon="Homo_sapiens" totalcount="4" value="AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
-        <sequence id="seq_Pan" taxon="Pan" totalcount="4" value="AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATTCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCTCGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAAGCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TATAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCACCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCGCGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAGCTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
-        <sequence id="seq_Gorilla" taxon="Gorilla" totalcount="4" value="AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGGACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCTCGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTCCTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTCCCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAAACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCTATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CGTAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTACCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCGCATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAGCTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT"/>
-        <sequence id="seq_Pongo" taxon="Pongo" totalcount="4" value="AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGGCCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCTTGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTCTTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTCTCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAAACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTTATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAACATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGATAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAACAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCGCTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCGCATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAACCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT"/>
-        <sequence id="seq_Hylobates" taxon="Hylobates" totalcount="4" value="AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATTCTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGGGCTCCAAGCCTTACTCCCACTGATAGCCTTCTGATGACTCGCAGCAAGCCTCGCTAACCTCGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTCCTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTCCCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAAACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCTAACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAACATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CACAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAGCCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTGCCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAACCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT"/>
-        <sequence id="seq_Macaca_fuscata" taxon="Macaca_fuscata" totalcount="4" value="AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGGACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTCCTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTCTCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAAGCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAACACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT"/>
-        <sequence id="seq_M._mulatta" taxon="M._mulatta" totalcount="4" value="AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGGACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTCCTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTCCCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCTATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAACATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CGCGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT"/>
-        <sequence id="seq_M._fascicularis" taxon="M._fascicularis" totalcount="4" value="AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTTCTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGTACCATACTACTATCCCGAGGACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTCCTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTCTCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAACATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTGCCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAATATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAACAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT"/>
-        <sequence id="seq_M._sylvanus" taxon="M._sylvanus" totalcount="4" value="AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTTCTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGCATCATACTACTATCCCGAGGACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCTTGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTCCTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTCTCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAAACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCTATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAACATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TGCAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCGCTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAATATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAACAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT"/>
-        <sequence id="seq_Saimiri_sciureus" taxon="Saimiri_sciureus" totalcount="4" value="AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTCTATGCTATTCTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAATAACATTTACTCGAGGGCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCTCGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTCTTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTCACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAAACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCTTACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAACATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CGCAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGATAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAATA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAGCTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCATCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAATCAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT"/>
-        <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4" value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
-    </data>
-
-    <run chainLength="5000000" id="mcmc" spec="MCMC">
-        <state id="state" storeEvery="5000">
-            <tree id="Tree.t:primate" name="stateNode">
-                <taxonset id="TaxonSet.coding" spec="TaxonSet">
-                    <alignment filter="2-457,660-896" id="coding" spec="beast.base.spec.evolution.alignment.FilteredAlignment">
-                        <data idref="primate-mtDNA"/>
-                    </alignment>
-                </taxonset>
-            </tree>
-            <parameter id="birthRate.t:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-            <parameter id="rateGT.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-            <parameter id="rateTransitions.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-            <parameter id="rateAT.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-            <parameter id="rateCG.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-            <parameter dimension="4" id="freqParameter.s:primate" name="stateNode" value="0.25" spec="beast.base.spec.inference.parameter.SimplexParam"/>
-        </state>
-
-        <init estimate="false" id="RandomTree.t:primate" initial="@Tree.t:primate" spec="beast.base.spec.evolution.tree.coalescent.RandomTree" taxa="@coding">
-            <populationModel id="ConstantPopulation0.t:primate" spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
-                <parameter id="randomPopSize.t:primate" name="popSize" value="1" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-            </populationModel>
-        </init>
-
-        <distribution id="posterior" spec="CompoundDistribution">
-            <distribution id="prior" spec="CompoundDistribution">
-                <distribution birthDiffRate="@birthRate.t:primate" id="YuleModel.t:primate" spec="beast.base.spec.evolution.speciation.YuleModel" tree="@Tree.t:primate"/>
-                <distribution id="Uniform.0" spec="beast.base.spec.inference.distribution.Uniform" param="@birthRate.t:primate" upper="1.0E6"/>
-                <distribution id="LogNormalDistributionModel.0" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateGT.s:primate">
-                        <parameter estimate="false" id="RealParameter.0" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="RealParameter.01" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </distribution>
-                <distribution id="LogNormalDistributionModel.01" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateTransitions.s:primate">
-                        <parameter estimate="false" id="RealParameter.02" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="RealParameter.03" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </distribution>
-                <distribution id="LogNormalDistributionModel.02" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateAT.s:primate">
-                        <parameter estimate="false" id="RealParameter.04" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="RealParameter.05" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </distribution>
-                <distribution id="LogNormalDistributionModel.03" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateCG.s:primate">
-                        <parameter estimate="false" id="RealParameter.06" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="RealParameter.07" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </distribution>
-            </distribution>
-
-            <distribution id="likelihood" spec="CompoundDistribution">
-                <distribution data="@coding" id="treeLikelihood.coding" spec="beast.base.spec.evolution.likelihood.TreeLikelihood" tree="@Tree.t:primate">
-                    <siteModel id="SiteModel.s:primate" spec="beast.base.spec.evolution.sitemodel.SiteModel">
-                        <parameter estimate="false" id="mutationRate.s:primate" name="mutationRate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="gammaShape.s:primate" name="shape" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                        <parameter estimate="false" id="proportionInvariant.s:primate" name="proportionInvariant" value="0.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="UnitInterval"/>
-                        <substModel id="tvm.s:primate" rateGT="@rateGT.s:primate" rateTransitions="@rateTransitions.s:primate" rateAT="@rateAT.s:primate" rateCG="@rateCG.s:primate" spec="beast.base.spec.evolution.substitutionmodel.TVM">
-                            <parameter estimate="false" id="rateAC.s:primate" name="rateAC" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
-                            <frequencies frequencies="@freqParameter.s:primate" id="estimatedFreqs.s:primate" spec="beast.base.spec.evolution.substitutionmodel.Frequencies"/>
-                        </substModel>
-                    </siteModel>
-                    <branchRateModel id="StrictClock.c:primate" spec="beast.base.spec.evolution.branchratemodel.StrictClockModel">
-                        <parameter estimate="false" id="clockRate.c:primate" name="clock.rate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-                    </branchRateModel>
-                </distribution>
-                <distribution branchRateModel="@StrictClock.c:primate" id="treeLikelihood.noncoding" siteModel="@SiteModel.s:primate" spec="beast.base.spec.evolution.likelihood.TreeLikelihood" tree="@Tree.t:primate">
-                    <data data="@primate-mtDNA" filter="1,458-659,897-898" id="noncoding" spec="beast.base.spec.evolution.alignment.FilteredAlignment"/>
-                </distribution>
-            </distribution>
-        </distribution>
-
-        <operator id="YuleBirthRateScaler.t:primate" parameter="@birthRate.t:primate" scaleFactor="0.75" weight="3.0" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator id="treeScaler.t:primate" scaleFactor="0.5" tree="@Tree.t:primate" weight="3.0" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
-
-        <operator id="treeRootScaler.t:primate" rootOnly="true" scaleFactor="0.5" tree="@Tree.t:primate" weight="3.0" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
-
-        <operator id="UniformOperator.t:primate" tree="@Tree.t:primate" weight="30.0" spec="beast.base.evolution.operator.Uniform"/>
-
-        <operator id="SubtreeSlide.t:primate" spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" tree="@Tree.t:primate" weight="15.0"/>
-
-        <operator id="narrow.t:primate" spec="Exchange" tree="@Tree.t:primate" weight="15.0"/>
-
-        <operator id="wide.t:primate" isNarrow="false" spec="Exchange" tree="@Tree.t:primate" weight="3.0"/>
-
-        <operator id="WilsonBalding.t:primate" spec="WilsonBalding" tree="@Tree.t:primate" weight="3.0"/>
-
-        <operator id="RateGTScaler.s:primate" parameter="@rateGT.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator id="RateATScaler.s:primate" parameter="@rateAT.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator id="RateCGScaler.s:primate" parameter="@rateCG.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator id="RateTransitionsScaler.s:primate" parameter="@rateTransitions.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
-
-        <operator delta="0.01" id="FrequenciesExchanger.s:primate" spec="beast.base.spec.inference.operator.DeltaExchangeOperator" weight="0.1">
-            <parameter idref="freqParameter.s:primate"/>
-        </operator>
-
-        <logger fileName="primate-mtDNA-TVM.log" id="tracelog" logEvery="5000" model="@posterior" sanitiseHeaders="true" sort="smart">
-            <log idref="posterior"/>
-            <log idref="likelihood"/>
-            <log idref="prior"/>
-            <log idref="treeLikelihood.noncoding"/>
-            <log idref="treeLikelihood.coding"/>
-            <log id="TreeHeight.t:primate" spec="beast.base.evolution.tree.TreeStatLogger" tree="@Tree.t:primate"/>
-            <log idref="YuleModel.t:primate"/>
-            <parameter idref="birthRate.t:primate" name="log"/>
-            <parameter idref="rateGT.s:primate" name="log"/>
-            <parameter idref="rateTransitions.s:primate" name="log"/>
-            <parameter idref="rateAT.s:primate" name="log"/>
-            <parameter idref="rateCG.s:primate" name="log"/>
-            <parameter idref="freqParameter.s:primate" name="log"/>
-        </logger>
-
-        <logger id="screenlog" logEvery="5000">
-            <log idref="posterior"/>
-            <log arg="@posterior" id="ESS.0" spec="beast.base.spec.inference.util.ESS"/>
-            <log idref="likelihood"/>
-            <log idref="prior"/>
-        </logger>
-
-        <logger fileName="$(tree).trees" id="treelog.t:primate" logEvery="5000" mode="tree">
-            <log id="TreeWithMetaDataLogger.t:primate" spec="beast.base.spec.evolution.TreeWithMetaDataLogger" tree="@Tree.t:primate"/>
-        </logger>
-
-    </run>
-</beast>
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/testYuleOneSite.xml b/beast-base/src/test/resources/beast.base/examples/spec/testYuleOneSite.xml
deleted file mode 100644
index 92e4b88f..00000000
--- a/beast-base/src/test/resources/beast.base/examples/spec/testYuleOneSite.xml
+++ /dev/null
@@ -1,89 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!-- test Yule birth model and Birth Death model per Gernhard 2008-->
-<beast version="2.8"
-       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt">
-
-    <data id="alignment" dataType="nucleotide">
-        <sequence taxon="A">A</sequence>
-        <sequence taxon="B">A</sequence>
-        <sequence taxon="C">A</sequence>
-        <sequence taxon="D">A</sequence>
-    </data>
-    
-    <!-- A prior on the distribution node heights defined given                  -->
-    <!-- a Yule speciation process (a pure birth process).                       -->
-    <input spec="beast.base.spec.evolution.speciation.YuleModel" id="yule">
-        <parameter name="birthDiffRate" idref="birthRate"/>
-	<tree spec="beast.base.evolution.tree.TreeParser" id="tree" IsLabelledNewick="true" taxa="@alignment" newick="((A:1.0,B:1.0):1.0,(C:1.0,D:1.0):1.0);"/>
-    </input>
-
-    <input spec="beast.base.spec.evolution.speciation.BirthDeathGernhard08Model" id="yulelike" type="unscaled" tree="@tree">
-        <parameter name="birthDiffRate" idref="birthRate"/>
-	    <parameter name="relativeDeathRate" idref="relativeDeathRate"/>
-    </input>
-
-    <!-- site model                                                              -->
-    <input spec="beast.base.spec.evolution.sitemodel.SiteModel" id="siteModel" gammaCategoryCount="1">
-	<substModel spec="beast.base.spec.evolution.substitutionmodel.HKY" id="hky">
-	    <kappa id="hky.kappa" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-	    <frequencies id="freqs" spec="beast.base.spec.evolution.substitutionmodel.Frequencies">
-	       <data idref="alignment"/>
-	    </frequencies>
-	</substModel>
-    </input>
-
-    <parameter id="birthRate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-    <parameter id="relativeDeathRate" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
-
-    <!-- initial yule prior = -6.0, yule-like prior = -2.8219461696520542 -->
-    <!-- expected yule prior = 1/(n.lambda)\sum_{k=1}^{n-1}k/(n-k) where lambda = birth rate, n = number of taxa
-	with lambda=1, n=-4 we expect 1/4(1/3+2/2+3/1)=1.155555555
- -->
-    <run spec="MCMC" chainLength="10">
-	<state>
-	    <stateNode idref="tree"/>
-	    <stateNode idref="birthRate"/>
-	    <stateNode id="tree-test-single-child-parsing" IsLabelledNewick="true" spec="beast.base.evolution.tree.TreeParser" singlechild="true" newick="((A:1.0):2,C:3);">
-			<taxonset spec="beast.base.evolution.alignment.TaxonSet">
-				<taxon spec="beast.base.evolution.alignment.Taxon" id="A"/>
-				<taxon spec="beast.base.evolution.alignment.Taxon" id="C"/>
-			</taxonset>
-		</stateNode>
-	</state>
-
-	<distribution spec="CompoundDistribution">
-	        <distribution id="yule.prior" idref="yule"/>
-<!--
-		<distribution spec='TreeLikelihood' id="treeLikelihood" data='@alignment' tree='@tree' siteModel='@siteModel'/>
--->
-	        <distribution id="yulelike.prior" idref="yulelike"/>
-	</distribution>
-
-        <operator spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" weight="5" size="1.0" tree="@tree"/>
-<!--
-        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" tree="@tree"/>
--->
-        <operator weight="10" tree="@tree" spec="beast.base.evolution.operator.Uniform"/>
-        <operator id="narrow" spec="Exchange" isNarrow="true" weight="1" tree="@tree"/>
-        <operator id="wide" spec="Exchange" isNarrow="false" weight="1" tree="@tree"/>
-        <operator spec="WilsonBalding" weight="1" tree="@tree"/>
-<!--
-        <operator spec='ScaleOperator' scaleFactor="0.75" weight="3">
-            <parameter idref="birthRate"/>
-        </operator>
--->
-	<logger logEvery="100">
-	    <log idref="yule.prior"/>
-	    <!--log idref='treeLikelihood'/-->
-	    <log idref="yulelike.prior"/>
-            <log spec="beast.base.evolution.tree.TreeStatLogger" tree="@tree"/>
-	</logger>
-	<logger logEvery="100" fileName="$(seed).log">
-	    <log idref="yule.prior"/>
-	    <!--log idref='treeLikelihood'/-->
-	    <!--log idref='yulelike.prior'/-->
-            <log spec="beast.base.evolution.tree.TreeStatLogger" tree="@tree"/>
-	</logger>
-    </run>
-
-</beast>
diff --git a/beast-base/src/test/resources/beast.base/examples/testGTR.xml b/beast-base/src/test/resources/beast.base/examples/testGTR.xml
index c39a57d2..50899ee6 100644
--- a/beast-base/src/test/resources/beast.base/examples/testGTR.xml
+++ b/beast-base/src/test/resources/beast.base/examples/testGTR.xml
@@ -1,155 +1,103 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<beast beautitemplate='Standard' beautistatus=''
-       namespace="beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.alignment:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood"
-       version="2.0">
-
+<?xml version='1.0' encoding='UTF-8'?>
+<beast version="2.8"
+       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt"
+       beautitemplate="Standard"
+       beautistatus="">
 
     <data id="primate-mtDNA">
-        <sequence id="seq_Lemur_catta" taxon="Lemur_catta" totalcount="4"
-                  value="AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATTCTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGGGATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCTAGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTCATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTCCCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAACCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATTTACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAACACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATGTATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGATAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTATAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTGCATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAACAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT"/>
-        <sequence id="seq_Homo_sapiens" taxon="Homo_sapiens" totalcount="4"
-                  value="AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
-        <sequence id="seq_Pan" taxon="Pan" totalcount="4"
-                  value="AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATTCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCTCGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAAGCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TATAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCACCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCGCGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAGCTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
-        <sequence id="seq_Gorilla" taxon="Gorilla" totalcount="4"
-                  value="AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGGACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCTCGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTCCTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTCCCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAAACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCTATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CGTAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTACCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCGCATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAGCTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT"/>
-        <sequence id="seq_Pongo" taxon="Pongo" totalcount="4"
-                  value="AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGGCCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCTTGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTCTTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTCTCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAAACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTTATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAACATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGATAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAACAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCGCTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCGCATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAACCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT"/>
-        <sequence id="seq_Hylobates" taxon="Hylobates" totalcount="4"
-                  value="AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATTCTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGGGCTCCAAGCCTTACTCCCACTGATAGCCTTCTGATGACTCGCAGCAAGCCTCGCTAACCTCGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTCCTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTCCCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAAACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCTAACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAACATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CACAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAGCCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTGCCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAACCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT"/>
-        <sequence id="seq_Macaca_fuscata" taxon="Macaca_fuscata" totalcount="4"
-                  value="AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGGACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTCCTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTCTCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAAGCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAACACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT"/>
-        <sequence id="seq_M._mulatta" taxon="M._mulatta" totalcount="4"
-                  value="AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGGACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTCCTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTCCCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCTATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAACATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CGCGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT"/>
-        <sequence id="seq_M._fascicularis" taxon="M._fascicularis" totalcount="4"
-                  value="AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTTCTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGTACCATACTACTATCCCGAGGACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTCCTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTCTCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAACATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTGCCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAATATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAACAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT"/>
-        <sequence id="seq_M._sylvanus" taxon="M._sylvanus" totalcount="4"
-                  value="AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTTCTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGCATCATACTACTATCCCGAGGACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCTTGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTCCTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTCTCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAAACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCTATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAACATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TGCAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCGCTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAATATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAACAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT"/>
-        <sequence id="seq_Saimiri_sciureus" taxon="Saimiri_sciureus" totalcount="4"
-                  value="AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTCTATGCTATTCTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAATAACATTTACTCGAGGGCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCTCGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTCTTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTCACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAAACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCTTACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAACATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CGCAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGATAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAATA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAGCTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCATCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAATCAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT"/>
-        <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4"
-                  value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
+        <sequence id="seq_Lemur_catta" taxon="Lemur_catta" totalcount="4" value="AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATTCTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGGGATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCTAGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTCATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTCCCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAACCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATTTACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAACACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATGTATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGATAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTATAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTGCATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAACAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT"/>
+        <sequence id="seq_Homo_sapiens" taxon="Homo_sapiens" totalcount="4" value="AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
+        <sequence id="seq_Pan" taxon="Pan" totalcount="4" value="AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATTCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCTCGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAAGCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TATAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCACCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCGCGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAGCTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
+        <sequence id="seq_Gorilla" taxon="Gorilla" totalcount="4" value="AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGGACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCTCGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTCCTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTCCCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAAACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCTATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CGTAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTACCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCGCATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAGCTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT"/>
+        <sequence id="seq_Pongo" taxon="Pongo" totalcount="4" value="AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGGCCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCTTGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTCTTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTCTCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAAACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTTATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAACATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGATAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAACAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCGCTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCGCATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAACCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT"/>
+        <sequence id="seq_Hylobates" taxon="Hylobates" totalcount="4" value="AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATTCTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGGGCTCCAAGCCTTACTCCCACTGATAGCCTTCTGATGACTCGCAGCAAGCCTCGCTAACCTCGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTCCTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTCCCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAAACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCTAACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAACATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CACAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAGCCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTGCCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAACCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT"/>
+        <sequence id="seq_Macaca_fuscata" taxon="Macaca_fuscata" totalcount="4" value="AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGGACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTCCTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTCTCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAAGCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAACACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT"/>
+        <sequence id="seq_M._mulatta" taxon="M._mulatta" totalcount="4" value="AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGGACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTCCTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTCCCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCTATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAACATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CGCGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT"/>
+        <sequence id="seq_M._fascicularis" taxon="M._fascicularis" totalcount="4" value="AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTTCTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGTACCATACTACTATCCCGAGGACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTCCTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTCTCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAACATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTGCCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAATATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAACAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT"/>
+        <sequence id="seq_M._sylvanus" taxon="M._sylvanus" totalcount="4" value="AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTTCTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGCATCATACTACTATCCCGAGGACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCTTGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTCCTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTCTCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAAACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCTATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAACATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TGCAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCGCTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAATATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAACAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT"/>
+        <sequence id="seq_Saimiri_sciureus" taxon="Saimiri_sciureus" totalcount="4" value="AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTCTATGCTATTCTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAATAACATTTACTCGAGGGCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCTCGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTCTTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTCACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAAACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCTTACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAACATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CGCAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGATAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAATA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAGCTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCATCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAATCAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT"/>
+        <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4" value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
     </data>
 
-
-    <map name="Beta">beast.base.inference.distribution.Beta</map>
-    <map name="Exponential">beast.base.inference.distribution.Exponential</map>
-    <map name="InverseGamma">beast.base.inference.distribution.InverseGamma</map>
-    <map name="LogNormal">beast.base.inference.distribution.LogNormalDistributionModel</map>
-    <map name="Gamma">beast.base.inference.distribution.Gamma</map>
-    <map name="Uniform">beast.base.inference.distribution.Uniform</map>
-    <map name="prior">beast.base.inference.distribution.Prior</map>
-    <map name="LaplaceDistribution">beast.base.inference.distribution.LaplaceDistribution</map>
-    <map name="OneOnX">beast.base.inference.distribution.OneOnX</map>
-    <map name="Normal">beast.base.inference.distribution.Normal</map>
-
-
     <run chainLength="5000000" id="mcmc" spec="MCMC">
         <state id="state" storeEvery="5000">
             <tree id="Tree.t:primate" name="stateNode">
                 <taxonset id="TaxonSet.coding" spec="TaxonSet">
-                    <alignment filter="2-457,660-896" id="coding" spec="FilteredAlignment">
+                    <alignment filter="2-457,660-896" id="coding" spec="beast.base.spec.evolution.alignment.FilteredAlignment">
                         <data idref="primate-mtDNA"/>
                     </alignment>
                 </taxonset>
             </tree>
-            <parameter id="birthRate.t:primate" name="stateNode" value="1.0"/>
-            <parameter id="rateAC.s:primate" lower="0.0" name="stateNode" value="1.0"/>
-            <parameter id="rateAG.s:primate" lower="0.0" name="stateNode" value="1.0"/>
-            <parameter id="rateAT.s:primate" lower="0.0" name="stateNode" value="1.0"/>
-            <parameter id="rateCG.s:primate" lower="0.0" name="stateNode" value="1.0"/>
-            <parameter id="rateGT.s:primate" lower="0.0" name="stateNode" value="1.0"/>
-            <parameter dimension="4" id="freqParameter.s:primate" lower="0.0" name="stateNode" upper="1.0"
-                       value="0.25"/>
+            <parameter id="birthRate.t:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+            <parameter id="rateAC.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+            <parameter id="rateAG.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+            <parameter id="rateAT.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+            <parameter id="rateCG.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+            <parameter id="rateGT.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+            <parameter dimension="4" id="freqParameter.s:primate" name="stateNode" value="0.25" spec="beast.base.spec.inference.parameter.SimplexParam"/>
         </state>
 
-        <init estimate="false" id="RandomTree.t:primate" initial="@Tree.t:primate"
-              spec="beast.base.evolution.tree.coalescent.RandomTree" taxa="@coding">
-            <populationModel id="ConstantPopulation0.t:primate" spec="ConstantPopulation">
-                <parameter id="randomPopSize.t:primate" name="popSize" value="1"/>
+        <init estimate="false" id="RandomTree.t:primate" initial="@Tree.t:primate" spec="beast.base.spec.evolution.tree.coalescent.RandomTree" taxa="@coding">
+            <populationModel id="ConstantPopulation0.t:primate" spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
+                <parameter id="randomPopSize.t:primate" name="popSize" value="1" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
             </populationModel>
         </init>
 
         <distribution id="posterior" spec="CompoundDistribution">
             <distribution id="prior" spec="CompoundDistribution">
-                <distribution birthDiffRate="@birthRate.t:primate" id="YuleModel.t:primate"
-                              spec="beast.base.evolution.speciation.YuleModel" tree="@Tree.t:primate"/>
-                <prior id="YuleBirthRatePrior.t:primate" name="distribution" x="@birthRate.t:primate">
-                    <Uniform id="Uniform.0" name="distr" upper="Infinity"/>
-                </prior>
-                <prior id="RateACPrior.s:primate" name="distribution" x="@rateAC.s:primate">
-                    <LogNormal id="LogNormalDistributionModel.0" name="distr">
-                        <parameter estimate="false" id="RealParameter.0" name="M" value="0"/>
-                        <parameter estimate="false" id="RealParameter.01" lower="0.0" name="S" upper="5.0"
-                                   value="1.25"/>
-                    </LogNormal>
-                </prior>
-                <prior id="RateAGPrior.s:primate" name="distribution" x="@rateAG.s:primate">
-                    <LogNormal id="LogNormalDistributionModel.01" name="distr">
-                        <parameter estimate="false" id="RealParameter.02" name="M" value="0"/>
-                        <parameter estimate="false" id="RealParameter.03" lower="0.0" name="S" upper="5.0"
-                                   value="1.25"/>
-                    </LogNormal>
-                </prior>
-                <prior id="RateATPrior.s:primate" name="distribution" x="@rateAT.s:primate">
-                    <LogNormal id="LogNormalDistributionModel.02" name="distr">
-                        <parameter estimate="false" id="RealParameter.04" name="M" value="0"/>
-                        <parameter estimate="false" id="RealParameter.05" lower="0.0" name="S" upper="5.0"
-                                   value="1.25"/>
-                    </LogNormal>
-                </prior>
-                <prior id="RateCGPrior.s:primate" name="distribution" x="@rateCG.s:primate">
-                    <LogNormal id="LogNormalDistributionModel.03" name="distr">
-                        <parameter estimate="false" id="RealParameter.06" name="M" value="0"/>
-                        <parameter estimate="false" id="RealParameter.07" lower="0.0" name="S" upper="5.0"
-                                   value="1.25"/>
-                    </LogNormal>
-                </prior>
-                <prior id="RateGTPrior.s:primate" name="distribution" x="@rateGT.s:primate">
-                    <LogNormal id="LogNormalDistributionModel.04" name="distr">
-                        <parameter estimate="false" id="RealParameter.08" name="M" value="0"/>
-                        <parameter estimate="false" id="RealParameter.09" lower="0.0" name="S" upper="5.0"
-                                   value="1.25"/>
-                    </LogNormal>
-                </prior>
+                <distribution birthDiffRate="@birthRate.t:primate" id="YuleModel.t:primate" spec="beast.base.spec.evolution.speciation.YuleModel" tree="@Tree.t:primate"/>
+                <distribution id="Uniform.0" spec="beast.base.spec.inference.distribution.Uniform" param="@birthRate.t:primate" upper="1.0E6"/>
+                <distribution id="LogNormalDistributionModel.0" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateAC.s:primate">
+                        <parameter estimate="false" id="RealParameter.0" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="RealParameter.01" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                    </distribution>
+                <distribution id="LogNormalDistributionModel.01" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateAG.s:primate">
+                        <parameter estimate="false" id="RealParameter.02" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="RealParameter.03" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                    </distribution>
+                <distribution id="LogNormalDistributionModel.02" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateAT.s:primate">
+                        <parameter estimate="false" id="RealParameter.04" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="RealParameter.05" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                    </distribution>
+                <distribution id="LogNormalDistributionModel.03" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateCG.s:primate">
+                        <parameter estimate="false" id="RealParameter.06" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="RealParameter.07" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                    </distribution>
+                <distribution id="LogNormalDistributionModel.04" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateGT.s:primate">
+                        <parameter estimate="false" id="RealParameter.08" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="RealParameter.09" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                    </distribution>
             </distribution>
             <distribution id="likelihood" spec="CompoundDistribution">
-                <distribution data="@coding" id="treeLikelihood.coding" spec="TreeLikelihood" tree="@Tree.t:primate">
-                    <siteModel id="SiteModel.s:primate" spec="SiteModel">
-                        <parameter estimate="false" id="mutationRate.s:primate" name="mutationRate" value="1.0"/>
-                        <parameter estimate="false" id="gammaShape.s:primate" name="shape" value="1.0"/>
-                        <parameter estimate="false" id="proportionInvariant.s:primate" lower="0.0"
-                                   name="proportionInvariant" upper="1.0" value="0.0"/>
-                        <substModel id="gtr.s:primate" rateAC="@rateAC.s:primate" rateAG="@rateAG.s:primate"
-                                    rateAT="@rateAT.s:primate" rateCG="@rateCG.s:primate" rateGT="@rateGT.s:primate"
-                                    spec="GTR">
-                            <parameter estimate="false" id="rateCT.s:primate" lower="0.0" name="rateCT" value="1.0"/>
-                            <frequencies frequencies="@freqParameter.s:primate" id="estimatedFreqs.s:primate"
-                                         spec="Frequencies"/>
+                <distribution data="@coding" id="treeLikelihood.coding" spec="beast.base.spec.evolution.likelihood.TreeLikelihood" tree="@Tree.t:primate">
+                    <siteModel id="SiteModel.s:primate" spec="beast.base.spec.evolution.sitemodel.SiteModel">
+                        <parameter estimate="false" id="mutationRate.s:primate" name="mutationRate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="gammaShape.s:primate" name="shape" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="proportionInvariant.s:primate" name="proportionInvariant" value="0.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="UnitInterval"/>
+                        <substModel id="gtr.s:primate" rateAC="@rateAC.s:primate" rateAG="@rateAG.s:primate" rateAT="@rateAT.s:primate" rateCG="@rateCG.s:primate" rateGT="@rateGT.s:primate" spec="beast.base.spec.evolution.substitutionmodel.GTR">
+                            <parameter estimate="false" id="rateCT.s:primate" name="rateCT" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+                            <frequencies frequencies="@freqParameter.s:primate" id="estimatedFreqs.s:primate" spec="beast.base.spec.evolution.substitutionmodel.Frequencies"/>
                         </substModel>
                     </siteModel>
-                    <branchRateModel id="StrictClock.c:primate" spec="beast.base.evolution.branchratemodel.StrictClockModel">
-                        <parameter estimate="false" id="clockRate.c:primate" name="clock.rate" value="1.0"/>
+                    <branchRateModel id="StrictClock.c:primate" spec="beast.base.spec.evolution.branchratemodel.StrictClockModel">
+                        <parameter estimate="false" id="clockRate.c:primate" name="clock.rate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
                     </branchRateModel>
                 </distribution>
-                <distribution branchRateModel="@StrictClock.c:primate" id="treeLikelihood.noncoding"
-                              siteModel="@SiteModel.s:primate" spec="TreeLikelihood" tree="@Tree.t:primate">
-                    <data data="@primate-mtDNA" filter="1,458-659,897-898" id="noncoding" spec="FilteredAlignment"/>
+                <distribution branchRateModel="@StrictClock.c:primate" id="treeLikelihood.noncoding" siteModel="@SiteModel.s:primate" spec="beast.base.spec.evolution.likelihood.TreeLikelihood" tree="@Tree.t:primate">
+                    <data data="@primate-mtDNA" filter="1,458-659,897-898" id="noncoding" spec="beast.base.spec.evolution.alignment.FilteredAlignment"/>
                 </distribution>
             </distribution>
         </distribution>
 
-        <operator id="YuleBirthRateScaler.t:primate" parameter="@birthRate.t:primate" scaleFactor="0.75"
-                  spec="ScaleOperator" weight="3.0"/>
+        <operator id="YuleBirthRateScaler.t:primate" parameter="@birthRate.t:primate" scaleFactor="0.75" weight="3.0" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator id="treeScaler.t:primate" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:primate" weight="3.0"/>
+        <operator id="treeScaler.t:primate" scaleFactor="0.5" tree="@Tree.t:primate" weight="3.0" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
 
-        <operator id="treeRootScaler.t:primate" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator"
-                  tree="@Tree.t:primate" weight="3.0"/>
+        <operator id="treeRootScaler.t:primate" rootOnly="true" scaleFactor="0.5" tree="@Tree.t:primate" weight="3.0" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
 
-        <operator id="UniformOperator.t:primate" spec="Uniform" tree="@Tree.t:primate" weight="30.0"/>
+        <operator id="UniformOperator.t:primate" tree="@Tree.t:primate" weight="30.0" spec="beast.base.evolution.operator.Uniform"/>
 
-        <operator id="SubtreeSlide.t:primate" spec="SubtreeSlide" tree="@Tree.t:primate" weight="15.0"/>
+        <operator id="SubtreeSlide.t:primate" spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" tree="@Tree.t:primate" weight="15.0"/>
 
         <operator id="narrow.t:primate" spec="Exchange" tree="@Tree.t:primate" weight="15.0"/>
 
@@ -157,27 +105,21 @@
 
         <operator id="WilsonBalding.t:primate" spec="WilsonBalding" tree="@Tree.t:primate" weight="3.0"/>
 
-        <operator id="RateACScaler.s:primate" parameter="@rateAC.s:primate" scaleFactor="0.5" spec="ScaleOperator"
-                  weight="0.1"/>
+        <operator id="RateACScaler.s:primate" parameter="@rateAC.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator id="RateAGScaler.s:primate" parameter="@rateAG.s:primate" scaleFactor="0.5" spec="ScaleOperator"
-                  weight="0.1"/>
+        <operator id="RateAGScaler.s:primate" parameter="@rateAG.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator id="RateATScaler.s:primate" parameter="@rateAT.s:primate" scaleFactor="0.5" spec="ScaleOperator"
-                  weight="0.1"/>
+        <operator id="RateATScaler.s:primate" parameter="@rateAT.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator id="RateCGScaler.s:primate" parameter="@rateCG.s:primate" scaleFactor="0.5" spec="ScaleOperator"
-                  weight="0.1"/>
+        <operator id="RateCGScaler.s:primate" parameter="@rateCG.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator id="RateGTScaler.s:primate" parameter="@rateGT.s:primate" scaleFactor="0.5" spec="ScaleOperator"
-                  weight="0.1"/>
+        <operator id="RateGTScaler.s:primate" parameter="@rateGT.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator delta="0.01" id="FrequenciesExchanger.s:primate" spec="DeltaExchangeOperator" weight="0.1">
+        <operator delta="0.01" id="FrequenciesExchanger.s:primate" spec="beast.base.spec.inference.operator.DeltaExchangeOperator" weight="0.1">
             <parameter idref="freqParameter.s:primate"/>
         </operator>
 
-        <logger fileName="primate-mtDNA.log" id="tracelog" logEvery="5000" model="@posterior" sanitiseHeaders="true"
-                sort="smart">
+        <logger fileName="primate-mtDNA.log" id="tracelog" logEvery="5000" model="@posterior" sanitiseHeaders="true" sort="smart">
             <log idref="posterior"/>
             <log idref="likelihood"/>
             <log idref="prior"/>
@@ -196,14 +138,13 @@
 
         <logger id="screenlog" logEvery="5000">
             <log idref="posterior"/>
-            <log arg="@posterior" id="ESS.0" spec="util.ESS"/>
+            <log arg="@posterior" id="ESS.0" spec="beast.base.spec.inference.util.ESS"/>
             <log idref="likelihood"/>
             <log idref="prior"/>
         </logger>
 
         <logger fileName="$(tree).trees" id="treelog.t:primate" logEvery="5000" mode="tree">
-            <log id="TreeWithMetaDataLogger.t:primate" spec="beast.base.evolution.TreeWithMetaDataLogger"
-                 tree="@Tree.t:primate"/>
+            <log id="TreeWithMetaDataLogger.t:primate" spec="beast.base.spec.evolution.TreeWithMetaDataLogger" tree="@Tree.t:primate"/>
         </logger>
 
     </run>
diff --git a/beast-base/src/test/resources/beast.base/examples/testHKY.json b/beast-base/src/test/resources/beast.base/examples/testHKY.json
index 12172ffa..80d6b121 100644
--- a/beast-base/src/test/resources/beast.base/examples/testHKY.json
+++ b/beast-base/src/test/resources/beast.base/examples/testHKY.json
@@ -1,86 +1,85 @@
-{version: "2.7",
-namespace: "beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.alignment:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood",
-
-// this is a comment, which is non-standard JSON
-// only commenst after double slashes are supported
-// but /* bla */ comments are not
-
-map: [
-	{name: "stateNode", value: "parameter.RealParameter"}
-],
+{version: "2.8",
+namespace: "beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt",
 
 beast: [
-	{id: "alignment",
-	 spec: "Alignment",
-	 sequence: [
-		 {spec: "Sequence", totalcount: 4, taxon: "human", value: "\n AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCCTTATTTCTACTAGGACTATGAGAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTG-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCGGAGCTTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGGCCTCCATGACTTTTTCAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAATTATAGGCT-AAATCCTATATATCTTA-CACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACACCTCTTTACAGTGA\n " },
-		 {spec: "Sequence", totalcount: 4, taxon: "chimp", value: "\n AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTCAAATCCCCTTATTTCTACTAGGACTATAAGAATCGAACTCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTAAGCACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCTCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AACCCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCGACACCTCTTTACAGTGA\n " },
-		 {spec: "Sequence", totalcount: 4, taxon: "bonobo", value: "\n AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTTAAATCCCCTTATTTCTACTAGGACTATGAGAGTCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCTCTCAGTAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAGC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTTGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCCCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCAACACCTCTTTACAGTGA\n " },
-		 {spec: "Sequence", totalcount: 4, taxon: "gorilla", value: "\n AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGAGGTTTAAACCCCCTTATTTCTACTAGGACTATGAGAATTGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTGTCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTCACATCCTTCCCGTACTAAGAAATTTAGGTTAAACATAGACCAAGAGCCTTCAAAGCCCTTAGTAAGTTA-CAACACTTAATTTCTGTAAGGACTGCAAAACCCTACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCAATGGGACTCAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAT-TCACCTCGGAGCTTGGTAAAAAGAGGCCCAGCCTCTGTCTTTAGATTTACAGTCCAATGCCTTA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGACCTTCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAGGTTAAATTACGGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCGTTAACCTTTTAAGTTAAAGATTAAGAGTATCGGCACCTCTTTGCAGTGA\n " },
-		 {spec: "Sequence", totalcount: 4, taxon: "orangutan", value: "\n AGAAATATGTCTGACAAAAGAGTTACTTTGATAGAGTAAAAAATAGAGGTCTAAATCCCCTTATTTCTACTAGGACTATGGGAATTGAACCCACCCCTGAGAATCCAAAATTCTCCGTGCCACCCATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTA--CACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTCA-CAGCACTTAATTTCTGTAAGGACTGCAAAACCCCACTTTGCATCAACTGAGCGCAAATCAGCCACTTTAATTAAGCTAAGCCCTCCTAGACCGATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAT-TGGCTTCAGTCCAAAGCCCCGGCAGGCCTTAAAGCTGCTCCTTCGAATTTGCAATTCAACATGACAA-TCACCTCAGGGCTTGGTAAAAAGAGGTCTGACCCCTGTTCTTAGATTTACAGCCTAATGCCTTAACTCGGCCATTTTACCGCAAAAAAGGAAGGAATCGAACCTCCTAAAGCTGGTTTCAAGCCAACCCCATAACCCCCATGACTTTTTCAAAAGGTACTAGAAAAACCATTTCGTAACTTTGTCAAAGTTAAATTACAGGTC-AGACCCTGTGTATCTTA-CATTGCAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACCAGCCTCTCTTTGCAATGA\n " },
-		 {spec: "Sequence", totalcount: 4, taxon: "siamang", value: "\n AGAAATACGTCTGACGAAAGAGTTACTTTGATAGAGTAAATAACAGGGGTTTAAATCCCCTTATTTCTACTAGAACCATAGGAGTCGAACCCATCCTTGAGAATCCAAAACTCTCCGTGCCACCCGTCGCACCCTGTTCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCATACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTAACAAAACTTAATTTCTGCAAGGGCTGCAAAACCCTACTTTGCATCAACCGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCGATGGGACTTAAACCCATAAAAATTTAGTTAACAGCTAAACACCCTAAACAACCTGGCTTCAATCTAAAGCCCCGGCAGA-GTTGAAGCTGCTTCTTTGAACTTGCAATTCAACGTGAAAAATCACTTCGGAGCTTGGCAAAAAGAGGTTTCACCTCTGTCCTTAGATTTACAGTCTAATGCTTTA-CTCAGCCACTTTACCACAAAAAAGGAAGGAATCGAACCCTCTAAAACCGGTTTCAAGCCAGCCCCATAACCTTTATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATCACAGGTCCAAACCCCGTATATCTTATCACTGTAGAGCTAGACCAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACTACCGCCTCTTTACAGTGA\n " }
-	  ]
-	},
+    {id: "alignment",
+     spec: "Alignment",
+     dataType: "nucleotide",
+     sequence: [
+         {spec: "Sequence", taxon: "human", value: "\n AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCCTTATTTCTACTAGGACTATGAGAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTG-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCGGAGCTTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGGCCTCCATGACTTTTTCAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAATTATAGGCT-AAATCCTATATATCTTA-CACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACACCTCTTTACAGTGA\n " },
+         {spec: "Sequence", taxon: "chimp", value: "\n AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTCAAATCCCCTTATTTCTACTAGGACTATAAGAATCGAACTCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTAAGCACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCTCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AACCCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCGACACCTCTTTACAGTGA\n " },
+         {spec: "Sequence", taxon: "bonobo", value: "\n AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTTAAATCCCCTTATTTCTACTAGGACTATGAGAGTCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCTCTCAGTAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAGC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTTGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCCCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCAACACCTCTTTACAGTGA\n " },
+         {spec: "Sequence", taxon: "gorilla", value: "\n AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGAGGTTTAAACCCCCTTATTTCTACTAGGACTATGAGAATTGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTGTCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTCACATCCTTCCCGTACTAAGAAATTTAGGTTAAACATAGACCAAGAGCCTTCAAAGCCCTTAGTAAGTTA-CAACACTTAATTTCTGTAAGGACTGCAAAACCCTACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCAATGGGACTCAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAT-TCACCTCGGAGCTTGGTAAAAAGAGGCCCAGCCTCTGTCTTTAGATTTACAGTCCAATGCCTTA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGACCTTCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAGGTTAAATTACGGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCGTTAACCTTTTAAGTTAAAGATTAAGAGTATCGGCACCTCTTTGCAGTGA\n " },
+         {spec: "Sequence", taxon: "orangutan", value: "\n AGAAATATGTCTGACAAAAGAGTTACTTTGATAGAGTAAAAAATAGAGGTCTAAATCCCCTTATTTCTACTAGGACTATGGGAATTGAACCCACCCCTGAGAATCCAAAATTCTCCGTGCCACCCATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTA--CACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTCA-CAGCACTTAATTTCTGTAAGGACTGCAAAACCCCACTTTGCATCAACTGAGCGCAAATCAGCCACTTTAATTAAGCTAAGCCCTCCTAGACCGATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAT-TGGCTTCAGTCCAAAGCCCCGGCAGGCCTTAAAGCTGCTCCTTCGAATTTGCAATTCAACATGACAA-TCACCTCAGGGCTTGGTAAAAAGAGGTCTGACCCCTGTTCTTAGATTTACAGCCTAATGCCTTAACTCGGCCATTTTACCGCAAAAAAGGAAGGAATCGAACCTCCTAAAGCTGGTTTCAAGCCAACCCCATAACCCCCATGACTTTTTCAAAAGGTACTAGAAAAACCATTTCGTAACTTTGTCAAAGTTAAATTACAGGTC-AGACCCTGTGTATCTTA-CATTGCAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACCAGCCTCTCTTTGCAATGA\n " },
+         {spec: "Sequence", taxon: "siamang", value: "\n AGAAATACGTCTGACGAAAGAGTTACTTTGATAGAGTAAATAACAGGGGTTTAAATCCCCTTATTTCTACTAGAACCATAGGAGTCGAACCCATCCTTGAGAATCCAAAACTCTCCGTGCCACCCGTCGCACCCTGTTCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCATACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTAACAAAACTTAATTTCTGCAAGGGCTGCAAAACCCTACTTTGCATCAACCGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCGATGGGACTTAAACCCATAAAAATTTAGTTAACAGCTAAACACCCTAAACAACCTGGCTTCAATCTAAAGCCCCGGCAGA-GTTGAAGCTGCTTCTTTGAACTTGCAATTCAACGTGAAAAATCACTTCGGAGCTTGGCAAAAAGAGGTTTCACCTCTGTCCTTAGATTTACAGTCTAATGCTTTA-CTCAGCCACTTTACCACAAAAAAGGAAGGAATCGAACCCTCTAAAACCGGTTTCAAGCCAGCCCCATAACCTTTATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATCACAGGTCCAAACCCCGTATATCTTATCACTGTAGAGCTAGACCAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACTACCGCCTCTTTACAGTGA\n " }
+      ]
+    },
 
-	{id: "mcmc",
-	 spec: "MCMC", chainLength: "5000000", preBurnin: 50000,
-	 init: [
-		{id: "coalescentSimulator",
-		 spec: "beast.base.evolution.tree.coalescent.RandomTree", taxa: "@alignment",
-			 populationModel: {spec: "ConstantPopulation", popSize: "1.0" },
-			 initial: {id: "tree", spec: "beast.base.evolution.tree.Tree" }
-		}
-	  ],
-	 distribution: {id: "posterior",
-		 spec: "CompoundDistribution",
-		 distribution: [
-			{spec: "beast.base.inference.distribution.Prior",
-				 x: {id: "hky.kappa", spec: "parameter.RealParameter", lower: 0.0, value: [ 1.0 ] },
-				 distr: {spec: "beast.base.inference.distribution.OneOnX" }
-			},
-			{id: "treeLikelihood",
-			 spec: "TreeLikelihood", data: "@alignment", tree: "@tree",
-			 siteModel: {id: "siteModel",
-				 spec: "SiteModel", gammaCategoryCount: 1,
-				 substModel: {id: "hky",
-					 spec: "HKY", kappa: "@hky.kappa",
-						 frequencies: {id: "freqs", spec: "Frequencies", data: "@alignment" }
-					}
-				}
-			}
-		  ]
-		},
-	 operator: [
-		 {id: "kappaScaler", spec: "ScaleOperator", parameter: "@hky.kappa", scaleFactor: 0.5, weight: 1.0 },
-		 {id: "treeScaler", spec: "ScaleOperator", tree: "@tree", scaleFactor: 0.5, weight: 1.0 },
-		 {id: "subtreeSlide", spec: "SubtreeSlide", tree: "@tree", weight: 5.0 },
-		 {id: "uniform", spec: "Uniform", tree: "@tree", weight: 10.0 },
-		 {id: "narrow", spec: "Exchange", tree: "@tree", weight: 1.0 },
-		 {id: "wide", spec: "Exchange", isNarrow: false, tree: "@tree", weight: 1.0 },
-		 {id: "wilsonBalding", spec: "WilsonBalding", tree: "@tree", weight: 1.0 }
-	  ],
-	 logger: [
-		{spec: "Logger", fileName: "test.$(seed).log", logEvery: 10000, model: "@treeLikelihood",
-		 log: [
-			 {idref: "treeLikelihood" },
-			 {idref: "hky.kappa" },
-			 {spec: "beast.base.evolution.tree.TreeStatLogger", tree: "@tree" }
-		  ]
-		},
-		{spec: "Logger", fileName: "test.$(seed).trees", logEvery: 10000,
-		 log: [
-			 {idref: "tree" }
-		  ]
-		},
-		{spec: "Logger", logEvery: 10000, model: "@treeLikelihood",
-		 log: [
-			 {idref: "treeLikelihood" },
-			 {spec: "beast.base.inference.util.ESS", arg: "@treeLikelihood" },
-			 {idref: "hky.kappa" },
-			 {spec: "beast.base.inference.util.ESS", arg: "@hky.kappa" }
-		  ]
-		}
-	  ]
-	}
+    {id: "mcmc",
+     spec: "MCMC", chainLength: "5000000", preBurnin: 50000,
+     init: [
+        {id: "coalescentSimulator",
+         spec: "beast.base.spec.evolution.tree.coalescent.RandomTree",
+         taxa: "@alignment",
+         populationModel: {spec: "beast.base.spec.evolution.tree.coalescent.ConstantPopulation",
+             popSize: {spec: "beast.base.spec.inference.parameter.RealScalarParam", domain: "Real", value: "1"}
+         },
+         initial: {id: "tree", spec: "beast.base.evolution.tree.Tree"}
+        }
+      ],
+     distribution: {id: "posterior",
+         spec: "CompoundDistribution",
+         distribution: [
+            {spec: "beast.base.spec.inference.distribution.LogNormal",
+                 param: {id: "hky.kappa", spec: "beast.base.spec.inference.parameter.RealScalarParam", domain: "PositiveReal", value: "1.0"},
+                 M: {spec: "beast.base.spec.inference.parameter.RealScalarParam", domain: "Real", value: "1.0"},
+                 S: {spec: "beast.base.spec.inference.parameter.RealScalarParam", domain: "PositiveReal", value: "0.5"}
+            },
+            {id: "treeLikelihood",
+             spec: "beast.base.spec.evolution.likelihood.TreeLikelihood",
+             data: "@alignment", tree: "@tree",
+             siteModel: {id: "siteModel",
+                 spec: "beast.base.spec.evolution.sitemodel.SiteModel", gammaCategoryCount: 1,
+                 substModel: {id: "hky",
+                     spec: "beast.base.spec.evolution.substitutionmodel.HKY", kappa: "@hky.kappa",
+                     frequencies: {id: "freqs",
+                         spec: "beast.base.spec.evolution.substitutionmodel.Frequencies",
+                         data: "@alignment"
+                     }
+                 }
+             }
+            }
+          ]
+        },
+     operator: [
+         {id: "kappaScaler", spec: "beast.base.spec.inference.operator.ScaleOperator", parameter: "@hky.kappa", scaleFactor: 0.5, weight: 1.0},
+         {id: "treeScaler", spec: "beast.base.spec.evolution.operator.ScaleTreeOperator", tree: "@tree", scaleFactor: 0.5, weight: 1.0},
+         {id: "subtreeSlide", spec: "beast.base.evolution.operator.kernel.BactrianSubtreeSlide", tree: "@tree", weight: 5.0, size: 1.0},
+         {id: "uniform", spec: "beast.base.evolution.operator.Uniform", tree: "@tree", weight: 10.0},
+         {id: "narrow", spec: "Exchange", isNarrow: true, tree: "@tree", weight: 1.0},
+         {id: "wide", spec: "Exchange", isNarrow: false, tree: "@tree", weight: 1.0},
+         {id: "wilsonBalding", spec: "WilsonBalding", tree: "@tree", weight: 1.0}
+      ],
+     logger: [
+        {spec: "Logger", fileName: "test.$(seed).log", logEvery: 10000, model: "@treeLikelihood",
+         log: [
+             {idref: "treeLikelihood"},
+             {idref: "hky.kappa"},
+             {spec: "beast.base.evolution.tree.TreeStatLogger", tree: "@tree"}
+          ]
+        },
+        {spec: "Logger", fileName: "test.$(seed).trees", logEvery: 10000,
+         log: [{idref: "tree"}]
+        },
+        {spec: "Logger", logEvery: 10000, model: "@treeLikelihood",
+         log: [
+             {idref: "treeLikelihood"},
+             {spec: "beast.base.spec.inference.util.ESS", arg: "@treeLikelihood"},
+             {idref: "hky.kappa"},
+             {spec: "beast.base.spec.inference.util.ESS", arg: "@hky.kappa"}
+          ]
+        }
+      ]
+    }
 ]
 }
diff --git a/beast-base/src/test/resources/beast.base/examples/testHKY.xml b/beast-base/src/test/resources/beast.base/examples/testHKY.xml
index 4377e018..a6a83b28 100644
--- a/beast-base/src/test/resources/beast.base/examples/testHKY.xml
+++ b/beast-base/src/test/resources/beast.base/examples/testHKY.xml
@@ -1,6 +1,6 @@
-<beast version='2.0'
-       namespace='beast.base.evolution.alignment:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
-
+<?xml version='1.0' encoding='UTF-8'?>
+<beast version="2.8"
+       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt">
 
     <!-- The sequence alignment                                                  -->
     <!-- ntax=6 nchar=768                                                        -->
@@ -27,77 +27,74 @@
     </data>
 
     <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
-    <input spec='HKY' id='hky'>
-        <kappa idref='hky.kappa'/>
-        <frequencies id='freqs' spec='Frequencies'>
-            <data idref='alignment'/>
+    <input spec="beast.base.spec.evolution.substitutionmodel.HKY" id="hky">
+        <kappa idref="hky.kappa"/>
+        <frequencies id="freqs" spec="beast.base.spec.evolution.substitutionmodel.Frequencies">
+            <data idref="alignment"/>
         </frequencies>
     </input>
 
     <!-- site model                                                              -->
-    <input spec='SiteModel' id="siteModel" gammaCategoryCount='1'>
+    <input spec="beast.base.spec.evolution.sitemodel.SiteModel" id="siteModel" gammaCategoryCount="1">
         <!--
             <parameter name='shape' id='shape' value='0.5'/>
             <parameter name='proportionInvariant' id='propInvar' value='0.2'/>
         -->
-        <substModel idref='hky'/>
+        <substModel idref="hky"/>
     </input>
 
-    <input spec='TreeLikelihood' id="treeLikelihood">
+    <input spec="beast.base.spec.evolution.likelihood.TreeLikelihood" id="treeLikelihood">
         <data idref="alignment"/>
         <tree idref="tree"/>
         <siteModel idref="siteModel"/>
     </input>
 
-    <parameter id="hky.kappa" value="1.0" lower="0.0"/>
+    <parameter id="hky.kappa" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
 
-    <tree id='tree'/>
+    <tree id="tree"/>
 
-    <tree spec='beast.base.evolution.tree.ClusterTree' id='upgmatree' clusterType='upgma' initial='@tree'>
-        <taxa idref='alignment'/>
+    <tree spec="beast.base.spec.evolution.tree.ClusterTree" id="upgmatree" clusterType="upgma" initial="@tree">
+        <taxa idref="alignment"/>
     </tree>
-    <tree spec='beast.base.evolution.tree.coalescent.RandomTree' id='coalescentSimulator' initial='@tree' taxa='@alignment'>
-        <populationModel spec='ConstantPopulation'>
-            <popSize spec='parameter.RealParameter' value='1'/>
+    <tree spec="beast.base.spec.evolution.tree.coalescent.RandomTree" id="coalescentSimulator" initial="@tree" taxa="@alignment">
+        <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
+            <popSize value="1" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
         </populationModel>
     </tree>
 
-
     <run spec="MCMC" id="mcmc" chainLength="5000000" preBurnin="50000">
 
-        <init idref='coalescentSimulator'/>
-        <distribution spec='CompoundDistribution' id='posterior'>
-            <distribution spec='beast.base.inference.distribution.Prior' x='@hky.kappa'>
-                <distr spec='beast.base.inference.distribution.OneOnX'/>
-            </distribution>
-            <distribution id='likelihood' idref="treeLikelihood"/>
+        <init idref="coalescentSimulator"/>
+        <distribution spec="CompoundDistribution" id="posterior">
+            <distribution spec="beast.base.spec.inference.distribution.LogNormal" param="@hky.kappa"><M spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real" value="1.0"/><S spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal" value="0.5"/></distribution>
+            <distribution id="likelihood" idref="treeLikelihood"/>
         </distribution>
 
-        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" parameter="@hky.kappa"/>
-        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" tree="@tree"/>
+        <operator id="kappaScaler" scaleFactor="0.5" weight="1" parameter="@hky.kappa" spec="beast.base.spec.inference.operator.ScaleOperator"/>
+        <operator id="treeScaler" scaleFactor="0.5" weight="1" tree="@tree" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
 
-        <operator id='subtreeSlide' spec='SubtreeSlide' weight="5" gaussian="true" size="1.0" tree="@tree"/>
+        <operator id="subtreeSlide" spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" weight="5" size="1.0" tree="@tree"/>
 
-        <operator id='uniform' spec='Uniform' weight="10" tree="@tree"/>
-        <operator id='narrow' spec='Exchange' isNarrow='true' weight="1" tree="@tree"/>
-        <operator id='wide' spec='Exchange' isNarrow='false' weight="1" tree="@tree"/>
-        <operator id='wilsonBalding' spec='WilsonBalding' weight="1" tree="@tree"/>
+        <operator id="uniform" weight="10" tree="@tree" spec="beast.base.evolution.operator.Uniform"/>
+        <operator id="narrow" spec="Exchange" isNarrow="true" weight="1" tree="@tree"/>
+        <operator id="wide" spec="Exchange" isNarrow="false" weight="1" tree="@tree"/>
+        <operator id="wilsonBalding" spec="WilsonBalding" weight="1" tree="@tree"/>
 
         <logger logEvery="10000" fileName="test.$(seed).log">
-            <model idref='likelihood'/>
+            <model idref="likelihood"/>
             <log idref="likelihood"/>
-            <log idref='hky.kappa'/>
-            <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree'/>
+            <log idref="hky.kappa"/>
+            <log spec="beast.base.evolution.tree.TreeStatLogger" tree="@tree"/>
         </logger>
         <logger logEvery="10000" fileName="test.$(seed).trees">
             <log idref="tree"/>
         </logger>
         <logger logEvery="10000">
-            <model idref='likelihood'/>
+            <model idref="likelihood"/>
             <log idref="likelihood"/>
-            <ESS spec='ESS' name='log' arg="@likelihood"/>
-            <log idref='hky.kappa'/>
-            <ESS spec='ESS' name='log' arg="@hky.kappa"/>
+            <ESS spec="beast.base.spec.inference.util.ESS" name="log" arg="@likelihood"/>
+            <log idref="hky.kappa"/>
+            <ESS spec="beast.base.spec.inference.util.ESS" name="log" arg="@hky.kappa"/>
         </logger>
     </run>
 
diff --git a/beast-base/src/test/resources/beast.base/examples/testJukesCantor.xml b/beast-base/src/test/resources/beast.base/examples/testJukesCantor.xml
index 3fcf586b..559ba59a 100644
--- a/beast-base/src/test/resources/beast.base/examples/testJukesCantor.xml
+++ b/beast-base/src/test/resources/beast.base/examples/testJukesCantor.xml
@@ -1,6 +1,6 @@
-<beast version='2.0'
-       namespace='beast.base.evolution.alignment:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
-
+<?xml version='1.0' encoding='UTF-8'?>
+<beast version="2.8"
+       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt">
 
     <!-- The sequence alignment                                                  -->
     <!-- ntax=6 nchar=768                                                        -->
@@ -27,58 +27,58 @@
     </data>
 
     <!-- The Jukes-Cantor substitution model (Jukes & Cantor, 1969)             -->
-    <input spec='JukesCantor' id='jc69'/>
+    <input spec="beast.base.spec.evolution.substitutionmodel.JukesCantor" id="jc69"/>
 
     <!-- site model                                                              -->
-    <input spec='SiteModel' id="siteModel" gammaCategoryCount='1'>
-        <substModel idref='jc69'/>
+    <input spec="beast.base.spec.evolution.sitemodel.SiteModel" id="siteModel" gammaCategoryCount="1">
+        <substModel idref="jc69"/>
     </input>
 
-    <input spec='TreeLikelihood' id="treeLikelihood">
+    <input spec="beast.base.spec.evolution.likelihood.TreeLikelihood" id="treeLikelihood">
         <data idref="alignment"/>
         <tree idref="tree"/>
         <siteModel idref="siteModel"/>
     </input>
 
-    <tree id='tree'/>
+    <tree id="tree"/>
 
-    <tree spec='beast.base.evolution.tree.ClusterTree' id='upgmatree' clusterType='upgma' initial='@tree'>
-        <taxa idref='alignment'/>
+    <tree spec="beast.base.spec.evolution.tree.ClusterTree" id="upgmatree" clusterType="upgma" initial="@tree">
+        <taxa idref="alignment"/>
     </tree>
-    <tree spec='beast.base.evolution.tree.coalescent.RandomTree' id='coalescentSimulator' initial='@tree' taxa='@alignment'>
-        <populationModel spec='ConstantPopulation'>
-            <popSize spec='parameter.RealParameter' value='0.05'/>
+    <tree spec="beast.base.spec.evolution.tree.coalescent.RandomTree" id="coalescentSimulator" initial="@tree" taxa="@alignment">
+        <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
+            <popSize value="0.05" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
         </populationModel>
     </tree>
 
     <run spec="MCMC" id="mcmc" chainLength="5000000" preBurnin="50000">
 
-        <init idref='coalescentSimulator'/>
-        <distribution spec='CompoundDistribution' id='posterior'>
-            <distribution id='likelihood' idref="treeLikelihood"/>
+        <init idref="coalescentSimulator"/>
+        <distribution spec="CompoundDistribution" id="posterior">
+            <distribution id="likelihood" idref="treeLikelihood"/>
         </distribution>
 
-        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" tree="@tree"/>
+        <operator id="treeScaler" scaleFactor="0.5" weight="1" tree="@tree" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
 
-        <operator spec='SubtreeSlide' weight="5" gaussian="true" size="1.0" tree="@tree"/>
+        <operator spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" weight="5" size="1.0" tree="@tree"/>
 
-        <operator spec='Uniform' weight="10" tree="@tree"/>
-        <operator id='narrow' spec='Exchange' isNarrow='true' weight="1" tree="@tree"/>
-        <operator id='wide' spec='Exchange' isNarrow='false' weight="1" tree="@tree"/>
-        <operator spec='WilsonBalding' weight="1" tree="@tree"/>
+        <operator weight="10" tree="@tree" spec="beast.base.evolution.operator.Uniform"/>
+        <operator id="narrow" spec="Exchange" isNarrow="true" weight="1" tree="@tree"/>
+        <operator id="wide" spec="Exchange" isNarrow="false" weight="1" tree="@tree"/>
+        <operator spec="WilsonBalding" weight="1" tree="@tree"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
-            <model idref='likelihood'/>
+            <model idref="likelihood"/>
             <log idref="likelihood"/>
-            <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree'/>
+            <log spec="beast.base.evolution.tree.TreeStatLogger" tree="@tree"/>
         </logger>
         <logger logEvery="1000" fileName="test.$(seed).trees">
             <log idref="tree"/>
         </logger>
         <logger logEvery="20000">
-            <model idref='likelihood'/>
+            <model idref="likelihood"/>
             <log idref="likelihood"/>
-            <ESS spec='ESS' name='log' arg="@likelihood"/>
+            <ESS spec="beast.base.spec.inference.util.ESS" name="log" arg="@likelihood"/>
         </logger>
     </run>
 
diff --git a/beast-base/src/test/resources/beast.base/examples/testJukesCantorShort.xml b/beast-base/src/test/resources/beast.base/examples/testJukesCantorShort.xml
index 5975f6bd..ca09b44a 100644
--- a/beast-base/src/test/resources/beast.base/examples/testJukesCantorShort.xml
+++ b/beast-base/src/test/resources/beast.base/examples/testJukesCantorShort.xml
@@ -1,6 +1,6 @@
-<beast version='2.0'
-       namespace='beast.base.evolution.alignment:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
-
+<?xml version='1.0' encoding='UTF-8'?>
+<beast version="2.8"
+       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt">
 
     <!-- A shortened version of the mitochondrial DNA alignment in testJukesCantor.xml, leading to higher uncertainty regarding the splits in the tree.  -->
     <!-- ntax=6 nchar=415                                                        -->
@@ -26,58 +26,58 @@
     </data>
 
     <!-- The Jukes-Cantor substitution model (Jukes & Cantor, 1969)             -->
-    <input spec='JukesCantor' id='jc69'/>
+    <input spec="beast.base.spec.evolution.substitutionmodel.JukesCantor" id="jc69"/>
 
     <!-- site model                                                              -->
-    <input spec='SiteModel' id="siteModel" gammaCategoryCount='1'>
-        <substModel idref='jc69'/>
+    <input spec="beast.base.spec.evolution.sitemodel.SiteModel" id="siteModel" gammaCategoryCount="1">
+        <substModel idref="jc69"/>
     </input>
 
-    <input spec='TreeLikelihood' id="treeLikelihood">
+    <input spec="beast.base.spec.evolution.likelihood.TreeLikelihood" id="treeLikelihood">
         <data idref="alignment"/>
         <tree idref="tree"/>
         <siteModel idref="siteModel"/>
     </input>
 
-    <tree id='tree'/>
+    <tree id="tree"/>
 
-    <tree spec='beast.base.evolution.tree.ClusterTree' id='upgmatree' clusterType='upgma' initial='@tree'>
-        <taxa idref='alignment'/>
+    <tree spec="beast.base.spec.evolution.tree.ClusterTree" id="upgmatree" clusterType="upgma" initial="@tree">
+        <taxa idref="alignment"/>
     </tree>
-    <tree spec='beast.base.evolution.tree.coalescent.RandomTree' id='coalescentSimulator' initial='@tree' taxa='@alignment'>
-        <populationModel spec='ConstantPopulation'>
-            <popSize spec='parameter.RealParameter' value='0.05'/>
+    <tree spec="beast.base.spec.evolution.tree.coalescent.RandomTree" id="coalescentSimulator" initial="@tree" taxa="@alignment">
+        <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
+            <popSize value="0.05" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
         </populationModel>
     </tree>
 
     <run spec="MCMC" id="mcmc" chainLength="5000000" preBurnin="50000">
 
-        <init idref='coalescentSimulator'/>
-        <distribution spec='CompoundDistribution' id='posterior'>
-            <distribution id='likelihood' idref="treeLikelihood"/>
+        <init idref="coalescentSimulator"/>
+        <distribution spec="CompoundDistribution" id="posterior">
+            <distribution id="likelihood" idref="treeLikelihood"/>
         </distribution>
 
-        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" tree="@tree"/>
+        <operator id="treeScaler" scaleFactor="0.5" weight="1" tree="@tree" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
 
-        <operator spec='SubtreeSlide' weight="5" gaussian="true" size="1.0" tree="@tree"/>
+        <operator spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" weight="5" size="1.0" tree="@tree"/>
 
-        <operator spec='Uniform' weight="10" tree="@tree"/>
-        <operator id='narrow' spec='Exchange' isNarrow='true' weight="1" tree="@tree"/>
-        <operator id='wide' spec='Exchange' isNarrow='false' weight="1" tree="@tree"/>
-        <operator spec='WilsonBalding' weight="1" tree="@tree"/>
+        <operator weight="10" tree="@tree" spec="beast.base.evolution.operator.Uniform"/>
+        <operator id="narrow" spec="Exchange" isNarrow="true" weight="1" tree="@tree"/>
+        <operator id="wide" spec="Exchange" isNarrow="false" weight="1" tree="@tree"/>
+        <operator spec="WilsonBalding" weight="1" tree="@tree"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
-            <model idref='likelihood'/>
+            <model idref="likelihood"/>
             <log idref="likelihood"/>
-            <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree'/>
+            <log spec="beast.base.evolution.tree.TreeStatLogger" tree="@tree"/>
         </logger>
         <logger logEvery="1000" fileName="test.$(seed).trees">
             <log idref="tree"/>
         </logger>
         <logger logEvery="20000">
-            <model idref='likelihood'/>
+            <model idref="likelihood"/>
             <log idref="likelihood"/>
-            <ESS spec='ESS' name='log' arg="@likelihood"/>
+            <ESS spec="beast.base.spec.inference.util.ESS" name="log" arg="@likelihood"/>
         </logger>
     </run>
 
diff --git a/beast-base/src/test/resources/beast.base/examples/testJukesCantorShortUncertain.xml b/beast-base/src/test/resources/beast.base/examples/testJukesCantorShortUncertain.xml
index d9cc153d..ed12c1b6 100644
--- a/beast-base/src/test/resources/beast.base/examples/testJukesCantorShortUncertain.xml
+++ b/beast-base/src/test/resources/beast.base/examples/testJukesCantorShortUncertain.xml
@@ -1,6 +1,6 @@
-<beast version='2.0'
-       namespace='beast.base.evolution.alignment:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
-
+<?xml version='1.0' encoding='UTF-8'?>
+<beast version="2.8"
+       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt">
 
     <!-- The sequence alignment from testJukesCantorShort.xml, after converting to tip likelihoods.
 	These tip likelihoods denote the likelihood of observed data (e.g. read counts) given a particular base call.
@@ -37,58 +37,58 @@
     </data>
 
     <!-- The Jukes-Cantor substitution model (Jukes & Cantor, 1969)             -->
-    <input spec='JukesCantor' id='jc69'/>
+    <input spec="beast.base.spec.evolution.substitutionmodel.JukesCantor" id="jc69"/>
 
     <!-- site model                                                              -->
-    <input spec='SiteModel' id="siteModel" gammaCategoryCount='1'>
-        <substModel idref='jc69'/>
+    <input spec="beast.base.spec.evolution.sitemodel.SiteModel" id="siteModel" gammaCategoryCount="1">
+        <substModel idref="jc69"/>
     </input>
 
-    <input spec='TreeLikelihood' id="treeLikelihood" useTipLikelihoods="true">
+    <input spec="beast.base.spec.evolution.likelihood.TreeLikelihood" id="treeLikelihood" useTipLikelihoods="true">
         <data idref="alignment"/>
         <tree idref="tree"/>
         <siteModel idref="siteModel"/>
     </input>
 
-    <tree id='tree'/>
+    <tree id="tree"/>
 
-    <tree spec='beast.base.evolution.tree.ClusterTree' id='upgmatree' clusterType='upgma' initial='@tree'>
-        <taxa idref='alignment'/>
+    <tree spec="beast.base.spec.evolution.tree.ClusterTree" id="upgmatree" clusterType="upgma" initial="@tree">
+        <taxa idref="alignment"/>
     </tree>
-    <tree spec='beast.base.evolution.tree.coalescent.RandomTree' id='coalescentSimulator' initial='@tree' taxa='@alignment'>
-        <populationModel spec='ConstantPopulation'>
-            <popSize spec='parameter.RealParameter' value='0.05'/>
+    <tree spec="beast.base.spec.evolution.tree.coalescent.RandomTree" id="coalescentSimulator" initial="@tree" taxa="@alignment">
+        <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
+            <popSize value="0.05" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
         </populationModel>
     </tree>
 
     <run spec="MCMC" id="mcmc" chainLength="5000000" preBurnin="50000">
 
-        <init idref='coalescentSimulator'/>
-        <distribution spec='CompoundDistribution' id='posterior'>
-            <distribution id='likelihood' idref="treeLikelihood"/>
+        <init idref="coalescentSimulator"/>
+        <distribution spec="CompoundDistribution" id="posterior">
+            <distribution id="likelihood" idref="treeLikelihood"/>
         </distribution>
 
-        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" tree="@tree"/>
+        <operator id="treeScaler" scaleFactor="0.5" weight="1" tree="@tree" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
 
-        <operator spec='SubtreeSlide' weight="5" gaussian="true" size="1.0" tree="@tree"/>
+        <operator spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" weight="5" size="1.0" tree="@tree"/>
 
-        <operator spec='Uniform' weight="10" tree="@tree"/>
-        <operator id='narrow' spec='Exchange' isNarrow='true' weight="1" tree="@tree"/>
-        <operator id='wide' spec='Exchange' isNarrow='false' weight="1" tree="@tree"/>
-        <operator spec='WilsonBalding' weight="1" tree="@tree"/>
+        <operator weight="10" tree="@tree" spec="beast.base.evolution.operator.Uniform"/>
+        <operator id="narrow" spec="Exchange" isNarrow="true" weight="1" tree="@tree"/>
+        <operator id="wide" spec="Exchange" isNarrow="false" weight="1" tree="@tree"/>
+        <operator spec="WilsonBalding" weight="1" tree="@tree"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
-            <model idref='likelihood'/>
+            <model idref="likelihood"/>
             <log idref="likelihood"/>
-            <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree'/>
+            <log spec="beast.base.evolution.tree.TreeStatLogger" tree="@tree"/>
         </logger>
         <logger logEvery="1000" fileName="test.$(seed).trees">
             <log idref="tree"/>
         </logger>
         <logger logEvery="20000">
-            <model idref='likelihood'/>
+            <model idref="likelihood"/>
             <log idref="likelihood"/>
-            <ESS spec='ESS' name='log' arg="@likelihood"/>
+            <ESS spec="beast.base.spec.inference.util.ESS" name="log" arg="@likelihood"/>
         </logger>
     </run>
 
diff --git a/beast-base/src/test/resources/beast.base/examples/testJukesCantorShortUncertain2.xml b/beast-base/src/test/resources/beast.base/examples/testJukesCantorShortUncertain2.xml
index 59e72041..3f45e0dc 100644
--- a/beast-base/src/test/resources/beast.base/examples/testJukesCantorShortUncertain2.xml
+++ b/beast-base/src/test/resources/beast.base/examples/testJukesCantorShortUncertain2.xml
@@ -1,6 +1,6 @@
-<beast version='2.0'
-       namespace='beast.base.evolution.alignment:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
-
+<?xml version='1.0' encoding='UTF-8'?>
+<beast version="2.8"
+       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt">
 
     <!-- The sequence alignment from testJukesCantorShort.xml, after converting to tip likelihoods.
 	These tip likelihoods denote the likelihood of observed data (e.g. read counts) given a particular base call.
@@ -38,58 +38,58 @@
 </data>
 
     <!-- The Jukes-Cantor substitution model (Jukes & Cantor, 1969)             -->
-    <input spec='JukesCantor' id='jc69'/>
+    <input spec="beast.base.spec.evolution.substitutionmodel.JukesCantor" id="jc69"/>
 
     <!-- site model                                                              -->
-    <input spec='SiteModel' id="siteModel" gammaCategoryCount='1'>
-        <substModel idref='jc69'/>
+    <input spec="beast.base.spec.evolution.sitemodel.SiteModel" id="siteModel" gammaCategoryCount="1">
+        <substModel idref="jc69"/>
     </input>
 
-    <input spec='TreeLikelihood' id="treeLikelihood" useTipLikelihoods="true">
+    <input spec="beast.base.spec.evolution.likelihood.TreeLikelihood" id="treeLikelihood" useTipLikelihoods="true">
         <data idref="alignment"/>
         <tree idref="tree"/>
         <siteModel idref="siteModel"/>
     </input>
 
-    <tree id='tree'/>
+    <tree id="tree"/>
 
-    <tree spec='beast.base.evolution.tree.ClusterTree' id='upgmatree' clusterType='upgma' initial='@tree'>
-        <taxa idref='alignment'/>
+    <tree spec="beast.base.spec.evolution.tree.ClusterTree" id="upgmatree" clusterType="upgma" initial="@tree">
+        <taxa idref="alignment"/>
     </tree>
-    <tree spec='beast.base.evolution.tree.coalescent.RandomTree' id='coalescentSimulator' initial='@tree' taxa='@alignment'>
-        <populationModel spec='ConstantPopulation'>
-            <popSize spec='parameter.RealParameter' value='0.05'/>
+    <tree spec="beast.base.spec.evolution.tree.coalescent.RandomTree" id="coalescentSimulator" initial="@tree" taxa="@alignment">
+        <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
+            <popSize value="0.05" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
         </populationModel>
     </tree>
 
     <run spec="MCMC" id="mcmc" chainLength="5000000" preBurnin="50000">
 
-        <init idref='coalescentSimulator'/>
-        <distribution spec='CompoundDistribution' id='posterior'>
-            <distribution id='likelihood' idref="treeLikelihood"/>
+        <init idref="coalescentSimulator"/>
+        <distribution spec="CompoundDistribution" id="posterior">
+            <distribution id="likelihood" idref="treeLikelihood"/>
         </distribution>
 
-        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" tree="@tree"/>
+        <operator id="treeScaler" scaleFactor="0.5" weight="1" tree="@tree" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
 
-        <operator spec='SubtreeSlide' weight="5" gaussian="true" size="1.0" tree="@tree"/>
+        <operator spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" weight="5" size="1.0" tree="@tree"/>
 
-        <operator spec='Uniform' weight="10" tree="@tree"/>
-        <operator id='narrow' spec='Exchange' isNarrow='true' weight="1" tree="@tree"/>
-        <operator id='wide' spec='Exchange' isNarrow='false' weight="1" tree="@tree"/>
-        <operator spec='WilsonBalding' weight="1" tree="@tree"/>
+        <operator weight="10" tree="@tree" spec="beast.base.evolution.operator.Uniform"/>
+        <operator id="narrow" spec="Exchange" isNarrow="true" weight="1" tree="@tree"/>
+        <operator id="wide" spec="Exchange" isNarrow="false" weight="1" tree="@tree"/>
+        <operator spec="WilsonBalding" weight="1" tree="@tree"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
-            <model idref='likelihood'/>
+            <model idref="likelihood"/>
             <log idref="likelihood"/>
-            <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree'/>
+            <log spec="beast.base.evolution.tree.TreeStatLogger" tree="@tree"/>
         </logger>
         <logger logEvery="1000" fileName="test.$(seed).trees">
             <log idref="tree"/>
         </logger>
         <logger logEvery="20000">
-            <model idref='likelihood'/>
+            <model idref="likelihood"/>
             <log idref="likelihood"/>
-            <ESS spec='ESS' name='log' arg="@likelihood"/>
+            <ESS spec="beast.base.spec.inference.util.ESS" name="log" arg="@likelihood"/>
         </logger>
     </run>
 
diff --git a/beast-base/src/test/resources/beast.base/examples/testJukesCantorShortUncertain2MLE.xml b/beast-base/src/test/resources/beast.base/examples/testJukesCantorShortUncertain2MLE.xml
index 117f3115..53849976 100644
--- a/beast-base/src/test/resources/beast.base/examples/testJukesCantorShortUncertain2MLE.xml
+++ b/beast-base/src/test/resources/beast.base/examples/testJukesCantorShortUncertain2MLE.xml
@@ -1,6 +1,6 @@
-<beast version='2.0'
-       namespace='beast.base.evolution.alignment:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
-
+<?xml version='1.0' encoding='UTF-8'?>
+<beast version="2.8"
+       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt">
 
     <!-- The sequence alignment from testJukesCantorShortUncertain2.xml, after 
     reconstructing the MLE for the sequences from the noisy simulated read data.
@@ -29,58 +29,58 @@
     </data>
 
     <!-- The Jukes-Cantor substitution model (Jukes & Cantor, 1969)             -->
-    <input spec='JukesCantor' id='jc69'/>
+    <input spec="beast.base.spec.evolution.substitutionmodel.JukesCantor" id="jc69"/>
 
     <!-- site model                                                              -->
-    <input spec='SiteModel' id="siteModel" gammaCategoryCount='1'>
-        <substModel idref='jc69'/>
+    <input spec="beast.base.spec.evolution.sitemodel.SiteModel" id="siteModel" gammaCategoryCount="1">
+        <substModel idref="jc69"/>
     </input>
 
-    <input spec='TreeLikelihood' id="treeLikelihood">
+    <input spec="beast.base.spec.evolution.likelihood.TreeLikelihood" id="treeLikelihood">
         <data idref="alignment"/>
         <tree idref="tree"/>
         <siteModel idref="siteModel"/>
     </input>
 
-    <tree id='tree'/>
+    <tree id="tree"/>
 
-    <tree spec='beast.base.evolution.tree.ClusterTree' id='upgmatree' clusterType='upgma' initial='@tree'>
-        <taxa idref='alignment'/>
+    <tree spec="beast.base.spec.evolution.tree.ClusterTree" id="upgmatree" clusterType="upgma" initial="@tree">
+        <taxa idref="alignment"/>
     </tree>
-    <tree spec='beast.base.evolution.tree.coalescent.RandomTree' id='coalescentSimulator' initial='@tree' taxa='@alignment'>
-        <populationModel spec='ConstantPopulation'>
-            <popSize spec='parameter.RealParameter' value='0.05'/>
+    <tree spec="beast.base.spec.evolution.tree.coalescent.RandomTree" id="coalescentSimulator" initial="@tree" taxa="@alignment">
+        <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
+            <popSize value="0.05" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
         </populationModel>
     </tree>
 
     <run spec="MCMC" id="mcmc" chainLength="5000000" preBurnin="50000">
 
-        <init idref='coalescentSimulator'/>
-        <distribution spec='CompoundDistribution' id='posterior'>
-            <distribution id='likelihood' idref="treeLikelihood"/>
+        <init idref="coalescentSimulator"/>
+        <distribution spec="CompoundDistribution" id="posterior">
+            <distribution id="likelihood" idref="treeLikelihood"/>
         </distribution>
 
-        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" tree="@tree"/>
+        <operator id="treeScaler" scaleFactor="0.5" weight="1" tree="@tree" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
 
-        <operator spec='SubtreeSlide' weight="5" gaussian="true" size="1.0" tree="@tree"/>
+        <operator spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" weight="5" size="1.0" tree="@tree"/>
 
-        <operator spec='Uniform' weight="10" tree="@tree"/>
-        <operator id='narrow' spec='Exchange' isNarrow='true' weight="1" tree="@tree"/>
-        <operator id='wide' spec='Exchange' isNarrow='false' weight="1" tree="@tree"/>
-        <operator spec='WilsonBalding' weight="1" tree="@tree"/>
+        <operator weight="10" tree="@tree" spec="beast.base.evolution.operator.Uniform"/>
+        <operator id="narrow" spec="Exchange" isNarrow="true" weight="1" tree="@tree"/>
+        <operator id="wide" spec="Exchange" isNarrow="false" weight="1" tree="@tree"/>
+        <operator spec="WilsonBalding" weight="1" tree="@tree"/>
 
         <logger logEvery="1000" fileName="test.$(seed).log">
-            <model idref='likelihood'/>
+            <model idref="likelihood"/>
             <log idref="likelihood"/>
-            <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree'/>
+            <log spec="beast.base.evolution.tree.TreeStatLogger" tree="@tree"/>
         </logger>
         <logger logEvery="1000" fileName="test.$(seed).trees">
             <log idref="tree"/>
         </logger>
         <logger logEvery="20000">
-            <model idref='likelihood'/>
+            <model idref="likelihood"/>
             <log idref="likelihood"/>
-            <ESS spec='ESS' name='log' arg="@likelihood"/>
+            <ESS spec="beast.base.spec.inference.util.ESS" name="log" arg="@likelihood"/>
         </logger>
     </run>
 
diff --git a/beast-base/src/test/resources/beast.base/examples/testOpSubSchedule.xml b/beast-base/src/test/resources/beast.base/examples/testOpSubSchedule.xml
index e49dfc59..f828101e 100644
--- a/beast-base/src/test/resources/beast.base/examples/testOpSubSchedule.xml
+++ b/beast-base/src/test/resources/beast.base/examples/testOpSubSchedule.xml
@@ -1,6 +1,6 @@
-<beast version='2.0'
-       namespace='beast.base.evolution.alignment:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
-
+<?xml version='1.0' encoding='UTF-8'?>
+<beast version="2.8"
+       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt">
 
     <!-- The sequence alignment                                                  -->
     <!-- ntax=6 nchar=768                                                        -->
@@ -27,50 +27,47 @@
     </data>
 
     <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
-    <input spec='HKY' id='hky'>
-        <kappa idref='hky.kappa'/>
-        <frequencies id='freqs' spec='Frequencies'>
-            <data idref='alignment'/>
+    <input spec="beast.base.spec.evolution.substitutionmodel.HKY" id="hky">
+        <kappa idref="hky.kappa"/>
+        <frequencies id="freqs" spec="beast.base.spec.evolution.substitutionmodel.Frequencies">
+            <data idref="alignment"/>
         </frequencies>
     </input>
 
     <!-- site model                                                              -->
-    <input spec='SiteModel' id="siteModel" gammaCategoryCount='1'>
+    <input spec="beast.base.spec.evolution.sitemodel.SiteModel" id="siteModel" gammaCategoryCount="1">
         <!--
             <parameter name='shape' id='shape' value='0.5'/>
             <parameter name='proportionInvariant' id='propInvar' value='0.2'/>
         -->
-        <substModel idref='hky'/>
+        <substModel idref="hky"/>
     </input>
 
-    <input spec='TreeLikelihood' id="treeLikelihood">
+    <input spec="beast.base.spec.evolution.likelihood.TreeLikelihood" id="treeLikelihood">
         <data idref="alignment"/>
         <tree idref="tree"/>
         <siteModel idref="siteModel"/>
     </input>
 
-    <parameter id="hky.kappa" value="1.0" lower="0.0"/>
+    <parameter id="hky.kappa" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
 
-    <tree id='tree'/>
+    <tree id="tree"/>
 
-    <tree spec='beast.base.evolution.tree.ClusterTree' id='upgmatree' clusterType='upgma' initial='@tree'>
-        <taxa idref='alignment'/>
+    <tree spec="beast.base.spec.evolution.tree.ClusterTree" id="upgmatree" clusterType="upgma" initial="@tree">
+        <taxa idref="alignment"/>
     </tree>
-    <tree spec='beast.base.evolution.tree.coalescent.RandomTree' id='coalescentSimulator' initial='@tree' taxa='@alignment'>
-        <populationModel spec='ConstantPopulation'>
-            <popSize spec='parameter.RealParameter' value='1'/>
+    <tree spec="beast.base.spec.evolution.tree.coalescent.RandomTree" id="coalescentSimulator" initial="@tree" taxa="@alignment">
+        <populationModel spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
+            <popSize value="1" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
         </populationModel>
     </tree>
 
-
     <run spec="MCMC" id="mcmc" chainLength="1000000" preBurnin="50000">
 
-        <init idref='coalescentSimulator'/>
-        <distribution spec='CompoundDistribution' id='posterior'>
-            <distribution spec='beast.base.inference.distribution.Prior' x='@hky.kappa'>
-                <distr spec='beast.base.inference.distribution.OneOnX'/>
-            </distribution>
-            <distribution id='likelihood' idref="treeLikelihood"/>
+        <init idref="coalescentSimulator"/>
+        <distribution spec="CompoundDistribution" id="posterior">
+            <distribution spec="beast.base.spec.inference.distribution.LogNormal" param="@hky.kappa"><M spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real" value="1.0"/><S spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal" value="0.5"/></distribution>
+            <distribution id="likelihood" idref="treeLikelihood"/>
         </distribution>
 
          <operatorschedule id="operatorSchedule" spec="OperatorSchedule">
@@ -78,31 +75,31 @@
             <subschedule id="operatorTrees" spec="OperatorSchedule" weight="50" weightIsPercentage="true" operatorPattern="^.*tree.*"/>
          </operatorschedule>
 
-        <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" parameter="@hky.kappa"/>
-        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" tree="@tree"/>
+        <operator id="kappaScaler" scaleFactor="0.5" weight="1" parameter="@hky.kappa" spec="beast.base.spec.inference.operator.ScaleOperator"/>
+        <operator id="treeScaler" scaleFactor="0.5" weight="1" tree="@tree" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
 
-        <operator id='subtreeSlide' spec='SubtreeSlide' weight="5" gaussian="true" size="1.0" tree="@tree"/>
+        <operator id="subtreeSlide" spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" weight="5" size="1.0" tree="@tree"/>
 
-        <operator id='uniform' spec='Uniform' weight="10" tree="@tree"/>
-        <operator id='narrow' spec='Exchange' isNarrow='true' weight="1" tree="@tree"/>
-        <operator id='wide' spec='Exchange' isNarrow='false' weight="1" tree="@tree"/>
-        <operator id='wilsonBalding' spec='WilsonBalding' weight="1" tree="@tree"/>
+        <operator id="uniform" weight="10" tree="@tree" spec="beast.base.evolution.operator.Uniform"/>
+        <operator id="narrow" spec="Exchange" isNarrow="true" weight="1" tree="@tree"/>
+        <operator id="wide" spec="Exchange" isNarrow="false" weight="1" tree="@tree"/>
+        <operator id="wilsonBalding" spec="WilsonBalding" weight="1" tree="@tree"/>
 
         <logger logEvery="10000" fileName="test.$(seed).log">
-            <model idref='likelihood'/>
+            <model idref="likelihood"/>
             <log idref="likelihood"/>
-            <log idref='hky.kappa'/>
-            <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree'/>
+            <log idref="hky.kappa"/>
+            <log spec="beast.base.evolution.tree.TreeStatLogger" tree="@tree"/>
         </logger>
         <logger logEvery="10000" fileName="test.$(seed).trees">
             <log idref="tree"/>
         </logger>
         <logger logEvery="10000">
-            <model idref='likelihood'/>
+            <model idref="likelihood"/>
             <log idref="likelihood"/>
-            <ESS spec='ESS' name='log' arg="@likelihood"/>
-            <log idref='hky.kappa'/>
-            <ESS spec='ESS' name='log' arg="@hky.kappa"/>
+            <ESS spec="beast.base.spec.inference.util.ESS" name="log" arg="@likelihood"/>
+            <log idref="hky.kappa"/>
+            <ESS spec="beast.base.spec.inference.util.ESS" name="log" arg="@hky.kappa"/>
         </logger>
     </run>
 
diff --git a/beast-base/src/test/resources/beast.base/examples/testPlates.xml b/beast-base/src/test/resources/beast.base/examples/testPlates.xml
index 12a2e919..b5a0da18 100644
--- a/beast-base/src/test/resources/beast.base/examples/testPlates.xml
+++ b/beast-base/src/test/resources/beast.base/examples/testPlates.xml
@@ -1,6 +1,6 @@
-<beast version='2.0'
-       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
-
+<?xml version='1.0' encoding='UTF-8'?>
+<beast version="2.8"
+       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt">
 
     <!-- The sequence alignment                                                  -->
     <!-- ntax=6 nchar=768                                                        -->
@@ -57,69 +57,64 @@
         </sequence>
     </data>
 
-    <plate spec='util.Plate' var='n' range='.p1,.p2,.p3'>
+    <plate spec="util.Plate" var="n" range=".p1,.p2,.p3">
         <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985)             -->
-        <input spec='HKY' id='hky$(n)' kappa='@hky.kappa$(n)'>
-            <frequencies id='freqs$(n)' spec='Frequencies' data='@alignment$(n)'/>
+        <input spec="beast.base.spec.evolution.substitutionmodel.HKY" id="hky$(n)" kappa="@hky.kappa$(n)">
+            <frequencies id="freqs$(n)" spec="beast.base.spec.evolution.substitutionmodel.Frequencies" data="@alignment$(n)"/>
         </input>
 
         <!-- site model                                                              -->
-        <input spec='SiteModel' id="siteModel$(n)" substModel='@hky$(n)'/>
+        <input spec="beast.base.spec.evolution.sitemodel.SiteModel" id="siteModel$(n)" substModel="@hky$(n)"/>
 
-        <input spec='TreeLikelihood' id="treeLikelihood$(n)"
-            data="@alignment$(n)"
-            tree="@tree"
-            siteModel="@siteModel$(n)"
-        />
+        <input spec="beast.base.spec.evolution.likelihood.TreeLikelihood" id="treeLikelihood$(n)" data="@alignment$(n)" tree="@tree" siteModel="@siteModel$(n)"/>
 
-        <parameter id="hky.kappa$(n)" value="1.0" lower="0.0"/>
+        <parameter id="hky.kappa$(n)" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
     </plate>
 
-    <tree spec='beast.base.evolution.tree.ClusterTree' id='tree' clusterType='upgma' taxa='@alignment.p1'/>
-
+    <tree spec="beast.base.spec.evolution.tree.ClusterTree" id="tree" clusterType="upgma" taxa="@alignment.p1"/>
 
     <run spec="MCMC" id="mcmc" chainLength="10000000">
-        <state storeEvery='100000'>
+        <state storeEvery="100000">
             <stateNode idref="hky.kappa.p1"/>
             <stateNode idref="hky.kappa.p2"/>
             <stateNode idref="hky.kappa.p3"/>
             <stateNode idref="tree"/>
         </state>
 
-        <distribution spec='CompoundDistribution' id='likelihood'>
-            <plate var='n' range='.p1,.p2,.p3'>
-                <distribution id='likelihood$(n)' idref="treeLikelihood$(n)"/>
+        <distribution spec="CompoundDistribution" id="likelihood">
+            <plate var="n" range=".p1,.p2,.p3">
+                <distribution id="likelihood$(n)" idref="treeLikelihood$(n)"/>
             </plate>
         </distribution>
     
-        <plate var='n' range='.p1,.p2,.p3'>
-            <operator id='kappaScaler$(n)' spec='ScaleOperator' scaleFactor="0.5" weight="1" parameter="@hky.kappa$(n)"/>
+        <plate var="n" range=".p1,.p2,.p3">
+            <operator id="kappaScaler$(n)" scaleFactor="0.5" weight="1" parameter="@hky.kappa$(n)" spec="beast.base.spec.inference.operator.ScaleOperator"/>
         </plate>
-        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" tree="@tree"/>
-        <operator spec='Uniform' weight="10" tree="@tree"/>
-        <operator spec='SubtreeSlide' weight="5" gaussian="true" size="1.0" tree="@tree"/>
-        <operator id='narrow' spec='Exchange' isNarrow='true' weight="1" tree="@tree"/>
-        <operator id='wide' spec='Exchange' isNarrow='false' weight="1" tree="@tree"/>
-        <operator spec='WilsonBalding' weight="1" tree="@tree"/>
+        <operator id="treeScaler" scaleFactor="0.5" weight="1" tree="@tree" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
+        <operator weight="10" tree="@tree" spec="beast.base.evolution.operator.Uniform"/>
+        <operator spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" weight="5" size="1.0" tree="@tree"/>
+        <operator id="narrow" spec="Exchange" isNarrow="true" weight="1" tree="@tree"/>
+        <operator id="wide" spec="Exchange" isNarrow="false" weight="1" tree="@tree"/>
+        <operator spec="WilsonBalding" weight="1" tree="@tree"/>
 
         <logger logEvery="10000" fileName="test.$(seed).log">
-	        <model idref='likelihood'/>
+	        <model idref="likelihood"/>
             <log idref="likelihood"/>
-            <plate var='n' range='.p1,.p2,.p3'>
-                <log idref='hky.kappa$(n)'/>
+            <plate var="n" range=".p1,.p2,.p3">
+                <log idref="hky.kappa$(n)"/>
             </plate>
-            <log spec='beast.base.evolution.tree.TreeStatLogger'><tree idref='tree'/></log>
+            <log spec="beast.base.evolution.tree.TreeStatLogger"><tree idref="tree"/></log>
         </logger>
         <logger logEvery="10000" fileName="test.$(seed).trees">
             <log idref="tree"/>
         </logger>
         <logger logEvery="10000">
-	        <model idref='likelihood'/>
+	        <model idref="likelihood"/>
             <log idref="likelihood"/>
-    	    <ESS spec='ESS' name='log' arg="@likelihood"/>
-            <plate var='n' range='.p1,.p2,.p3'>
-                <log idref='hky.kappa$(n)'/>
-        	    <ESS spec='ESS' name='log' arg="@hky.kappa$(n)"/>
+    	    <ESS spec="beast.base.spec.inference.util.ESS" name="log" arg="@likelihood"/>
+            <plate var="n" range=".p1,.p2,.p3">
+                <log idref="hky.kappa$(n)"/>
+        	    <ESS spec="beast.base.spec.inference.util.ESS" name="log" arg="@hky.kappa$(n)"/>
             </plate>
         </logger>
 
diff --git a/beast-base/src/test/resources/beast.base/examples/testRNA.xml b/beast-base/src/test/resources/beast.base/examples/testRNA.xml
index 041817ff..9d7f7013 100644
--- a/beast-base/src/test/resources/beast.base/examples/testRNA.xml
+++ b/beast-base/src/test/resources/beast.base/examples/testRNA.xml
@@ -1,156 +1,105 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<beast beautitemplate='Standard' beautistatus=''
-       namespace="beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.alignment:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood"
-       version="2.0">
+<?xml version='1.0' encoding='UTF-8'?>
+<beast version="2.8"
+       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt"
+       beautitemplate="Standard"
+       beautistatus="">
 
 <!-- A fake RNA alignment.  Should give exactly the same result as testGTR.xml. -->
 
     <data id="primate-mtDNA">
-        <sequence id="seq_Lemur_catta" taxon="Lemur_catta" totalcount="4"
-                  value="AAGCUUCAUAGGAGCAACCAUUCUAAUAAUCGCACAUGGCCUUACAUCAUCCAUAUUAUUCUGUCUAGCCAACUCUAACUACGAACGAAUCCAUAGCCGUACAAUACUACUAGCACGAGGGAUCCAAACCAUUCUCCCUCUUAUAGCCACCUGAUGACUACUCGCCAGCCUAACUAACCUAGCCCUACCCACCUCUAUCAAUUUAAUUGGCGAACUAUUCGUCACUAUAGCAUCCUUCUCAUGAUCAAACAUUACAAUUAUCUUAAUAGGCUUAAAUAUGCUCAUCACCGCUCUCUAUUCCCUCUAUAUAUUAACUACUACACAACGAGGAAAACUCACAUAUCAUUCGCACAACCUAAACCCAUCCUUUACACGAGAAAACACCCUUAUAUCCAUACACAUACUCCCCCUUCUCCUAUUUACCUUAAACCCCAAAAUUAUUCUAGGACCCACGUACUGUAAAUAUAGUUUAAA-AAAACACUAGAUUGUGAAUCCAGAAAUAGAAGCUCAAAC-CUUCUUAUUUACCGAGAAAGUAAUGUAUGAACUGCUAACUCUGCACUCCGUAUAUAAAAAUACGGCUAUCUCAACUUUUAAAGGAUAGAAGUAAUCCAUUGGCCUUAGGAGCCAAAAA-AUUGGUGCAACUCCAAAUAAAAGUAAUAAAUCUAUUAUCCUCUUUCACCCUUGUCACACUGAUUAUCCUAACUUUACCUAUCAUUAUAAACGUUACAAACAUAUACAAAAACUACCCCUAUGCACCAUACGUAAAAUCUUCUAUUGCAUGUGCCUUCAUCACUAGCCUCAUCCCAACUAUAUUAUUUAUCUCCUCAGGACAAGAAACAAUCAUUUCCAACUGACAUUGAAUAACAAUCCAAACCCUAAAACUAUCUAUUAGCUU"/>
-        <sequence id="seq_Homo_sapiens" taxon="Homo_sapiens" totalcount="4"
-                  value="AAGCUUCACCGGCGCAGUCAUUCUCAUAAUCGCCCACGGGCUUACAUCCUCAUUACUAUUCUGCCUAGCAAACUCAAACUACGAACGCACUCACAGUCGCAUCAUAAUCCUCUCUCAAGGACUUCAAACUCUACUCCCACUAAUAGCUUUUUGAUGACUUCUAGCAAGCCUCGCUAACCUCGCCUUACCCCCCACUAUUAACCUACUGGGAGAACUCUCUGUGCUAGUAACCACGUUCUCCUGAUCAAAUAUCACUCUCCUACUUACAGGACUCAACAUACUAGUCACAGCCCUAUACUCCCUCUACAUAUUUACCACAACACAAUGGGGCUCACUCACCCACCACAUUAACAACAUAAAACCCUCAUUCACACGAGAAAACACCCUCAUGUUCAUACACCUAUCCCCCAUUCUCCUCCUAUCCCUCAACCCCGACAUCAUUACCGGGUUUUCCUCUUGUAAAUAUAGUUUAACCAAAACAUCAGAUUGUGAAUCUGACAACAGAGGCUUA-CGACCCCUUAUUUACCGAGAAAGCU-CACAAGAACUGCUAACUCAUGCCCCCAUGUCUAACAACAUGGCUUUCUCAACUUUUAAAGGAUAACAGCUAUCCAUUGGUCUUAGGCCCCAAAAAUUUUGGUGCAACUCCAAAUAAAAGUAAUAACCAUGCACACUACUAUAACCACCCUAACCCUGACUUCCCUAAUUCCCCCCAUCCUUACCACCCUCGUUAACCCUAACAAAAAAAACUCAUACCCCCAUUAUGUAAAAUCCAUUGUCGCAUCCACCUUUAUUAUCAGUCUCUUCCCCACAACAAUAUUCAUGUGCCUAGACCAAGAAGUUAUUAUCUCGAACUGACACUGAGCCACAACCCAAACAACCCAGCUCUCCCUAAGCUU"/>
-        <sequence id="seq_Pan" taxon="Pan" totalcount="4"
-                  value="AAGCUUCACCGGCGCAAUUAUCCUCAUAAUCGCCCACGGACUUACAUCCUCAUUAUUAUUCUGCCUAGCAAACUCAAAUUAUGAACGCACCCACAGUCGCAUCAUAAUUCUCUCCCAAGGACUUCAAACUCUACUCCCACUAAUAGCCUUUUGAUGACUCCUAGCAAGCCUCGCUAACCUCGCCCUACCCCCUACCAUUAAUCUCCUAGGGGAACUCUCCGUGCUAGUAACCUCAUUCUCCUGAUCAAAUACCACUCUCCUACUCACAGGAUUCAACAUACUAAUCACAGCCCUGUACUCCCUCUACAUGUUUACCACAACACAAUGAGGCUCACUCACCCACCACAUUAAUAACAUAAAGCCCUCAUUCACACGAGAAAAUACUCUCAUAUUUUUACACCUAUCCCCCAUCCUCCUUCUAUCCCUCAAUCCUGAUAUCAUCACUGGAUUCACCUCCUGUAAAUAUAGUUUAACCAAAACAUCAGAUUGUGAAUCUGACAACAGAGGCUCA-CGACCCCUUAUUUACCGAGAAAGCU-UAUAAGAACUGCUAAUUCAUAUCCCCAUGCCUGACAACAUGGCUUUCUCAACUUUUAAAGGAUAACAGCCAUCCGUUGGUCUUAGGCCCCAAAAAUUUUGGUGCAACUCCAAAUAAAAGUAAUAACCAUGUAUACUACCAUAACCACCUUAACCCUAACUCCCUUAAUUCUCCCCAUCCUCACCACCCUCAUUAACCCUAACAAAAAAAACUCAUAUCCCCAUUAUGUGAAAUCCAUUAUCGCGUCCACCUUUAUCAUUAGCCUUUUCCCCACAACAAUAUUCAUAUGCCUAGACCAAGAAGCUAUUAUCUCAAACUGGCACUGAGCAACAACCCAAACAACCCAGCUCUCCCUAAGCUU"/>
-        <sequence id="seq_Gorilla" taxon="Gorilla" totalcount="4"
-                  value="AAGCUUCACCGGCGCAGUUGUUCUUAUAAUUGCCCACGGACUUACAUCAUCAUUAUUAUUCUGCCUAGCAAACUCAAACUACGAACGAACCCACAGCCGCAUCAUAAUUCUCUCUCAAGGACUCCAAACCCUACUCCCACUAAUAGCCCUUUGAUGACUUCUGGCAAGCCUCGCCAACCUCGCCUUACCCCCCACCAUUAACCUACUAGGAGAGCUCUCCGUACUAGUAACCACAUUCUCCUGAUCAAACACCACCCUUUUACUUACAGGAUCUAACAUACUAAUUACAGCCCUGUACUCCCUUUAUAUAUUUACCACAACACAAUGAGGCCCACUCACACACCACAUCACCAACAUAAAACCCUCAUUUACACGAGAAAACAUCCUCAUAUUCAUGCACCUAUCCCCCAUCCUCCUCCUAUCCCUCAACCCCGAUAUUAUCACCGGGUUCACCUCCUGUAAAUAUAGUUUAACCAAAACAUCAGAUUGUGAAUCUGAUAACAGAGGCUCA-CAACCCCUUAUUUACCGAGAAAGCU-CGUAAGAGCUGCUAACUCAUACCCCCGUGCUUGACAACAUGGCUUUCUCAACUUUUAAAGGAUAACAGCUAUCCAUUGGUCUUAGGACCCAAAAAUUUUGGUGCAACUCCAAAUAAAAGUAAUAACUAUGUACGCUACCAUAACCACCUUAGCCCUAACUUCCUUAAUUCCCCCUAUCCUUACCACCUUCAUCAAUCCUAACAAAAAAAGCUCAUACCCCCAUUACGUAAAAUCUAUCGUCGCAUCCACCUUUAUCAUCAGCCUCUUCCCCACAACAAUAUUUCUAUGCCUAGACCAAGAAGCUAUUAUCUCAAGCUGACACUGAGCAACAACCCAAACAAUUCAACUCUCCCUAAGCUU"/>
-        <sequence id="seq_Pongo" taxon="Pongo" totalcount="4"
-                  value="AAGCUUCACCGGCGCAACCACCCUCAUGAUUGCCCAUGGACUCACAUCCUCCCUACUGUUCUGCCUAGCAAACUCAAACUACGAACGAACCCACAGCCGCAUCAUAAUCCUCUCUCAAGGCCUUCAAACUCUACUCCCCCUAAUAGCCCUCUGAUGACUUCUAGCAAGCCUCACUAACCUUGCCCUACCACCCACCAUCAACCUUCUAGGAGAACUCUCCGUACUAAUAGCCAUAUUCUCUUGAUCUAACAUCACCAUCCUACUAACAGGACUCAACAUACUAAUCACAACCCUAUACUCUCUCUAUAUAUUCACCACAACACAACGAGGUACACCCACACACCACAUCAACAACAUAAAACCUUCUUUCACACGCGAAAAUACCCUCAUGCUCAUACACCUAUCCCCCAUCCUCCUCUUAUCCCUCAACCCCAGCAUCAUCGCUGGGUUCGCCUACUGUAAAUAUAGUUUAACCAAAACAUUAGAUUGUGAAUCUAAUAAUAGGGCCCCA-CAACCCCUUAUUUACCGAGAAAGCU-CACAAGAACUGCUAACUCUCACU-CCAUGUGUGACAACAUGGCUUUCUCAGCUUUUAAAGGAUAACAGCUAUCCCUUGGUCUUAGGAUCCAAAAAUUUUGGUGCAACUCCAAAUAAAAGUAACAGCCAUGUUUACCACCAUAACUGCCCUCACCUUAACUUCCCUAAUCCCCCCCAUUACCGCUACCCUCAUUAACCCCAACAAAAAAAACCCAUACCCCCACUAUGUAAAAACGGCCAUCGCAUCCGCCUUUACUAUCAGCCUUAUCCCAACAACAAUAUUUAUCUGCCUAGGACAAGAAACCAUCGUCACAAACUGAUGCUGAACAACCACCCAGACACUACAACUCUCACUAAGCUU"/>
-        <sequence id="seq_Hylobates" taxon="Hylobates" totalcount="4"
-                  value="AAGCUUUACAGGUGCAACCGUCCUCAUAAUCGCCCACGGACUAACCUCUUCCCUGCUAUUCUGCCUUGCAAACUCAAACUACGAACGAACUCACAGCCGCAUCAUAAUCCUAUCUCGAGGGCUCCAAGCCUUACUCCCACUGAUAGCCUUCUGAUGACUCGCAGCAAGCCUCGCUAACCUCGCCCUACCCCCCACUAUUAACCUCCUAGGUGAACUCUUCGUACUAAUGGCCUCCUUCUCCUGGGCAAACACUACUAUUACACUCACCGGGCUCAACGUACUAAUCACGGCCCUAUACUCCCUUUACAUAUUUAUCAUAACACAACGAGGCACACUUACACACCACAUUAAAAACAUAAAACCCUCACUCACACGAGAAAACAUAUUAAUACUUAUGCACCUCUUCCCCCUCCUCCUCCUAACCCUCAACCCUAACAUCAUUACUGGCUUUACUCCCUGUAAACAUAGUUUAAUCAAAACAUUAGAUUGUGAAUCUAACAAUAGAGGCUCG-AAACCUCUUGCUUACCGAGAAAGCC-CACAAGAACUGCUAACUCACUAUCCCAUGUAUGACAACAUGGCUUUCUCAACUUUUAAAGGAUAACAGCUAUCCAUUGGUCUUAGGACCCAAAAAUUUUGGUGCAACUCCAAAUAAAAGUAAUAGCAAUGUACACCACCAUAGCCAUUCUAACGCUAACCUCCCUAAUUCCCCCCAUUACAGCCACCCUUAUUAACCCCAAUAAAAAGAACUUAUACCCGCACUACGUAAAAAUGACCAUUGCCUCUACCUUUAUAAUCAGCCUAUUUCCCACAAUAAUAUUCAUGUGCACAGACCAAGAAACCAUUAUUUCAAACUGACACUGAACUGCAACCCAAACGCUAGAACUCUCCCUAAGCUU"/>
-        <sequence id="seq_Macaca_fuscata" taxon="Macaca_fuscata" totalcount="4"
-                  value="AAGCUUUUCCGGCGCAACCAUCCUUAUGAUCGCUCACGGACUCACCUCUUCCAUAUAUUUCUGCCUAGCCAAUUCAAACUAUGAACGCACUCACAACCGUACCAUACUACUGUCCCGAGGACUUCAAAUCCUACUUCCACUAACAGCCUUUUGAUGAUUAACAGCAAGCCUUACUAACCUUGCCCUACCCCCCACUAUCAAUCUACUAGGUGAACUCUUUGUAAUCGCAACCUCAUUCUCCUGAUCCCAUAUCACCAUUAUGCUAACAGGACUUAACAUAUUAAUUACGGCCCUCUACUCUCUCCACAUAUUCACUACAACACAACGAGGAACACUCACACAUCACAUAAUCAACAUAAAGCCCCCCUUCACACGAGAAAACACAUUAAUAUUCAUACACCUCGCUCCAAUUAUCCUUCUAUCCCUCAACCCCAACAUCAUCCUGGGGUUUACCUCCUGUAGAUAUAGUUUAACUAAAACACUAGAUUGUGAAUCUAACCAUAGAGACUCA-CCACCUCUUAUUUACCGAGAAAACU-CGCAAGGACUGCUAACCCAUGUACCCGUACCUAAAAUUACGGUUUUCUCAACUUUUAAAGGAUAACAGCUAUCCAUUGACCUUAGGAGUCAAAAACAUUGGUGCAACUCCAAAUAAAAGUAAUAAUCAUGCACACCCCCAUCAUUAUAACAACCCUUAUCUCCCUAACUCUCCCAAUUUUUGCCACCCUCAUCAACCCUUACAAAAAACGUCCAUACCCAGAUUACGUAAAAACAACCGUAAUAUAUGCUUUCAUCAUCAGCCUCCCCUCAACAACUUUAUUCAUCUUCUCAAACCAAGAAACAACCAUUUGGAGCUGACAUUGAAUAAUGACCCAAACACUAGACCUAACGCUAAGCUU"/>
-        <sequence id="seq_M._mulatta" taxon="M._mulatta" totalcount="4"
-                  value="AAGCUUUUCUGGCGCAACCAUCCUCAUGAUUGCUCACGGACUCACCUCUUCCAUAUAUUUCUGCCUAGCCAAUUCAAACUAUGAACGCACUCACAACCGUACCAUACUACUGUCCCGGGGACUUCAAAUCCUACUUCCACUAACAGCUUUCUGAUGAUUAACAGCAAGCCUUACUAACCUUGCCCUACCCCCCACUAUCAACCUACUAGGUGAACUCUUUGUAAUCGCGACCUCAUUCUCCUGGUCCCAUAUCACCAUUAUAUUAACAGGAUUUAACAUACUAAUUACGGCCCUCUACUCCCUCCACAUAUUCACCACAACACAACGAGGAGCACUCACACAUCACAUAAUCAACAUAAAACCCCCCUUCACACGAGAAAACAUAUUAAUAUUCAUACACCUCGCUCCAAUCAUCCUCCUAUCUCUCAACCCCAACAUCAUCCUGGGGUUUACUUCCUGUAGAUAUAGUUUAACUAAAACAUUAGAUUGUGAAUCUAACCAUAGAGACUUA-CCACCUCUUAUUUACCGAGAAAACU-CGCGAGGACUGCUAACCCAUGUAUCCGUACCUAAAAUUACGGUUUUCUCAACUUUUAAAGGAUAACAGCUAUCCAUUGACCUUAGGAGUCAAAAAUAUUGGUGCAACUCCAAAUAAAAGUAAUAAUCAUGCACACCCCUAUCAUAAUAACAACCCUUAUCUCCCUAACUCUCCCAAUUUUUGCCACCCUCAUCAACCCUUACAAAAAACGUCCAUACCCAGAUUACGUAAAAACAACCGUAAUAUAUGCUUUCAUCAUCAGCCUCCCCUCAACAACUUUAUUCAUCUUCUCAAACCAAGAAACAACCAUUUGAAGCUGACAUUGAAUAAUAACCCAAACACUAGACCUAACACUAAGCUU"/>
-        <sequence id="seq_M._fascicularis" taxon="M._fascicularis" totalcount="4"
-                  value="AAGCUUCUCCGGCGCAACCACCCUUAUAAUCGCCCACGGGCUCACCUCUUCCAUGUAUUUCUGCUUGGCCAAUUCAAACUAUGAGCGCACUCAUAACCGUACCAUACUACUAUCCCGAGGACUUCAAAUUCUACUUCCAUUGACAGCCUUCUGAUGACUCACAGCAAGCCUUACUAACCUUGCCCUACCCCCCACUAUUAAUCUACUAGGCGAACUCUUUGUAAUCACAACUUCAUUUUCCUGAUCCCAUAUCACCAUUGUGUUAACGGGCCUUAAUAUACUAAUCACAGCCCUCUACUCUCUCCACAUGUUCAUUACAGUACAACGAGGAACACUCACACACCACAUAAUCAAUAUAAAACCCCCCUUCACACGAGAAAACAUAUUAAUAUUCAUACACCUCGCUCCAAUUAUCCUUCUAUCUCUCAACCCCAACAUCAUCCUGGGGUUUACCUCCUGUAAAUAUAGUUUAACUAAAACAUUAGAUUGUGAAUCUAACUAUAGAGGCCUA-CCACUUCUUAUUUACCGAGAAAACU-CGCAAGGACUGCUAAUCCAUGCCUCCGUACUUAAAACUACGGUUUCCUCAACUUUUAAAGGAUAACAGCUAUCCAUUGACCUUAGGAGUCAAAAACAUUGGUGCAACUCCAAAUAAAAGUAAUAAUCAUGCACACCCCCAUCAUAAUAACAACCCUCAUCUCCCUGACCCUUCCAAUUUUUGCCACCCUCACCAACCCCUAUAAAAAACGUUCAUACCCAGACUACGUAAAAACAACCGUAAUAUAUGCUUUUAUUACCAGUCUCCCCUCAACAACCCUAUUCAUCCUCUCAAACCAAGAAACAACCAUUUGGAGUUGACAUUGAAUAACAACCCAAACAUUAGACCUAACACUAAGCUU"/>
-        <sequence id="seq_M._sylvanus" taxon="M._sylvanus" totalcount="4"
-                  value="AAGCUUCUCCGGUGCAACUAUCCUUAUAGUUGCCCAUGGACUCACCUCUUCCAUAUACUUCUGCUUGGCCAACUCAAACUACGAACGCACCCACAGCCGCAUCAUACUACUAUCCCGAGGACUCCAAAUCCUACUCCCACUAACAGCCUUCUGAUGAUUCACAGCAAGCCUUACUAAUCUUGCUCUACCCUCCACUAUUAAUCUACUGGGCGAACUCUUCGUAAUCGCAACCUCAUUUUCCUGAUCCCACAUCACCAUCAUACUAACAGGACUGAACAUACUAAUUACAGCCCUCUACUCUCUUCACAUAUUCACCACAACACAACGAGGAGCGCUCACACACCACAUAAUUAACAUAAAACCACCUUUCACACGAGAAAACAUAUUAAUACUCAUACACCUCGCUCCAAUUAUUCUUCUAUCUCUUAACCCCAACAUCAUUCUAGGAUUUACUUCCUGUAAAUAUAGUUUAAUUAAAACAUUAGACUGUGAAUCUAACUAUAGAAGCUUA-CCACUUCUUAUUUACCGAGAAAACU-UGCAAGGACCGCUAAUCCACACCUCCGUACUUAAAACUACGGUUUUCUCAACUUUUAAAGGAUAACAGCUAUCCAUUGGCCUUAGGAGUCAAAAAUAUUGGUGCAACUCCAAAUAAAAGUAAUAAUCAUGUAUACCCCCAUCAUAAUAACAACUCUCAUCUCCCUAACUCUUCCAAUUUUCGCUACCCUUAUCAACCCCAACAAAAAACACCUAUAUCCAAACUACGUAAAAACAGCCGUAAUAUAUGCUUUCAUUACCAGCCUCUCUUCAACAACUUUAUAUAUAUUCUUAAACCAAGAAACAAUCAUCUGAAGCUGGCACUGAAUAAUAACCCAAACACUAAGCCUAACAUUAAGCUU"/>
-        <sequence id="seq_Saimiri_sciureus" taxon="Saimiri_sciureus" totalcount="4"
-                  value="AAGCUUCACCGGCGCAAUGAUCCUAAUAAUCGCUCACGGGUUUACUUCGUCUAUGCUAUUCUGCCUAGCAAACUCAAAUUACGAACGAAUUCACAGCCGAACAAUAACAUUUACUCGAGGGCUCCAAACACUAUUCCCGCUUAUAGGCCUCUGAUGACUCCUAGCAAAUCUCGCUAACCUCGCCCUACCCACAGCUAUUAAUCUAGUAGGAGAAUUACUCACAAUCGUAUCUUCCUUCUCUUGAUCCAACUUUACUAUUAUAUUCACAGGACUUAAUAUACUAAUUACAGCACUCUACUCACUUCAUAUGUAUGCCUCUACACAGCGAGGUCCACUUACAUACAGCACCAGCAAUAUAAAACCAAUAUUUACACGAGAAAAUACGCUAAUAUUUAUACAUAUAACACCAAUCCUCCUCCUUACCUUGAGCCCCAAGGUAAUUAUAGGACCCUCACCUUGUAAUUAUAGUUUAGCUAAAACAUUAGAUUGUGAAUCUAAUAAUAGAAGAAUA-UAACUUCUUAAUUACCGAGAAAGUG-CGCAAGAACUGCUAAUUCAUGCUCCCAAGACUAACAACUUGGCUUCCUCAACUUUUAAAGGAUAGUAGUUAUCCAUUGGUCUUAGGAGCCAAAAACAUUGGUGCAACUCCAAAUAAAAGUAAUA---AUACACUUCUCCAUCACUCUAAUAACACUAAUUAGCCUACUAGCGCCAAUCCUAGCUACCCUCAUUAACCCUAACAAAAGCACACUAUACCCGUACUACGUAAAACUAGCCAUCAUCUACGCCCUCAUUACCAGUACCUUAUCUAUAAUAUUCUUUAUCCUUACAGGCCAAGAAUCAAUAAUUUCAAACUGACACUGAAUAACUAUCCAAACCAUCAAACUAUCCCUAAGCUU"/>
-        <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4"
-                  value="AAGUUUCAUUGGAGCCACCACUCUUAUAAUUGCCCAUGGCCUCACCUCCUCCCUAUUAUUUUGCCUAGCAAAUACAAACUACGAACGAGUCCACAGUCGAACAAUAGCACUAGCCCGUGGCCUUCAAACCCUAUUACCUCUUGCAGCAACAUGAUGACUCCUCGCCAGCUUAACCAACCUGGCCCUUCCCCCAACAAUUAAUUUAAUCGGUGAACUGUCCGUAAUAAUAGCAGCAUUUUCAUGGUCACACCUAACUAUUAUCUUAGUAGGCCUUAACACCCUUAUCACCGCCCUAUAUUCCCUAUAUAUACUAAUCAUAACUCAACGAGGAAAAUACACAUAUCAUAUCAACAAUAUCAUGCCCCCUUUCACCCGAGAAAAUACAUUAAUAAUCAUACACCUAUUUCCCUUAAUCCUACUAUCUACCAACCCCAAAGUAAUUAUAGGAACCAUGUACUGUAAAUAUAGUUUAAACAAAACAUUAGAUUGUGAGUCUAAUAAUAGAAGCCCAAAGAUUUCUUAUUUACCAAGAAAGUA-UGCAAGAACUGCUAACUCAUGCCUCCAUAUAUAACAAUGUGGCUUUCUU-ACUUUUAAAGGAUAGAAGUAAUCCAUCGGUCUUAGGAACCGAAAA-AUUGGUGCAACUCCAAAUAAAAGUAAUAAAUUUAUUUUCAUCCUCCAUUUUACUAUCACUUACACUCUUAAUUACCCCAUUUAUUAUUACAACAACUAAAAAAUAUGAAACACAUGCAUACCCUUACUACGUAAAAAACUCUAUCGCCUGCGCAUUUAUAACAAGCCUAGUCCCAAUGCUCAUAUUUCUAUACACAAAUCAAGAAAUAAUCAUUUCCAACUGACAUUGAAUAACGAUUCAUACUAUCAAAUUAUGCCUAAGCUU"/>
+        <sequence id="seq_Lemur_catta" taxon="Lemur_catta" totalcount="4" value="AAGCUUCAUAGGAGCAACCAUUCUAAUAAUCGCACAUGGCCUUACAUCAUCCAUAUUAUUCUGUCUAGCCAACUCUAACUACGAACGAAUCCAUAGCCGUACAAUACUACUAGCACGAGGGAUCCAAACCAUUCUCCCUCUUAUAGCCACCUGAUGACUACUCGCCAGCCUAACUAACCUAGCCCUACCCACCUCUAUCAAUUUAAUUGGCGAACUAUUCGUCACUAUAGCAUCCUUCUCAUGAUCAAACAUUACAAUUAUCUUAAUAGGCUUAAAUAUGCUCAUCACCGCUCUCUAUUCCCUCUAUAUAUUAACUACUACACAACGAGGAAAACUCACAUAUCAUUCGCACAACCUAAACCCAUCCUUUACACGAGAAAACACCCUUAUAUCCAUACACAUACUCCCCCUUCUCCUAUUUACCUUAAACCCCAAAAUUAUUCUAGGACCCACGUACUGUAAAUAUAGUUUAAA-AAAACACUAGAUUGUGAAUCCAGAAAUAGAAGCUCAAAC-CUUCUUAUUUACCGAGAAAGUAAUGUAUGAACUGCUAACUCUGCACUCCGUAUAUAAAAAUACGGCUAUCUCAACUUUUAAAGGAUAGAAGUAAUCCAUUGGCCUUAGGAGCCAAAAA-AUUGGUGCAACUCCAAAUAAAAGUAAUAAAUCUAUUAUCCUCUUUCACCCUUGUCACACUGAUUAUCCUAACUUUACCUAUCAUUAUAAACGUUACAAACAUAUACAAAAACUACCCCUAUGCACCAUACGUAAAAUCUUCUAUUGCAUGUGCCUUCAUCACUAGCCUCAUCCCAACUAUAUUAUUUAUCUCCUCAGGACAAGAAACAAUCAUUUCCAACUGACAUUGAAUAACAAUCCAAACCCUAAAACUAUCUAUUAGCUU"/>
+        <sequence id="seq_Homo_sapiens" taxon="Homo_sapiens" totalcount="4" value="AAGCUUCACCGGCGCAGUCAUUCUCAUAAUCGCCCACGGGCUUACAUCCUCAUUACUAUUCUGCCUAGCAAACUCAAACUACGAACGCACUCACAGUCGCAUCAUAAUCCUCUCUCAAGGACUUCAAACUCUACUCCCACUAAUAGCUUUUUGAUGACUUCUAGCAAGCCUCGCUAACCUCGCCUUACCCCCCACUAUUAACCUACUGGGAGAACUCUCUGUGCUAGUAACCACGUUCUCCUGAUCAAAUAUCACUCUCCUACUUACAGGACUCAACAUACUAGUCACAGCCCUAUACUCCCUCUACAUAUUUACCACAACACAAUGGGGCUCACUCACCCACCACAUUAACAACAUAAAACCCUCAUUCACACGAGAAAACACCCUCAUGUUCAUACACCUAUCCCCCAUUCUCCUCCUAUCCCUCAACCCCGACAUCAUUACCGGGUUUUCCUCUUGUAAAUAUAGUUUAACCAAAACAUCAGAUUGUGAAUCUGACAACAGAGGCUUA-CGACCCCUUAUUUACCGAGAAAGCU-CACAAGAACUGCUAACUCAUGCCCCCAUGUCUAACAACAUGGCUUUCUCAACUUUUAAAGGAUAACAGCUAUCCAUUGGUCUUAGGCCCCAAAAAUUUUGGUGCAACUCCAAAUAAAAGUAAUAACCAUGCACACUACUAUAACCACCCUAACCCUGACUUCCCUAAUUCCCCCCAUCCUUACCACCCUCGUUAACCCUAACAAAAAAAACUCAUACCCCCAUUAUGUAAAAUCCAUUGUCGCAUCCACCUUUAUUAUCAGUCUCUUCCCCACAACAAUAUUCAUGUGCCUAGACCAAGAAGUUAUUAUCUCGAACUGACACUGAGCCACAACCCAAACAACCCAGCUCUCCCUAAGCUU"/>
+        <sequence id="seq_Pan" taxon="Pan" totalcount="4" value="AAGCUUCACCGGCGCAAUUAUCCUCAUAAUCGCCCACGGACUUACAUCCUCAUUAUUAUUCUGCCUAGCAAACUCAAAUUAUGAACGCACCCACAGUCGCAUCAUAAUUCUCUCCCAAGGACUUCAAACUCUACUCCCACUAAUAGCCUUUUGAUGACUCCUAGCAAGCCUCGCUAACCUCGCCCUACCCCCUACCAUUAAUCUCCUAGGGGAACUCUCCGUGCUAGUAACCUCAUUCUCCUGAUCAAAUACCACUCUCCUACUCACAGGAUUCAACAUACUAAUCACAGCCCUGUACUCCCUCUACAUGUUUACCACAACACAAUGAGGCUCACUCACCCACCACAUUAAUAACAUAAAGCCCUCAUUCACACGAGAAAAUACUCUCAUAUUUUUACACCUAUCCCCCAUCCUCCUUCUAUCCCUCAAUCCUGAUAUCAUCACUGGAUUCACCUCCUGUAAAUAUAGUUUAACCAAAACAUCAGAUUGUGAAUCUGACAACAGAGGCUCA-CGACCCCUUAUUUACCGAGAAAGCU-UAUAAGAACUGCUAAUUCAUAUCCCCAUGCCUGACAACAUGGCUUUCUCAACUUUUAAAGGAUAACAGCCAUCCGUUGGUCUUAGGCCCCAAAAAUUUUGGUGCAACUCCAAAUAAAAGUAAUAACCAUGUAUACUACCAUAACCACCUUAACCCUAACUCCCUUAAUUCUCCCCAUCCUCACCACCCUCAUUAACCCUAACAAAAAAAACUCAUAUCCCCAUUAUGUGAAAUCCAUUAUCGCGUCCACCUUUAUCAUUAGCCUUUUCCCCACAACAAUAUUCAUAUGCCUAGACCAAGAAGCUAUUAUCUCAAACUGGCACUGAGCAACAACCCAAACAACCCAGCUCUCCCUAAGCUU"/>
+        <sequence id="seq_Gorilla" taxon="Gorilla" totalcount="4" value="AAGCUUCACCGGCGCAGUUGUUCUUAUAAUUGCCCACGGACUUACAUCAUCAUUAUUAUUCUGCCUAGCAAACUCAAACUACGAACGAACCCACAGCCGCAUCAUAAUUCUCUCUCAAGGACUCCAAACCCUACUCCCACUAAUAGCCCUUUGAUGACUUCUGGCAAGCCUCGCCAACCUCGCCUUACCCCCCACCAUUAACCUACUAGGAGAGCUCUCCGUACUAGUAACCACAUUCUCCUGAUCAAACACCACCCUUUUACUUACAGGAUCUAACAUACUAAUUACAGCCCUGUACUCCCUUUAUAUAUUUACCACAACACAAUGAGGCCCACUCACACACCACAUCACCAACAUAAAACCCUCAUUUACACGAGAAAACAUCCUCAUAUUCAUGCACCUAUCCCCCAUCCUCCUCCUAUCCCUCAACCCCGAUAUUAUCACCGGGUUCACCUCCUGUAAAUAUAGUUUAACCAAAACAUCAGAUUGUGAAUCUGAUAACAGAGGCUCA-CAACCCCUUAUUUACCGAGAAAGCU-CGUAAGAGCUGCUAACUCAUACCCCCGUGCUUGACAACAUGGCUUUCUCAACUUUUAAAGGAUAACAGCUAUCCAUUGGUCUUAGGACCCAAAAAUUUUGGUGCAACUCCAAAUAAAAGUAAUAACUAUGUACGCUACCAUAACCACCUUAGCCCUAACUUCCUUAAUUCCCCCUAUCCUUACCACCUUCAUCAAUCCUAACAAAAAAAGCUCAUACCCCCAUUACGUAAAAUCUAUCGUCGCAUCCACCUUUAUCAUCAGCCUCUUCCCCACAACAAUAUUUCUAUGCCUAGACCAAGAAGCUAUUAUCUCAAGCUGACACUGAGCAACAACCCAAACAAUUCAACUCUCCCUAAGCUU"/>
+        <sequence id="seq_Pongo" taxon="Pongo" totalcount="4" value="AAGCUUCACCGGCGCAACCACCCUCAUGAUUGCCCAUGGACUCACAUCCUCCCUACUGUUCUGCCUAGCAAACUCAAACUACGAACGAACCCACAGCCGCAUCAUAAUCCUCUCUCAAGGCCUUCAAACUCUACUCCCCCUAAUAGCCCUCUGAUGACUUCUAGCAAGCCUCACUAACCUUGCCCUACCACCCACCAUCAACCUUCUAGGAGAACUCUCCGUACUAAUAGCCAUAUUCUCUUGAUCUAACAUCACCAUCCUACUAACAGGACUCAACAUACUAAUCACAACCCUAUACUCUCUCUAUAUAUUCACCACAACACAACGAGGUACACCCACACACCACAUCAACAACAUAAAACCUUCUUUCACACGCGAAAAUACCCUCAUGCUCAUACACCUAUCCCCCAUCCUCCUCUUAUCCCUCAACCCCAGCAUCAUCGCUGGGUUCGCCUACUGUAAAUAUAGUUUAACCAAAACAUUAGAUUGUGAAUCUAAUAAUAGGGCCCCA-CAACCCCUUAUUUACCGAGAAAGCU-CACAAGAACUGCUAACUCUCACU-CCAUGUGUGACAACAUGGCUUUCUCAGCUUUUAAAGGAUAACAGCUAUCCCUUGGUCUUAGGAUCCAAAAAUUUUGGUGCAACUCCAAAUAAAAGUAACAGCCAUGUUUACCACCAUAACUGCCCUCACCUUAACUUCCCUAAUCCCCCCCAUUACCGCUACCCUCAUUAACCCCAACAAAAAAAACCCAUACCCCCACUAUGUAAAAACGGCCAUCGCAUCCGCCUUUACUAUCAGCCUUAUCCCAACAACAAUAUUUAUCUGCCUAGGACAAGAAACCAUCGUCACAAACUGAUGCUGAACAACCACCCAGACACUACAACUCUCACUAAGCUU"/>
+        <sequence id="seq_Hylobates" taxon="Hylobates" totalcount="4" value="AAGCUUUACAGGUGCAACCGUCCUCAUAAUCGCCCACGGACUAACCUCUUCCCUGCUAUUCUGCCUUGCAAACUCAAACUACGAACGAACUCACAGCCGCAUCAUAAUCCUAUCUCGAGGGCUCCAAGCCUUACUCCCACUGAUAGCCUUCUGAUGACUCGCAGCAAGCCUCGCUAACCUCGCCCUACCCCCCACUAUUAACCUCCUAGGUGAACUCUUCGUACUAAUGGCCUCCUUCUCCUGGGCAAACACUACUAUUACACUCACCGGGCUCAACGUACUAAUCACGGCCCUAUACUCCCUUUACAUAUUUAUCAUAACACAACGAGGCACACUUACACACCACAUUAAAAACAUAAAACCCUCACUCACACGAGAAAACAUAUUAAUACUUAUGCACCUCUUCCCCCUCCUCCUCCUAACCCUCAACCCUAACAUCAUUACUGGCUUUACUCCCUGUAAACAUAGUUUAAUCAAAACAUUAGAUUGUGAAUCUAACAAUAGAGGCUCG-AAACCUCUUGCUUACCGAGAAAGCC-CACAAGAACUGCUAACUCACUAUCCCAUGUAUGACAACAUGGCUUUCUCAACUUUUAAAGGAUAACAGCUAUCCAUUGGUCUUAGGACCCAAAAAUUUUGGUGCAACUCCAAAUAAAAGUAAUAGCAAUGUACACCACCAUAGCCAUUCUAACGCUAACCUCCCUAAUUCCCCCCAUUACAGCCACCCUUAUUAACCCCAAUAAAAAGAACUUAUACCCGCACUACGUAAAAAUGACCAUUGCCUCUACCUUUAUAAUCAGCCUAUUUCCCACAAUAAUAUUCAUGUGCACAGACCAAGAAACCAUUAUUUCAAACUGACACUGAACUGCAACCCAAACGCUAGAACUCUCCCUAAGCUU"/>
+        <sequence id="seq_Macaca_fuscata" taxon="Macaca_fuscata" totalcount="4" value="AAGCUUUUCCGGCGCAACCAUCCUUAUGAUCGCUCACGGACUCACCUCUUCCAUAUAUUUCUGCCUAGCCAAUUCAAACUAUGAACGCACUCACAACCGUACCAUACUACUGUCCCGAGGACUUCAAAUCCUACUUCCACUAACAGCCUUUUGAUGAUUAACAGCAAGCCUUACUAACCUUGCCCUACCCCCCACUAUCAAUCUACUAGGUGAACUCUUUGUAAUCGCAACCUCAUUCUCCUGAUCCCAUAUCACCAUUAUGCUAACAGGACUUAACAUAUUAAUUACGGCCCUCUACUCUCUCCACAUAUUCACUACAACACAACGAGGAACACUCACACAUCACAUAAUCAACAUAAAGCCCCCCUUCACACGAGAAAACACAUUAAUAUUCAUACACCUCGCUCCAAUUAUCCUUCUAUCCCUCAACCCCAACAUCAUCCUGGGGUUUACCUCCUGUAGAUAUAGUUUAACUAAAACACUAGAUUGUGAAUCUAACCAUAGAGACUCA-CCACCUCUUAUUUACCGAGAAAACU-CGCAAGGACUGCUAACCCAUGUACCCGUACCUAAAAUUACGGUUUUCUCAACUUUUAAAGGAUAACAGCUAUCCAUUGACCUUAGGAGUCAAAAACAUUGGUGCAACUCCAAAUAAAAGUAAUAAUCAUGCACACCCCCAUCAUUAUAACAACCCUUAUCUCCCUAACUCUCCCAAUUUUUGCCACCCUCAUCAACCCUUACAAAAAACGUCCAUACCCAGAUUACGUAAAAACAACCGUAAUAUAUGCUUUCAUCAUCAGCCUCCCCUCAACAACUUUAUUCAUCUUCUCAAACCAAGAAACAACCAUUUGGAGCUGACAUUGAAUAAUGACCCAAACACUAGACCUAACGCUAAGCUU"/>
+        <sequence id="seq_M._mulatta" taxon="M._mulatta" totalcount="4" value="AAGCUUUUCUGGCGCAACCAUCCUCAUGAUUGCUCACGGACUCACCUCUUCCAUAUAUUUCUGCCUAGCCAAUUCAAACUAUGAACGCACUCACAACCGUACCAUACUACUGUCCCGGGGACUUCAAAUCCUACUUCCACUAACAGCUUUCUGAUGAUUAACAGCAAGCCUUACUAACCUUGCCCUACCCCCCACUAUCAACCUACUAGGUGAACUCUUUGUAAUCGCGACCUCAUUCUCCUGGUCCCAUAUCACCAUUAUAUUAACAGGAUUUAACAUACUAAUUACGGCCCUCUACUCCCUCCACAUAUUCACCACAACACAACGAGGAGCACUCACACAUCACAUAAUCAACAUAAAACCCCCCUUCACACGAGAAAACAUAUUAAUAUUCAUACACCUCGCUCCAAUCAUCCUCCUAUCUCUCAACCCCAACAUCAUCCUGGGGUUUACUUCCUGUAGAUAUAGUUUAACUAAAACAUUAGAUUGUGAAUCUAACCAUAGAGACUUA-CCACCUCUUAUUUACCGAGAAAACU-CGCGAGGACUGCUAACCCAUGUAUCCGUACCUAAAAUUACGGUUUUCUCAACUUUUAAAGGAUAACAGCUAUCCAUUGACCUUAGGAGUCAAAAAUAUUGGUGCAACUCCAAAUAAAAGUAAUAAUCAUGCACACCCCUAUCAUAAUAACAACCCUUAUCUCCCUAACUCUCCCAAUUUUUGCCACCCUCAUCAACCCUUACAAAAAACGUCCAUACCCAGAUUACGUAAAAACAACCGUAAUAUAUGCUUUCAUCAUCAGCCUCCCCUCAACAACUUUAUUCAUCUUCUCAAACCAAGAAACAACCAUUUGAAGCUGACAUUGAAUAAUAACCCAAACACUAGACCUAACACUAAGCUU"/>
+        <sequence id="seq_M._fascicularis" taxon="M._fascicularis" totalcount="4" value="AAGCUUCUCCGGCGCAACCACCCUUAUAAUCGCCCACGGGCUCACCUCUUCCAUGUAUUUCUGCUUGGCCAAUUCAAACUAUGAGCGCACUCAUAACCGUACCAUACUACUAUCCCGAGGACUUCAAAUUCUACUUCCAUUGACAGCCUUCUGAUGACUCACAGCAAGCCUUACUAACCUUGCCCUACCCCCCACUAUUAAUCUACUAGGCGAACUCUUUGUAAUCACAACUUCAUUUUCCUGAUCCCAUAUCACCAUUGUGUUAACGGGCCUUAAUAUACUAAUCACAGCCCUCUACUCUCUCCACAUGUUCAUUACAGUACAACGAGGAACACUCACACACCACAUAAUCAAUAUAAAACCCCCCUUCACACGAGAAAACAUAUUAAUAUUCAUACACCUCGCUCCAAUUAUCCUUCUAUCUCUCAACCCCAACAUCAUCCUGGGGUUUACCUCCUGUAAAUAUAGUUUAACUAAAACAUUAGAUUGUGAAUCUAACUAUAGAGGCCUA-CCACUUCUUAUUUACCGAGAAAACU-CGCAAGGACUGCUAAUCCAUGCCUCCGUACUUAAAACUACGGUUUCCUCAACUUUUAAAGGAUAACAGCUAUCCAUUGACCUUAGGAGUCAAAAACAUUGGUGCAACUCCAAAUAAAAGUAAUAAUCAUGCACACCCCCAUCAUAAUAACAACCCUCAUCUCCCUGACCCUUCCAAUUUUUGCCACCCUCACCAACCCCUAUAAAAAACGUUCAUACCCAGACUACGUAAAAACAACCGUAAUAUAUGCUUUUAUUACCAGUCUCCCCUCAACAACCCUAUUCAUCCUCUCAAACCAAGAAACAACCAUUUGGAGUUGACAUUGAAUAACAACCCAAACAUUAGACCUAACACUAAGCUU"/>
+        <sequence id="seq_M._sylvanus" taxon="M._sylvanus" totalcount="4" value="AAGCUUCUCCGGUGCAACUAUCCUUAUAGUUGCCCAUGGACUCACCUCUUCCAUAUACUUCUGCUUGGCCAACUCAAACUACGAACGCACCCACAGCCGCAUCAUACUACUAUCCCGAGGACUCCAAAUCCUACUCCCACUAACAGCCUUCUGAUGAUUCACAGCAAGCCUUACUAAUCUUGCUCUACCCUCCACUAUUAAUCUACUGGGCGAACUCUUCGUAAUCGCAACCUCAUUUUCCUGAUCCCACAUCACCAUCAUACUAACAGGACUGAACAUACUAAUUACAGCCCUCUACUCUCUUCACAUAUUCACCACAACACAACGAGGAGCGCUCACACACCACAUAAUUAACAUAAAACCACCUUUCACACGAGAAAACAUAUUAAUACUCAUACACCUCGCUCCAAUUAUUCUUCUAUCUCUUAACCCCAACAUCAUUCUAGGAUUUACUUCCUGUAAAUAUAGUUUAAUUAAAACAUUAGACUGUGAAUCUAACUAUAGAAGCUUA-CCACUUCUUAUUUACCGAGAAAACU-UGCAAGGACCGCUAAUCCACACCUCCGUACUUAAAACUACGGUUUUCUCAACUUUUAAAGGAUAACAGCUAUCCAUUGGCCUUAGGAGUCAAAAAUAUUGGUGCAACUCCAAAUAAAAGUAAUAAUCAUGUAUACCCCCAUCAUAAUAACAACUCUCAUCUCCCUAACUCUUCCAAUUUUCGCUACCCUUAUCAACCCCAACAAAAAACACCUAUAUCCAAACUACGUAAAAACAGCCGUAAUAUAUGCUUUCAUUACCAGCCUCUCUUCAACAACUUUAUAUAUAUUCUUAAACCAAGAAACAAUCAUCUGAAGCUGGCACUGAAUAAUAACCCAAACACUAAGCCUAACAUUAAGCUU"/>
+        <sequence id="seq_Saimiri_sciureus" taxon="Saimiri_sciureus" totalcount="4" value="AAGCUUCACCGGCGCAAUGAUCCUAAUAAUCGCUCACGGGUUUACUUCGUCUAUGCUAUUCUGCCUAGCAAACUCAAAUUACGAACGAAUUCACAGCCGAACAAUAACAUUUACUCGAGGGCUCCAAACACUAUUCCCGCUUAUAGGCCUCUGAUGACUCCUAGCAAAUCUCGCUAACCUCGCCCUACCCACAGCUAUUAAUCUAGUAGGAGAAUUACUCACAAUCGUAUCUUCCUUCUCUUGAUCCAACUUUACUAUUAUAUUCACAGGACUUAAUAUACUAAUUACAGCACUCUACUCACUUCAUAUGUAUGCCUCUACACAGCGAGGUCCACUUACAUACAGCACCAGCAAUAUAAAACCAAUAUUUACACGAGAAAAUACGCUAAUAUUUAUACAUAUAACACCAAUCCUCCUCCUUACCUUGAGCCCCAAGGUAAUUAUAGGACCCUCACCUUGUAAUUAUAGUUUAGCUAAAACAUUAGAUUGUGAAUCUAAUAAUAGAAGAAUA-UAACUUCUUAAUUACCGAGAAAGUG-CGCAAGAACUGCUAAUUCAUGCUCCCAAGACUAACAACUUGGCUUCCUCAACUUUUAAAGGAUAGUAGUUAUCCAUUGGUCUUAGGAGCCAAAAACAUUGGUGCAACUCCAAAUAAAAGUAAUA---AUACACUUCUCCAUCACUCUAAUAACACUAAUUAGCCUACUAGCGCCAAUCCUAGCUACCCUCAUUAACCCUAACAAAAGCACACUAUACCCGUACUACGUAAAACUAGCCAUCAUCUACGCCCUCAUUACCAGUACCUUAUCUAUAAUAUUCUUUAUCCUUACAGGCCAAGAAUCAAUAAUUUCAAACUGACACUGAAUAACUAUCCAAACCAUCAAACUAUCCCUAAGCUU"/>
+        <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4" value="AAGUUUCAUUGGAGCCACCACUCUUAUAAUUGCCCAUGGCCUCACCUCCUCCCUAUUAUUUUGCCUAGCAAAUACAAACUACGAACGAGUCCACAGUCGAACAAUAGCACUAGCCCGUGGCCUUCAAACCCUAUUACCUCUUGCAGCAACAUGAUGACUCCUCGCCAGCUUAACCAACCUGGCCCUUCCCCCAACAAUUAAUUUAAUCGGUGAACUGUCCGUAAUAAUAGCAGCAUUUUCAUGGUCACACCUAACUAUUAUCUUAGUAGGCCUUAACACCCUUAUCACCGCCCUAUAUUCCCUAUAUAUACUAAUCAUAACUCAACGAGGAAAAUACACAUAUCAUAUCAACAAUAUCAUGCCCCCUUUCACCCGAGAAAAUACAUUAAUAAUCAUACACCUAUUUCCCUUAAUCCUACUAUCUACCAACCCCAAAGUAAUUAUAGGAACCAUGUACUGUAAAUAUAGUUUAAACAAAACAUUAGAUUGUGAGUCUAAUAAUAGAAGCCCAAAGAUUUCUUAUUUACCAAGAAAGUA-UGCAAGAACUGCUAACUCAUGCCUCCAUAUAUAACAAUGUGGCUUUCUU-ACUUUUAAAGGAUAGAAGUAAUCCAUCGGUCUUAGGAACCGAAAA-AUUGGUGCAACUCCAAAUAAAAGUAAUAAAUUUAUUUUCAUCCUCCAUUUUACUAUCACUUACACUCUUAAUUACCCCAUUUAUUAUUACAACAACUAAAAAAUAUGAAACACAUGCAUACCCUUACUACGUAAAAAACUCUAUCGCCUGCGCAUUUAUAACAAGCCUAGUCCCAAUGCUCAUAUUUCUAUACACAAAUCAAGAAAUAAUCAUUUCCAACUGACAUUGAAUAACGAUUCAUACUAUCAAAUUAUGCCUAAGCUU"/>
     </data>
 
-
-    <map name="Beta">beast.base.inference.distribution.Beta</map>
-    <map name="Exponential">beast.base.inference.distribution.Exponential</map>
-    <map name="InverseGamma">beast.base.inference.distribution.InverseGamma</map>
-    <map name="LogNormal">beast.base.inference.distribution.LogNormalDistributionModel</map>
-    <map name="Gamma">beast.base.inference.distribution.Gamma</map>
-    <map name="Uniform">beast.base.inference.distribution.Uniform</map>
-    <map name="prior">beast.base.inference.distribution.Prior</map>
-    <map name="LaplaceDistribution">beast.base.inference.distribution.LaplaceDistribution</map>
-    <map name="OneOnX">beast.base.inference.distribution.OneOnX</map>
-    <map name="Normal">beast.base.inference.distribution.Normal</map>
-
-
     <run chainLength="5000000" id="mcmc" spec="MCMC">
         <state id="state" storeEvery="5000">
             <tree id="Tree.t:primate" name="stateNode">
                 <taxonset id="TaxonSet.coding" spec="TaxonSet">
-                    <alignment filter="2-457,660-896" id="coding" spec="FilteredAlignment">
+                    <alignment filter="2-457,660-896" id="coding" spec="beast.base.spec.evolution.alignment.FilteredAlignment">
                         <data idref="primate-mtDNA"/>
                     </alignment>
                 </taxonset>
             </tree>
-            <parameter id="birthRate.t:primate" name="stateNode" value="1.0"/>
-            <parameter id="rateAC.s:primate" lower="0.0" name="stateNode" value="1.0"/>
-            <parameter id="rateAG.s:primate" lower="0.0" name="stateNode" value="1.0"/>
-            <parameter id="rateAT.s:primate" lower="0.0" name="stateNode" value="1.0"/>
-            <parameter id="rateCG.s:primate" lower="0.0" name="stateNode" value="1.0"/>
-            <parameter id="rateGT.s:primate" lower="0.0" name="stateNode" value="1.0"/>
-            <parameter dimension="4" id="freqParameter.s:primate" lower="0.0" name="stateNode" upper="1.0"
-                       value="0.25"/>
+            <parameter id="birthRate.t:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+            <parameter id="rateAC.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+            <parameter id="rateAG.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+            <parameter id="rateAT.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+            <parameter id="rateCG.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+            <parameter id="rateGT.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+            <parameter dimension="4" id="freqParameter.s:primate" name="stateNode" value="0.25" spec="beast.base.spec.inference.parameter.SimplexParam"/>
         </state>
 
-        <init estimate="false" id="RandomTree.t:primate" initial="@Tree.t:primate"
-              spec="beast.base.evolution.tree.coalescent.RandomTree" taxa="@coding">
-            <populationModel id="ConstantPopulation0.t:primate" spec="ConstantPopulation">
-                <parameter id="randomPopSize.t:primate" name="popSize" value="1"/>
+        <init estimate="false" id="RandomTree.t:primate" initial="@Tree.t:primate" spec="beast.base.spec.evolution.tree.coalescent.RandomTree" taxa="@coding">
+            <populationModel id="ConstantPopulation0.t:primate" spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
+                <parameter id="randomPopSize.t:primate" name="popSize" value="1" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
             </populationModel>
         </init>
 
         <distribution id="posterior" spec="CompoundDistribution">
             <distribution id="prior" spec="CompoundDistribution">
-                <distribution birthDiffRate="@birthRate.t:primate" id="YuleModel.t:primate"
-                              spec="beast.base.evolution.speciation.YuleModel" tree="@Tree.t:primate"/>
-                <prior id="YuleBirthRatePrior.t:primate" name="distribution" x="@birthRate.t:primate">
-                    <Uniform id="Uniform.0" name="distr" upper="Infinity"/>
-                </prior>
-                <prior id="RateACPrior.s:primate" name="distribution" x="@rateAC.s:primate">
-                    <LogNormal id="LogNormalDistributionModel.0" name="distr">
-                        <parameter estimate="false" id="RealParameter.0" name="M" value="0"/>
-                        <parameter estimate="false" id="RealParameter.01" lower="0.0" name="S" upper="5.0"
-                                   value="1.25"/>
-                    </LogNormal>
-                </prior>
-                <prior id="RateAGPrior.s:primate" name="distribution" x="@rateAG.s:primate">
-                    <LogNormal id="LogNormalDistributionModel.01" name="distr">
-                        <parameter estimate="false" id="RealParameter.02" name="M" value="0"/>
-                        <parameter estimate="false" id="RealParameter.03" lower="0.0" name="S" upper="5.0"
-                                   value="1.25"/>
-                    </LogNormal>
-                </prior>
-                <prior id="RateATPrior.s:primate" name="distribution" x="@rateAT.s:primate">
-                    <LogNormal id="LogNormalDistributionModel.02" name="distr">
-                        <parameter estimate="false" id="RealParameter.04" name="M" value="0"/>
-                        <parameter estimate="false" id="RealParameter.05" lower="0.0" name="S" upper="5.0"
-                                   value="1.25"/>
-                    </LogNormal>
-                </prior>
-                <prior id="RateCGPrior.s:primate" name="distribution" x="@rateCG.s:primate">
-                    <LogNormal id="LogNormalDistributionModel.03" name="distr">
-                        <parameter estimate="false" id="RealParameter.06" name="M" value="0"/>
-                        <parameter estimate="false" id="RealParameter.07" lower="0.0" name="S" upper="5.0"
-                                   value="1.25"/>
-                    </LogNormal>
-                </prior>
-                <prior id="RateGTPrior.s:primate" name="distribution" x="@rateGT.s:primate">
-                    <LogNormal id="LogNormalDistributionModel.04" name="distr">
-                        <parameter estimate="false" id="RealParameter.08" name="M" value="0"/>
-                        <parameter estimate="false" id="RealParameter.09" lower="0.0" name="S" upper="5.0"
-                                   value="1.25"/>
-                    </LogNormal>
-                </prior>
+                <distribution birthDiffRate="@birthRate.t:primate" id="YuleModel.t:primate" spec="beast.base.spec.evolution.speciation.YuleModel" tree="@Tree.t:primate"/>
+                <distribution id="Uniform.0" spec="beast.base.spec.inference.distribution.Uniform" param="@birthRate.t:primate" upper="1.0E6"/>
+                <distribution id="LogNormalDistributionModel.0" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateAC.s:primate">
+                        <parameter estimate="false" id="RealParameter.0" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="RealParameter.01" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                    </distribution>
+                <distribution id="LogNormalDistributionModel.01" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateAG.s:primate">
+                        <parameter estimate="false" id="RealParameter.02" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="RealParameter.03" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                    </distribution>
+                <distribution id="LogNormalDistributionModel.02" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateAT.s:primate">
+                        <parameter estimate="false" id="RealParameter.04" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="RealParameter.05" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                    </distribution>
+                <distribution id="LogNormalDistributionModel.03" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateCG.s:primate">
+                        <parameter estimate="false" id="RealParameter.06" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="RealParameter.07" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                    </distribution>
+                <distribution id="LogNormalDistributionModel.04" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateGT.s:primate">
+                        <parameter estimate="false" id="RealParameter.08" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="RealParameter.09" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                    </distribution>
             </distribution>
             <distribution id="likelihood" spec="CompoundDistribution">
-                <distribution data="@coding" id="treeLikelihood.coding" spec="TreeLikelihood" tree="@Tree.t:primate">
-                    <siteModel id="SiteModel.s:primate" spec="SiteModel">
-                        <parameter estimate="false" id="mutationRate.s:primate" name="mutationRate" value="1.0"/>
-                        <parameter estimate="false" id="gammaShape.s:primate" name="shape" value="1.0"/>
-                        <parameter estimate="false" id="proportionInvariant.s:primate" lower="0.0"
-                                   name="proportionInvariant" upper="1.0" value="0.0"/>
-                        <substModel id="gtr.s:primate" rateAC="@rateAC.s:primate" rateAG="@rateAG.s:primate"
-                                    rateAT="@rateAT.s:primate" rateCG="@rateCG.s:primate" rateGT="@rateGT.s:primate"
-                                    spec="GTR">
-                            <parameter estimate="false" id="rateCT.s:primate" lower="0.0" name="rateCT" value="1.0"/>
-                            <frequencies frequencies="@freqParameter.s:primate" id="estimatedFreqs.s:primate"
-                                         spec="Frequencies"/>
+                <distribution data="@coding" id="treeLikelihood.coding" spec="beast.base.spec.evolution.likelihood.TreeLikelihood" tree="@Tree.t:primate">
+                    <siteModel id="SiteModel.s:primate" spec="beast.base.spec.evolution.sitemodel.SiteModel">
+                        <parameter estimate="false" id="mutationRate.s:primate" name="mutationRate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="gammaShape.s:primate" name="shape" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="proportionInvariant.s:primate" name="proportionInvariant" value="0.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="UnitInterval"/>
+                        <substModel id="gtr.s:primate" rateAC="@rateAC.s:primate" rateAG="@rateAG.s:primate" rateAT="@rateAT.s:primate" rateCG="@rateCG.s:primate" rateGT="@rateGT.s:primate" spec="beast.base.spec.evolution.substitutionmodel.GTR">
+                            <parameter estimate="false" id="rateCT.s:primate" name="rateCT" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+                            <frequencies frequencies="@freqParameter.s:primate" id="estimatedFreqs.s:primate" spec="beast.base.spec.evolution.substitutionmodel.Frequencies"/>
                         </substModel>
                     </siteModel>
-                    <branchRateModel id="StrictClock.c:primate" spec="beast.base.evolution.branchratemodel.StrictClockModel">
-                        <parameter estimate="false" id="clockRate.c:primate" name="clock.rate" value="1.0"/>
+                    <branchRateModel id="StrictClock.c:primate" spec="beast.base.spec.evolution.branchratemodel.StrictClockModel">
+                        <parameter estimate="false" id="clockRate.c:primate" name="clock.rate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
                     </branchRateModel>
                 </distribution>
-                <distribution branchRateModel="@StrictClock.c:primate" id="treeLikelihood.noncoding"
-                              siteModel="@SiteModel.s:primate" spec="TreeLikelihood" tree="@Tree.t:primate">
-                    <data data="@primate-mtDNA" filter="1,458-659,897-898" id="noncoding" spec="FilteredAlignment"/>
+                <distribution branchRateModel="@StrictClock.c:primate" id="treeLikelihood.noncoding" siteModel="@SiteModel.s:primate" spec="beast.base.spec.evolution.likelihood.TreeLikelihood" tree="@Tree.t:primate">
+                    <data data="@primate-mtDNA" filter="1,458-659,897-898" id="noncoding" spec="beast.base.spec.evolution.alignment.FilteredAlignment"/>
                 </distribution>
             </distribution>
         </distribution>
 
-        <operator id="YuleBirthRateScaler.t:primate" parameter="@birthRate.t:primate" scaleFactor="0.75"
-                  spec="ScaleOperator" weight="3.0"/>
+        <operator id="YuleBirthRateScaler.t:primate" parameter="@birthRate.t:primate" scaleFactor="0.75" weight="3.0" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator id="treeScaler.t:primate" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:primate" weight="3.0"/>
+        <operator id="treeScaler.t:primate" scaleFactor="0.5" tree="@Tree.t:primate" weight="3.0" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
 
-        <operator id="treeRootScaler.t:primate" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator"
-                  tree="@Tree.t:primate" weight="3.0"/>
+        <operator id="treeRootScaler.t:primate" rootOnly="true" scaleFactor="0.5" tree="@Tree.t:primate" weight="3.0" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
 
-        <operator id="UniformOperator.t:primate" spec="Uniform" tree="@Tree.t:primate" weight="30.0"/>
+        <operator id="UniformOperator.t:primate" tree="@Tree.t:primate" weight="30.0" spec="beast.base.evolution.operator.Uniform"/>
 
-        <operator id="SubtreeSlide.t:primate" spec="SubtreeSlide" tree="@Tree.t:primate" weight="15.0"/>
+        <operator id="SubtreeSlide.t:primate" spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" tree="@Tree.t:primate" weight="15.0"/>
 
         <operator id="narrow.t:primate" spec="Exchange" tree="@Tree.t:primate" weight="15.0"/>
 
@@ -158,27 +107,21 @@
 
         <operator id="WilsonBalding.t:primate" spec="WilsonBalding" tree="@Tree.t:primate" weight="3.0"/>
 
-        <operator id="RateACScaler.s:primate" parameter="@rateAC.s:primate" scaleFactor="0.5" spec="ScaleOperator"
-                  weight="0.1"/>
+        <operator id="RateACScaler.s:primate" parameter="@rateAC.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator id="RateAGScaler.s:primate" parameter="@rateAG.s:primate" scaleFactor="0.5" spec="ScaleOperator"
-                  weight="0.1"/>
+        <operator id="RateAGScaler.s:primate" parameter="@rateAG.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator id="RateATScaler.s:primate" parameter="@rateAT.s:primate" scaleFactor="0.5" spec="ScaleOperator"
-                  weight="0.1"/>
+        <operator id="RateATScaler.s:primate" parameter="@rateAT.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator id="RateCGScaler.s:primate" parameter="@rateCG.s:primate" scaleFactor="0.5" spec="ScaleOperator"
-                  weight="0.1"/>
+        <operator id="RateCGScaler.s:primate" parameter="@rateCG.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator id="RateGTScaler.s:primate" parameter="@rateGT.s:primate" scaleFactor="0.5" spec="ScaleOperator"
-                  weight="0.1"/>
+        <operator id="RateGTScaler.s:primate" parameter="@rateGT.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator delta="0.01" id="FrequenciesExchanger.s:primate" spec="DeltaExchangeOperator" weight="0.1">
+        <operator delta="0.01" id="FrequenciesExchanger.s:primate" spec="beast.base.spec.inference.operator.DeltaExchangeOperator" weight="0.1">
             <parameter idref="freqParameter.s:primate"/>
         </operator>
 
-        <logger fileName="testRNA.log" id="tracelog" logEvery="5000" model="@posterior" sanitiseHeaders="true"
-                sort="smart">
+        <logger fileName="testRNA.log" id="tracelog" logEvery="5000" model="@posterior" sanitiseHeaders="true" sort="smart">
             <log idref="posterior"/>
             <log idref="likelihood"/>
             <log idref="prior"/>
@@ -197,14 +140,13 @@
 
         <logger id="screenlog" logEvery="5000">
             <log idref="posterior"/>
-            <log arg="@posterior" id="ESS.0" spec="util.ESS"/>
+            <log arg="@posterior" id="ESS.0" spec="beast.base.spec.inference.util.ESS"/>
             <log idref="likelihood"/>
             <log idref="prior"/>
         </logger>
 
         <logger fileName="testRNA.trees" id="treelog.t:primate" logEvery="5000" mode="tree">
-            <log id="TreeWithMetaDataLogger.t:primate" spec="beast.base.evolution.TreeWithMetaDataLogger"
-                 tree="@Tree.t:primate"/>
+            <log id="TreeWithMetaDataLogger.t:primate" spec="beast.base.spec.evolution.TreeWithMetaDataLogger" tree="@Tree.t:primate"/>
         </logger>
 
     </run>
diff --git a/beast-base/src/test/resources/beast.base/examples/testRestrictedGTR.xml b/beast-base/src/test/resources/beast.base/examples/testRestrictedGTR.xml
index d5734fa6..f14f49d4 100644
--- a/beast-base/src/test/resources/beast.base/examples/testRestrictedGTR.xml
+++ b/beast-base/src/test/resources/beast.base/examples/testRestrictedGTR.xml
@@ -1,135 +1,88 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<beast beautitemplate='Standard' beautistatus=''
-       namespace="beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.alignment:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood"
-       version="2.0">
-
+<?xml version='1.0' encoding='UTF-8'?>
+<beast version="2.8"
+       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt"
+       beautitemplate="Standard"
+       beautistatus="">
 
     <data id="primate-mtDNA">
-        <sequence id="seq_Lemur_catta" taxon="Lemur_catta" totalcount="4"
-                  value="AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATTCTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGGGATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCTAGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTCATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTCCCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAACCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATTTACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAACACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATGTATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGATAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTATAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTGCATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAACAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT"/>
-        <sequence id="seq_Homo_sapiens" taxon="Homo_sapiens" totalcount="4"
-                  value="AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
-        <sequence id="seq_Pan" taxon="Pan" totalcount="4"
-                  value="AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATTCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCTCGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAAGCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TATAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCACCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCGCGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAGCTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
-        <sequence id="seq_Gorilla" taxon="Gorilla" totalcount="4"
-                  value="AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGGACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCTCGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTCCTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTCCCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAAACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCTATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CGTAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTACCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCGCATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAGCTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT"/>
-        <sequence id="seq_Pongo" taxon="Pongo" totalcount="4"
-                  value="AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGGCCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCTTGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTCTTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTCTCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAAACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTTATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAACATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGATAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAACAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCGCTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCGCATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAACCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT"/>
-        <sequence id="seq_Hylobates" taxon="Hylobates" totalcount="4"
-                  value="AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATTCTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGGGCTCCAAGCCTTACTCCCACTGATAGCCTTCTGATGACTCGCAGCAAGCCTCGCTAACCTCGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTCCTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTCCCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAAACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCTAACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAACATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CACAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAGCCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTGCCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAACCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT"/>
-        <sequence id="seq_Macaca_fuscata" taxon="Macaca_fuscata" totalcount="4"
-                  value="AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGGACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTCCTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTCTCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAAGCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAACACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT"/>
-        <sequence id="seq_M._mulatta" taxon="M._mulatta" totalcount="4"
-                  value="AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGGACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTCCTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTCCCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCTATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAACATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CGCGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT"/>
-        <sequence id="seq_M._fascicularis" taxon="M._fascicularis" totalcount="4"
-                  value="AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTTCTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGTACCATACTACTATCCCGAGGACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTCCTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTCTCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAACATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTGCCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAATATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAACAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT"/>
-        <sequence id="seq_M._sylvanus" taxon="M._sylvanus" totalcount="4"
-                  value="AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTTCTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGCATCATACTACTATCCCGAGGACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCTTGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTCCTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTCTCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAAACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCTATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAACATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TGCAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCGCTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAATATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAACAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT"/>
-        <sequence id="seq_Saimiri_sciureus" taxon="Saimiri_sciureus" totalcount="4"
-                  value="AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTCTATGCTATTCTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAATAACATTTACTCGAGGGCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCTCGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTCTTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTCACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAAACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCTTACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAACATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CGCAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGATAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAATA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAGCTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCATCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAATCAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT"/>
-        <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4"
-                  value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
+        <sequence id="seq_Lemur_catta" taxon="Lemur_catta" totalcount="4" value="AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATTCTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGGGATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCTAGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTCATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTCCCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAACCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATTTACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAACACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATGTATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGATAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTATAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTGCATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAACAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT"/>
+        <sequence id="seq_Homo_sapiens" taxon="Homo_sapiens" totalcount="4" value="AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
+        <sequence id="seq_Pan" taxon="Pan" totalcount="4" value="AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATTCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCTCGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAAGCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TATAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCACCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCGCGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAGCTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
+        <sequence id="seq_Gorilla" taxon="Gorilla" totalcount="4" value="AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGGACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCTCGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTCCTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTCCCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAAACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCTATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CGTAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTACCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCGCATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAGCTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT"/>
+        <sequence id="seq_Pongo" taxon="Pongo" totalcount="4" value="AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGGCCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCTTGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTCTTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTCTCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAAACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTTATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAACATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGATAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAACAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCGCTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCGCATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAACCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT"/>
+        <sequence id="seq_Hylobates" taxon="Hylobates" totalcount="4" value="AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATTCTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGGGCTCCAAGCCTTACTCCCACTGATAGCCTTCTGATGACTCGCAGCAAGCCTCGCTAACCTCGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTCCTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTCCCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAAACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCTAACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAACATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CACAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAGCCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTGCCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAACCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT"/>
+        <sequence id="seq_Macaca_fuscata" taxon="Macaca_fuscata" totalcount="4" value="AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGGACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTCCTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTCTCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAAGCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAACACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT"/>
+        <sequence id="seq_M._mulatta" taxon="M._mulatta" totalcount="4" value="AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGGACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTCCTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTCCCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCTATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAACATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CGCGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT"/>
+        <sequence id="seq_M._fascicularis" taxon="M._fascicularis" totalcount="4" value="AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTTCTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGTACCATACTACTATCCCGAGGACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTCCTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTCTCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAACATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTGCCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAATATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAACAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT"/>
+        <sequence id="seq_M._sylvanus" taxon="M._sylvanus" totalcount="4" value="AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTTCTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGCATCATACTACTATCCCGAGGACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCTTGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTCCTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTCTCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAAACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCTATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAACATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TGCAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCGCTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAATATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAACAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT"/>
+        <sequence id="seq_Saimiri_sciureus" taxon="Saimiri_sciureus" totalcount="4" value="AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTCTATGCTATTCTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAATAACATTTACTCGAGGGCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCTCGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTCTTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTCACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAAACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCTTACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAACATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CGCAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGATAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAATA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAGCTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCATCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAATCAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT"/>
+        <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4" value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
     </data>
 
-
-    <map name="Beta">beast.base.inference.distribution.Beta</map>
-    <map name="Exponential">beast.base.inference.distribution.Exponential</map>
-    <map name="InverseGamma">beast.base.inference.distribution.InverseGamma</map>
-    <map name="LogNormal">beast.base.inference.distribution.LogNormalDistributionModel</map>
-    <map name="Gamma">beast.base.inference.distribution.Gamma</map>
-    <map name="Uniform">beast.base.inference.distribution.Uniform</map>
-    <map name="prior">beast.base.inference.distribution.Prior</map>
-    <map name="LaplaceDistribution">beast.base.inference.distribution.LaplaceDistribution</map>
-    <map name="OneOnX">beast.base.inference.distribution.OneOnX</map>
-    <map name="Normal">beast.base.inference.distribution.Normal</map>
-
-
     <run chainLength="5000000" id="mcmc" spec="MCMC">
         <state id="state" storeEvery="5000">
             <tree id="Tree.t:primate" name="stateNode">
                 <taxonset id="TaxonSet.coding" spec="TaxonSet">
-                    <alignment filter="2-457,660-896" id="coding" spec="FilteredAlignment">
+                    <alignment filter="2-457,660-896" id="coding" spec="beast.base.spec.evolution.alignment.FilteredAlignment">
                         <data idref="primate-mtDNA"/>
                     </alignment>
                 </taxonset>
             </tree>
-            <parameter id="birthRate.t:primate" name="stateNode" value="1.0"/>
-            <parameter id="rateTransversion.s:primate" lower="0.0" name="stateNode" value="1.0"/>
-            <parameter id="rateAG.s:primate" lower="0.0" name="stateNode" value="1.0"/>
-            <parameter dimension="4" id="freqParameter.s:primate" lower="0.0" name="stateNode" upper="1.0"
-                       value="0.25"/>
+            <parameter id="birthRate.t:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+            <parameter id="rateTransversion.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+            <parameter id="rateAG.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+            <parameter dimension="4" id="freqParameter.s:primate" name="stateNode" value="0.25" spec="beast.base.spec.inference.parameter.SimplexParam"/>
         </state>
 
-        <init estimate="false" id="RandomTree.t:primate" initial="@Tree.t:primate"
-              spec="beast.base.evolution.tree.coalescent.RandomTree" taxa="@coding">
-            <populationModel id="ConstantPopulation0.t:primate" spec="ConstantPopulation">
-                <parameter id="randomPopSize.t:primate" name="popSize" value="1"/>
+        <init estimate="false" id="RandomTree.t:primate" initial="@Tree.t:primate" spec="beast.base.spec.evolution.tree.coalescent.RandomTree" taxa="@coding">
+            <populationModel id="ConstantPopulation0.t:primate" spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
+                <parameter id="randomPopSize.t:primate" name="popSize" value="1" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
             </populationModel>
         </init>
 
         <distribution id="posterior" spec="CompoundDistribution">
             <distribution id="prior" spec="CompoundDistribution">
-                <distribution birthDiffRate="@birthRate.t:primate" id="YuleModel.t:primate"
-                              spec="beast.base.evolution.speciation.YuleModel" tree="@Tree.t:primate"/>
-                <prior id="YuleBirthRatePrior.t:primate" name="distribution" x="@birthRate.t:primate">
-                    <Uniform id="Uniform.0" name="distr" upper="Infinity"/>
-                </prior>
-                <prior id="RateTransversionPrior.s:primate" name="distribution" x="@rateTransversion.s:primate">
-                    <LogNormal id="LogNormalDistributionModel.0" name="distr">
-                        <parameter estimate="false" id="RealParameter.0" name="M" value="0"/>
-                        <parameter estimate="false" id="RealParameter.01" lower="0.0" name="S" upper="5.0"
-                                   value="1.25"/>
-                    </LogNormal>
-                </prior>
-                <prior id="RateAGPrior.s:primate" name="distribution" x="@rateAG.s:primate">
-                    <LogNormal id="LogNormalDistributionModel.01" name="distr">
-                        <parameter estimate="false" id="RealParameter.02" name="M" value="0"/>
-                        <parameter estimate="false" id="RealParameter.03" lower="0.0" name="S" upper="5.0"
-                                   value="1.25"/>
-                    </LogNormal>
-                </prior>
+                <distribution birthDiffRate="@birthRate.t:primate" id="YuleModel.t:primate" spec="beast.base.spec.evolution.speciation.YuleModel" tree="@Tree.t:primate"/>
+                <distribution id="Uniform.0" spec="beast.base.spec.inference.distribution.Uniform" param="@birthRate.t:primate" upper="1.0E6"/>
+                <distribution id="LogNormalDistributionModel.0" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateTransversion.s:primate">
+                        <parameter estimate="false" id="RealParameter.0" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="RealParameter.01" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                    </distribution>
+                <distribution id="LogNormalDistributionModel.01" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateAG.s:primate">
+                        <parameter estimate="false" id="RealParameter.02" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="RealParameter.03" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                    </distribution>
             </distribution>
             <distribution id="likelihood" spec="CompoundDistribution">
-                <distribution data="@coding" id="treeLikelihood.coding" spec="TreeLikelihood" tree="@Tree.t:primate">
-                    <siteModel id="SiteModel.s:primate" spec="SiteModel">
-                        <parameter estimate="false" id="mutationRate.s:primate" name="mutationRate" value="1.0"/>
-                        <parameter estimate="false" id="gammaShape.s:primate" name="shape" value="1.0"/>
-                        <parameter estimate="false" id="proportionInvariant.s:primate" lower="0.0"
-                                   name="proportionInvariant" upper="1.0" value="0.0"/>
-                        <substModel id="gtr.s:primate"
-                                    rateAC="@rateTransversion.s:primate"
-                                    rateAG="@rateAG.s:primate"
-                                    rateAT="@rateTransversion.s:primate"
-                                    rateCG="@rateTransversion.s:primate"
-                                    rateGT="@rateTransversion.s:primate"
-                                    spec="GTR">
-                            <parameter estimate="false" id="rateCT.s:primate" lower="0.0" name="rateCT" value="1.0"/>
-                            <frequencies frequencies="@freqParameter.s:primate" id="estimatedFreqs.s:primate"
-                                         spec="Frequencies"/>
+                <distribution data="@coding" id="treeLikelihood.coding" spec="beast.base.spec.evolution.likelihood.TreeLikelihood" tree="@Tree.t:primate">
+                    <siteModel id="SiteModel.s:primate" spec="beast.base.spec.evolution.sitemodel.SiteModel">
+                        <parameter estimate="false" id="mutationRate.s:primate" name="mutationRate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="gammaShape.s:primate" name="shape" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="proportionInvariant.s:primate" name="proportionInvariant" value="0.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="UnitInterval"/>
+                        <substModel id="gtr.s:primate" rateAC="@rateTransversion.s:primate" rateAG="@rateAG.s:primate" rateAT="@rateTransversion.s:primate" rateCG="@rateTransversion.s:primate" rateGT="@rateTransversion.s:primate" spec="beast.base.spec.evolution.substitutionmodel.GTR">
+                            <parameter estimate="false" id="rateCT.s:primate" name="rateCT" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+                            <frequencies frequencies="@freqParameter.s:primate" id="estimatedFreqs.s:primate" spec="beast.base.spec.evolution.substitutionmodel.Frequencies"/>
                         </substModel>
                     </siteModel>
-                    <branchRateModel id="StrictClock.c:primate" spec="beast.base.evolution.branchratemodel.StrictClockModel">
-                        <parameter estimate="false" id="clockRate.c:primate" name="clock.rate" value="1.0"/>
+                    <branchRateModel id="StrictClock.c:primate" spec="beast.base.spec.evolution.branchratemodel.StrictClockModel">
+                        <parameter estimate="false" id="clockRate.c:primate" name="clock.rate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
                     </branchRateModel>
                 </distribution>
-                <distribution branchRateModel="@StrictClock.c:primate" id="treeLikelihood.noncoding"
-                              siteModel="@SiteModel.s:primate" spec="TreeLikelihood" tree="@Tree.t:primate">
-                    <data data="@primate-mtDNA" filter="1,458-659,897-898" id="noncoding" spec="FilteredAlignment"/>
+                <distribution branchRateModel="@StrictClock.c:primate" id="treeLikelihood.noncoding" siteModel="@SiteModel.s:primate" spec="beast.base.spec.evolution.likelihood.TreeLikelihood" tree="@Tree.t:primate">
+                    <data data="@primate-mtDNA" filter="1,458-659,897-898" id="noncoding" spec="beast.base.spec.evolution.alignment.FilteredAlignment"/>
                 </distribution>
             </distribution>
         </distribution>
 
-        <operator id="YuleBirthRateScaler.t:primate" parameter="@birthRate.t:primate" scaleFactor="0.75"
-                  spec="ScaleOperator" weight="3.0"/>
+        <operator id="YuleBirthRateScaler.t:primate" parameter="@birthRate.t:primate" scaleFactor="0.75" weight="3.0" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator id="treeScaler.t:primate" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:primate" weight="3.0"/>
+        <operator id="treeScaler.t:primate" scaleFactor="0.5" tree="@Tree.t:primate" weight="3.0" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
 
-        <operator id="treeRootScaler.t:primate" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator"
-                  tree="@Tree.t:primate" weight="3.0"/>
+        <operator id="treeRootScaler.t:primate" rootOnly="true" scaleFactor="0.5" tree="@Tree.t:primate" weight="3.0" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
 
-        <operator id="UniformOperator.t:primate" spec="Uniform" tree="@Tree.t:primate" weight="30.0"/>
+        <operator id="UniformOperator.t:primate" tree="@Tree.t:primate" weight="30.0" spec="beast.base.evolution.operator.Uniform"/>
 
-        <operator id="SubtreeSlide.t:primate" spec="SubtreeSlide" tree="@Tree.t:primate" weight="15.0"/>
+        <operator id="SubtreeSlide.t:primate" spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" tree="@Tree.t:primate" weight="15.0"/>
 
         <operator id="narrow.t:primate" spec="Exchange" tree="@Tree.t:primate" weight="15.0"/>
 
@@ -137,20 +90,15 @@
 
         <operator id="WilsonBalding.t:primate" spec="WilsonBalding" tree="@Tree.t:primate" weight="3.0"/>
 
-        <operator id="RateTransversionScaler.s:primate" parameter="@rateTransversion.s:primate" scaleFactor="0.5"
-                  spec="ScaleOperator"
-                  weight="0.1"/>
+        <operator id="RateTransversionScaler.s:primate" parameter="@rateTransversion.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator id="RateAGScaler.s:primate" parameter="@rateAG.s:primate" scaleFactor="0.5" spec="ScaleOperator"
-                  weight="0.1"/>
+        <operator id="RateAGScaler.s:primate" parameter="@rateAG.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator delta="0.01" id="FrequenciesExchanger.s:primate" spec="DeltaExchangeOperator" weight="0.1">
+        <operator delta="0.01" id="FrequenciesExchanger.s:primate" spec="beast.base.spec.inference.operator.DeltaExchangeOperator" weight="0.1">
             <parameter idref="freqParameter.s:primate"/>
         </operator>
 
-        <logger fileName="primate-mtDNA-restrictedGTR.log" id="tracelog" logEvery="5000" model="@posterior"
-                sanitiseHeaders="true"
-                sort="smart">
+        <logger fileName="primate-mtDNA-restrictedGTR.log" id="tracelog" logEvery="5000" model="@posterior" sanitiseHeaders="true" sort="smart">
             <log idref="posterior"/>
             <log idref="likelihood"/>
             <log idref="prior"/>
@@ -166,14 +114,13 @@
 
         <logger id="screenlog" logEvery="5000">
             <log idref="posterior"/>
-            <log arg="@posterior" id="ESS.0" spec="util.ESS"/>
+            <log arg="@posterior" id="ESS.0" spec="beast.base.spec.inference.util.ESS"/>
             <log idref="likelihood"/>
             <log idref="prior"/>
         </logger>
 
         <logger fileName="primate-mtDNA-restrictedGTR-$(tree).trees" id="treelog.t:primate" logEvery="5000" mode="tree">
-            <log id="TreeWithMetaDataLogger.t:primate" spec="beast.base.evolution.TreeWithMetaDataLogger"
-                 tree="@Tree.t:primate"/>
+            <log id="TreeWithMetaDataLogger.t:primate" spec="beast.base.spec.evolution.TreeWithMetaDataLogger" tree="@Tree.t:primate"/>
         </logger>
     </run>
 </beast>
diff --git a/beast-base/src/test/resources/beast.base/examples/testSYM.xml b/beast-base/src/test/resources/beast.base/examples/testSYM.xml
index 9b9c012d..3198b41a 100644
--- a/beast-base/src/test/resources/beast.base/examples/testSYM.xml
+++ b/beast-base/src/test/resources/beast.base/examples/testSYM.xml
@@ -1,155 +1,103 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<beast beautitemplate='Standard' beautistatus=''
-       namespace="beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.alignment:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood"
-       version="2.0">
-
+<?xml version='1.0' encoding='UTF-8'?>
+<beast version="2.8"
+       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt"
+       beautitemplate="Standard"
+       beautistatus="">
 
     <data id="primate-mtDNA">
-        <sequence id="seq_Lemur_catta" taxon="Lemur_catta" totalcount="4"
-                  value="AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATTCTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGGGATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCTAGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTCATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTCCCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAACCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATTTACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAACACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATGTATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGATAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTATAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTGCATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAACAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT"/>
-        <sequence id="seq_Homo_sapiens" taxon="Homo_sapiens" totalcount="4"
-                  value="AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
-        <sequence id="seq_Pan" taxon="Pan" totalcount="4"
-                  value="AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATTCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCTCGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAAGCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TATAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCACCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCGCGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAGCTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
-        <sequence id="seq_Gorilla" taxon="Gorilla" totalcount="4"
-                  value="AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGGACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCTCGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTCCTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTCCCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAAACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCTATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CGTAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTACCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCGCATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAGCTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT"/>
-        <sequence id="seq_Pongo" taxon="Pongo" totalcount="4"
-                  value="AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGGCCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCTTGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTCTTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTCTCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAAACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTTATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAACATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGATAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAACAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCGCTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCGCATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAACCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT"/>
-        <sequence id="seq_Hylobates" taxon="Hylobates" totalcount="4"
-                  value="AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATTCTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGGGCTCCAAGCCTTACTCCCACTGATAGCCTTCTGATGACTCGCAGCAAGCCTCGCTAACCTCGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTCCTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTCCCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAAACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCTAACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAACATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CACAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAGCCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTGCCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAACCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT"/>
-        <sequence id="seq_Macaca_fuscata" taxon="Macaca_fuscata" totalcount="4"
-                  value="AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGGACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTCCTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTCTCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAAGCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAACACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT"/>
-        <sequence id="seq_M._mulatta" taxon="M._mulatta" totalcount="4"
-                  value="AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGGACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTCCTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTCCCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCTATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAACATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CGCGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT"/>
-        <sequence id="seq_M._fascicularis" taxon="M._fascicularis" totalcount="4"
-                  value="AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTTCTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGTACCATACTACTATCCCGAGGACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTCCTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTCTCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAACATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTGCCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAATATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAACAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT"/>
-        <sequence id="seq_M._sylvanus" taxon="M._sylvanus" totalcount="4"
-                  value="AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTTCTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGCATCATACTACTATCCCGAGGACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCTTGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTCCTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTCTCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAAACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCTATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAACATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TGCAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCGCTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAATATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAACAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT"/>
-        <sequence id="seq_Saimiri_sciureus" taxon="Saimiri_sciureus" totalcount="4"
-                  value="AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTCTATGCTATTCTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAATAACATTTACTCGAGGGCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCTCGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTCTTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTCACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAAACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCTTACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAACATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CGCAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGATAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAATA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAGCTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCATCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAATCAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT"/>
-        <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4"
-                  value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
+        <sequence id="seq_Lemur_catta" taxon="Lemur_catta" totalcount="4" value="AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATTCTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGGGATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCTAGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTCATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTCCCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAACCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATTTACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAACACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATGTATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGATAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTATAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTGCATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAACAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT"/>
+        <sequence id="seq_Homo_sapiens" taxon="Homo_sapiens" totalcount="4" value="AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
+        <sequence id="seq_Pan" taxon="Pan" totalcount="4" value="AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATTCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCTCGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAAGCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TATAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCACCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCGCGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAGCTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
+        <sequence id="seq_Gorilla" taxon="Gorilla" totalcount="4" value="AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGGACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCTCGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTCCTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTCCCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAAACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCTATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CGTAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTACCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCGCATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAGCTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT"/>
+        <sequence id="seq_Pongo" taxon="Pongo" totalcount="4" value="AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGGCCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCTTGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTCTTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTCTCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAAACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTTATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAACATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGATAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAACAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCGCTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCGCATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAACCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT"/>
+        <sequence id="seq_Hylobates" taxon="Hylobates" totalcount="4" value="AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATTCTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGGGCTCCAAGCCTTACTCCCACTGATAGCCTTCTGATGACTCGCAGCAAGCCTCGCTAACCTCGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTCCTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTCCCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAAACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCTAACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAACATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CACAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAGCCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTGCCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAACCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT"/>
+        <sequence id="seq_Macaca_fuscata" taxon="Macaca_fuscata" totalcount="4" value="AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGGACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTCCTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTCTCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAAGCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAACACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT"/>
+        <sequence id="seq_M._mulatta" taxon="M._mulatta" totalcount="4" value="AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGGACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTCCTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTCCCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCTATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAACATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CGCGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT"/>
+        <sequence id="seq_M._fascicularis" taxon="M._fascicularis" totalcount="4" value="AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTTCTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGTACCATACTACTATCCCGAGGACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTCCTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTCTCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAACATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTGCCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAATATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAACAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT"/>
+        <sequence id="seq_M._sylvanus" taxon="M._sylvanus" totalcount="4" value="AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTTCTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGCATCATACTACTATCCCGAGGACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCTTGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTCCTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTCTCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAAACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCTATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAACATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TGCAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCGCTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAATATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAACAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT"/>
+        <sequence id="seq_Saimiri_sciureus" taxon="Saimiri_sciureus" totalcount="4" value="AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTCTATGCTATTCTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAATAACATTTACTCGAGGGCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCTCGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTCTTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTCACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAAACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCTTACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAACATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CGCAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGATAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAATA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAGCTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCATCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAATCAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT"/>
+        <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4" value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
     </data>
 
-
-    <map name="Beta">beast.base.inference.distribution.Beta</map>
-    <map name="Exponential">beast.base.inference.distribution.Exponential</map>
-    <map name="InverseGamma">beast.base.inference.distribution.InverseGamma</map>
-    <map name="LogNormal">beast.base.inference.distribution.LogNormalDistributionModel</map>
-    <map name="Gamma">beast.base.inference.distribution.Gamma</map>
-    <map name="Uniform">beast.base.inference.distribution.Uniform</map>
-    <map name="prior">beast.base.inference.distribution.Prior</map>
-    <map name="LaplaceDistribution">beast.base.inference.distribution.LaplaceDistribution</map>
-    <map name="OneOnX">beast.base.inference.distribution.OneOnX</map>
-    <map name="Normal">beast.base.inference.distribution.Normal</map>
-
-
     <run chainLength="5000000" id="mcmc" spec="MCMC">
         <state id="state" storeEvery="5000">
             <tree id="Tree.t:primate" name="stateNode">
                 <taxonset id="TaxonSet.coding" spec="TaxonSet">
-                    <alignment filter="2-457,660-896" id="coding" spec="FilteredAlignment">
+                    <alignment filter="2-457,660-896" id="coding" spec="beast.base.spec.evolution.alignment.FilteredAlignment">
                         <data idref="primate-mtDNA"/>
                     </alignment>
                 </taxonset>
             </tree>
-            <parameter id="birthRate.t:primate" name="stateNode" value="1.0"/>
-            <parameter id="rateAC.s:primate" lower="0.0" name="stateNode" value="1.0"/>
-            <parameter id="rateAG.s:primate" lower="0.0" name="stateNode" value="1.0"/>
-            <parameter id="rateAT.s:primate" lower="0.0" name="stateNode" value="1.0"/>
-            <parameter id="rateCG.s:primate" lower="0.0" name="stateNode" value="1.0"/>
-            <parameter id="rateGT.s:primate" lower="0.0" name="stateNode" value="1.0"/>
-            <parameter dimension="4" id="freqParameter.s:primate" lower="0.0" name="stateNode" upper="1.0"
-                       value="0.25"/>
+            <parameter id="birthRate.t:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+            <parameter id="rateAC.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+            <parameter id="rateAG.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+            <parameter id="rateAT.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+            <parameter id="rateCG.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+            <parameter id="rateGT.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+            <parameter dimension="4" id="freqParameter.s:primate" name="stateNode" value="0.25" spec="beast.base.spec.inference.parameter.SimplexParam"/>
         </state>
 
-        <init estimate="false" id="RandomTree.t:primate" initial="@Tree.t:primate"
-              spec="beast.base.evolution.tree.coalescent.RandomTree" taxa="@coding">
-            <populationModel id="ConstantPopulation0.t:primate" spec="ConstantPopulation">
-                <parameter id="randomPopSize.t:primate" name="popSize" value="1"/>
+        <init estimate="false" id="RandomTree.t:primate" initial="@Tree.t:primate" spec="beast.base.spec.evolution.tree.coalescent.RandomTree" taxa="@coding">
+            <populationModel id="ConstantPopulation0.t:primate" spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
+                <parameter id="randomPopSize.t:primate" name="popSize" value="1" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
             </populationModel>
         </init>
 
         <distribution id="posterior" spec="CompoundDistribution">
             <distribution id="prior" spec="CompoundDistribution">
-                <distribution birthDiffRate="@birthRate.t:primate" id="YuleModel.t:primate"
-                              spec="beast.base.evolution.speciation.YuleModel" tree="@Tree.t:primate"/>
-                <prior id="YuleBirthRatePrior.t:primate" name="distribution" x="@birthRate.t:primate">
-                    <Uniform id="Uniform.0" name="distr" upper="Infinity"/>
-                </prior>
-                <prior id="RateACPrior.s:primate" name="distribution" x="@rateAC.s:primate">
-                    <LogNormal id="LogNormalDistributionModel.0" name="distr">
-                        <parameter estimate="false" id="RealParameter.0" name="M" value="0"/>
-                        <parameter estimate="false" id="RealParameter.01" lower="0.0" name="S" upper="5.0"
-                                   value="1.25"/>
-                    </LogNormal>
-                </prior>
-                <prior id="RateAGPrior.s:primate" name="distribution" x="@rateAG.s:primate">
-                    <LogNormal id="LogNormalDistributionModel.01" name="distr">
-                        <parameter estimate="false" id="RealParameter.02" name="M" value="0"/>
-                        <parameter estimate="false" id="RealParameter.03" lower="0.0" name="S" upper="5.0"
-                                   value="1.25"/>
-                    </LogNormal>
-                </prior>
-                <prior id="RateATPrior.s:primate" name="distribution" x="@rateAT.s:primate">
-                    <LogNormal id="LogNormalDistributionModel.02" name="distr">
-                        <parameter estimate="false" id="RealParameter.04" name="M" value="0"/>
-                        <parameter estimate="false" id="RealParameter.05" lower="0.0" name="S" upper="5.0"
-                                   value="1.25"/>
-                    </LogNormal>
-                </prior>
-                <prior id="RateCGPrior.s:primate" name="distribution" x="@rateCG.s:primate">
-                    <LogNormal id="LogNormalDistributionModel.03" name="distr">
-                        <parameter estimate="false" id="RealParameter.06" name="M" value="0"/>
-                        <parameter estimate="false" id="RealParameter.07" lower="0.0" name="S" upper="5.0"
-                                   value="1.25"/>
-                    </LogNormal>
-                </prior>
-                <prior id="RateGTPrior.s:primate" name="distribution" x="@rateGT.s:primate">
-                    <LogNormal id="LogNormalDistributionModel.04" name="distr">
-                        <parameter estimate="false" id="RealParameter.08" name="M" value="0"/>
-                        <parameter estimate="false" id="RealParameter.09" lower="0.0" name="S" upper="5.0"
-                                   value="1.25"/>
-                    </LogNormal>
-                </prior>
+                <distribution birthDiffRate="@birthRate.t:primate" id="YuleModel.t:primate" spec="beast.base.spec.evolution.speciation.YuleModel" tree="@Tree.t:primate"/>
+                <distribution id="Uniform.0" spec="beast.base.spec.inference.distribution.Uniform" param="@birthRate.t:primate" upper="1.0E6"/>
+                <distribution id="LogNormalDistributionModel.0" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateAC.s:primate">
+                        <parameter estimate="false" id="RealParameter.0" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="RealParameter.01" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                    </distribution>
+                <distribution id="LogNormalDistributionModel.01" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateAG.s:primate">
+                        <parameter estimate="false" id="RealParameter.02" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="RealParameter.03" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                    </distribution>
+                <distribution id="LogNormalDistributionModel.02" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateAT.s:primate">
+                        <parameter estimate="false" id="RealParameter.04" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="RealParameter.05" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                    </distribution>
+                <distribution id="LogNormalDistributionModel.03" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateCG.s:primate">
+                        <parameter estimate="false" id="RealParameter.06" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="RealParameter.07" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                    </distribution>
+                <distribution id="LogNormalDistributionModel.04" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateGT.s:primate">
+                        <parameter estimate="false" id="RealParameter.08" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="RealParameter.09" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                    </distribution>
             </distribution>
             <distribution id="likelihood" spec="CompoundDistribution">
-                <distribution data="@coding" id="treeLikelihood.coding" spec="TreeLikelihood" tree="@Tree.t:primate">
-                    <siteModel id="SiteModel.s:primate" spec="SiteModel">
-                        <parameter estimate="false" id="mutationRate.s:primate" name="mutationRate" value="1.0"/>
-                        <parameter estimate="false" id="gammaShape.s:primate" name="shape" value="1.0"/>
-                        <parameter estimate="false" id="proportionInvariant.s:primate" lower="0.0"
-                                   name="proportionInvariant" upper="1.0" value="0.0"/>
-                        <substModel id="gtr.s:primate" rateAC="@rateAC.s:primate" rateAG="@rateAG.s:primate"
-                                    rateAT="@rateAT.s:primate" rateCG="@rateCG.s:primate" rateGT="@rateGT.s:primate"
-                                    spec="GTR">
-                            <parameter estimate="false" id="rateCT.s:primate" lower="0.0" name="rateCT" value="1.0"/>
-                            <frequencies frequencies="@freqParameter.s:primate" id="estimatedFreqs.s:primate"
-                                         spec="Frequencies"/>
+                <distribution data="@coding" id="treeLikelihood.coding" spec="beast.base.spec.evolution.likelihood.TreeLikelihood" tree="@Tree.t:primate">
+                    <siteModel id="SiteModel.s:primate" spec="beast.base.spec.evolution.sitemodel.SiteModel">
+                        <parameter estimate="false" id="mutationRate.s:primate" name="mutationRate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="gammaShape.s:primate" name="shape" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="proportionInvariant.s:primate" name="proportionInvariant" value="0.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="UnitInterval"/>
+                        <substModel id="gtr.s:primate" rateAC="@rateAC.s:primate" rateAG="@rateAG.s:primate" rateAT="@rateAT.s:primate" rateCG="@rateCG.s:primate" rateGT="@rateGT.s:primate" spec="beast.base.spec.evolution.substitutionmodel.GTR">
+                            <parameter estimate="false" id="rateCT.s:primate" name="rateCT" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+                            <frequencies frequencies="@freqParameter.s:primate" id="estimatedFreqs.s:primate" spec="beast.base.spec.evolution.substitutionmodel.Frequencies"/>
                         </substModel>
                     </siteModel>
-                    <branchRateModel id="StrictClock.c:primate" spec="beast.base.evolution.branchratemodel.StrictClockModel">
-                        <parameter estimate="false" id="clockRate.c:primate" name="clock.rate" value="1.0"/>
+                    <branchRateModel id="StrictClock.c:primate" spec="beast.base.spec.evolution.branchratemodel.StrictClockModel">
+                        <parameter estimate="false" id="clockRate.c:primate" name="clock.rate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
                     </branchRateModel>
                 </distribution>
-                <distribution branchRateModel="@StrictClock.c:primate" id="treeLikelihood.noncoding"
-                              siteModel="@SiteModel.s:primate" spec="TreeLikelihood" tree="@Tree.t:primate">
-                    <data data="@primate-mtDNA" filter="1,458-659,897-898" id="noncoding" spec="FilteredAlignment"/>
+                <distribution branchRateModel="@StrictClock.c:primate" id="treeLikelihood.noncoding" siteModel="@SiteModel.s:primate" spec="beast.base.spec.evolution.likelihood.TreeLikelihood" tree="@Tree.t:primate">
+                    <data data="@primate-mtDNA" filter="1,458-659,897-898" id="noncoding" spec="beast.base.spec.evolution.alignment.FilteredAlignment"/>
                 </distribution>
             </distribution>
         </distribution>
 
-        <operator id="YuleBirthRateScaler.t:primate" parameter="@birthRate.t:primate" scaleFactor="0.75"
-                  spec="ScaleOperator" weight="3.0"/>
+        <operator id="YuleBirthRateScaler.t:primate" parameter="@birthRate.t:primate" scaleFactor="0.75" weight="3.0" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator id="treeScaler.t:primate" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:primate" weight="3.0"/>
+        <operator id="treeScaler.t:primate" scaleFactor="0.5" tree="@Tree.t:primate" weight="3.0" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
 
-        <operator id="treeRootScaler.t:primate" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator"
-                  tree="@Tree.t:primate" weight="3.0"/>
+        <operator id="treeRootScaler.t:primate" rootOnly="true" scaleFactor="0.5" tree="@Tree.t:primate" weight="3.0" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
 
-        <operator id="UniformOperator.t:primate" spec="Uniform" tree="@Tree.t:primate" weight="30.0"/>
+        <operator id="UniformOperator.t:primate" tree="@Tree.t:primate" weight="30.0" spec="beast.base.evolution.operator.Uniform"/>
 
-        <operator id="SubtreeSlide.t:primate" spec="SubtreeSlide" tree="@Tree.t:primate" weight="15.0"/>
+        <operator id="SubtreeSlide.t:primate" spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" tree="@Tree.t:primate" weight="15.0"/>
 
         <operator id="narrow.t:primate" spec="Exchange" tree="@Tree.t:primate" weight="15.0"/>
 
@@ -157,23 +105,17 @@
 
         <operator id="WilsonBalding.t:primate" spec="WilsonBalding" tree="@Tree.t:primate" weight="3.0"/>
 
-        <operator id="RateACScaler.s:primate" parameter="@rateAC.s:primate" scaleFactor="0.5" spec="ScaleOperator"
-                  weight="0.1"/>
+        <operator id="RateACScaler.s:primate" parameter="@rateAC.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator id="RateAGScaler.s:primate" parameter="@rateAG.s:primate" scaleFactor="0.5" spec="ScaleOperator"
-                  weight="0.1"/>
+        <operator id="RateAGScaler.s:primate" parameter="@rateAG.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator id="RateATScaler.s:primate" parameter="@rateAT.s:primate" scaleFactor="0.5" spec="ScaleOperator"
-                  weight="0.1"/>
+        <operator id="RateATScaler.s:primate" parameter="@rateAT.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator id="RateCGScaler.s:primate" parameter="@rateCG.s:primate" scaleFactor="0.5" spec="ScaleOperator"
-                  weight="0.1"/>
+        <operator id="RateCGScaler.s:primate" parameter="@rateCG.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator id="RateGTScaler.s:primate" parameter="@rateGT.s:primate" scaleFactor="0.5" spec="ScaleOperator"
-                  weight="0.1"/>
+        <operator id="RateGTScaler.s:primate" parameter="@rateGT.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <logger fileName="primate-mtDNA-SYM.log" id="tracelog" logEvery="5000" model="@posterior" sanitiseHeaders="true"
-                sort="smart">
+        <logger fileName="primate-mtDNA-SYM.log" id="tracelog" logEvery="5000" model="@posterior" sanitiseHeaders="true" sort="smart">
             <log idref="posterior"/>
             <log idref="likelihood"/>
             <log idref="prior"/>
@@ -192,14 +134,13 @@
 
         <logger id="screenlog" logEvery="5000">
             <log idref="posterior"/>
-            <log arg="@posterior" id="ESS.0" spec="util.ESS"/>
+            <log arg="@posterior" id="ESS.0" spec="beast.base.spec.inference.util.ESS"/>
             <log idref="likelihood"/>
             <log idref="prior"/>
         </logger>
 
         <logger fileName="$(tree).trees" id="treelog.t:primate" logEvery="5000" mode="tree">
-            <log id="TreeWithMetaDataLogger.t:primate" spec="beast.base.evolution.TreeWithMetaDataLogger"
-                 tree="@Tree.t:primate"/>
+            <log id="TreeWithMetaDataLogger.t:primate" spec="beast.base.spec.evolution.TreeWithMetaDataLogger" tree="@Tree.t:primate"/>
         </logger>
 
     </run>
diff --git a/beast-base/src/test/resources/beast.base/examples/testTIM.xml b/beast-base/src/test/resources/beast.base/examples/testTIM.xml
index e8b380b8..e9882e7b 100644
--- a/beast-base/src/test/resources/beast.base/examples/testTIM.xml
+++ b/beast-base/src/test/resources/beast.base/examples/testTIM.xml
@@ -1,140 +1,93 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<beast beautitemplate='Standard' beautistatus=''
-       namespace="beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.alignment:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood"
-       version="2.0">
-
+<?xml version='1.0' encoding='UTF-8'?>
+<beast version="2.8"
+       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt"
+       beautitemplate="Standard"
+       beautistatus="">
 
     <data id="primate-mtDNA">
-        <sequence id="seq_Lemur_catta" taxon="Lemur_catta" totalcount="4"
-                  value="AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATTCTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGGGATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCTAGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTCATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTCCCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAACCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATTTACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAACACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATGTATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGATAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTATAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTGCATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAACAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT"/>
-        <sequence id="seq_Homo_sapiens" taxon="Homo_sapiens" totalcount="4"
-                  value="AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
-        <sequence id="seq_Pan" taxon="Pan" totalcount="4"
-                  value="AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATTCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCTCGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAAGCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TATAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCACCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCGCGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAGCTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
-        <sequence id="seq_Gorilla" taxon="Gorilla" totalcount="4"
-                  value="AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGGACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCTCGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTCCTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTCCCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAAACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCTATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CGTAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTACCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCGCATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAGCTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT"/>
-        <sequence id="seq_Pongo" taxon="Pongo" totalcount="4"
-                  value="AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGGCCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCTTGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTCTTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTCTCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAAACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTTATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAACATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGATAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAACAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCGCTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCGCATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAACCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT"/>
-        <sequence id="seq_Hylobates" taxon="Hylobates" totalcount="4"
-                  value="AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATTCTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGGGCTCCAAGCCTTACTCCCACTGATAGCCTTCTGATGACTCGCAGCAAGCCTCGCTAACCTCGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTCCTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTCCCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAAACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCTAACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAACATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CACAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAGCCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTGCCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAACCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT"/>
-        <sequence id="seq_Macaca_fuscata" taxon="Macaca_fuscata" totalcount="4"
-                  value="AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGGACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTCCTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTCTCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAAGCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAACACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT"/>
-        <sequence id="seq_M._mulatta" taxon="M._mulatta" totalcount="4"
-                  value="AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGGACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTCCTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTCCCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCTATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAACATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CGCGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT"/>
-        <sequence id="seq_M._fascicularis" taxon="M._fascicularis" totalcount="4"
-                  value="AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTTCTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGTACCATACTACTATCCCGAGGACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTCCTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTCTCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAACATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTGCCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAATATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAACAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT"/>
-        <sequence id="seq_M._sylvanus" taxon="M._sylvanus" totalcount="4"
-                  value="AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTTCTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGCATCATACTACTATCCCGAGGACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCTTGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTCCTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTCTCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAAACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCTATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAACATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TGCAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCGCTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAATATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAACAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT"/>
-        <sequence id="seq_Saimiri_sciureus" taxon="Saimiri_sciureus" totalcount="4"
-                  value="AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTCTATGCTATTCTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAATAACATTTACTCGAGGGCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCTCGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTCTTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTCACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAAACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCTTACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAACATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CGCAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGATAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAATA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAGCTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCATCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAATCAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT"/>
-        <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4"
-                  value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
+        <sequence id="seq_Lemur_catta" taxon="Lemur_catta" totalcount="4" value="AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATTCTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGGGATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCTAGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTCATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTCCCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAACCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATTTACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAACACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATGTATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGATAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTATAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTGCATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAACAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT"/>
+        <sequence id="seq_Homo_sapiens" taxon="Homo_sapiens" totalcount="4" value="AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
+        <sequence id="seq_Pan" taxon="Pan" totalcount="4" value="AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATTCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCTCGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAAGCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TATAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCACCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCGCGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAGCTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
+        <sequence id="seq_Gorilla" taxon="Gorilla" totalcount="4" value="AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGGACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCTCGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTCCTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTCCCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAAACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCTATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CGTAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTACCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCGCATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAGCTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT"/>
+        <sequence id="seq_Pongo" taxon="Pongo" totalcount="4" value="AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGGCCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCTTGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTCTTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTCTCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAAACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTTATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAACATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGATAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAACAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCGCTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCGCATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAACCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT"/>
+        <sequence id="seq_Hylobates" taxon="Hylobates" totalcount="4" value="AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATTCTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGGGCTCCAAGCCTTACTCCCACTGATAGCCTTCTGATGACTCGCAGCAAGCCTCGCTAACCTCGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTCCTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTCCCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAAACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCTAACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAACATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CACAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAGCCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTGCCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAACCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT"/>
+        <sequence id="seq_Macaca_fuscata" taxon="Macaca_fuscata" totalcount="4" value="AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGGACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTCCTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTCTCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAAGCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAACACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT"/>
+        <sequence id="seq_M._mulatta" taxon="M._mulatta" totalcount="4" value="AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGGACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTCCTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTCCCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCTATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAACATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CGCGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT"/>
+        <sequence id="seq_M._fascicularis" taxon="M._fascicularis" totalcount="4" value="AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTTCTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGTACCATACTACTATCCCGAGGACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTCCTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTCTCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAACATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTGCCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAATATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAACAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT"/>
+        <sequence id="seq_M._sylvanus" taxon="M._sylvanus" totalcount="4" value="AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTTCTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGCATCATACTACTATCCCGAGGACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCTTGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTCCTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTCTCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAAACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCTATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAACATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TGCAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCGCTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAATATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAACAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT"/>
+        <sequence id="seq_Saimiri_sciureus" taxon="Saimiri_sciureus" totalcount="4" value="AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTCTATGCTATTCTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAATAACATTTACTCGAGGGCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCTCGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTCTTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTCACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAAACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCTTACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAACATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CGCAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGATAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAATA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAGCTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCATCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAATCAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT"/>
+        <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4" value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
     </data>
 
-
-    <map name="Beta">beast.base.inference.distribution.Beta</map>
-    <map name="Exponential">beast.base.inference.distribution.Exponential</map>
-    <map name="InverseGamma">beast.base.inference.distribution.InverseGamma</map>
-    <map name="LogNormal">beast.base.inference.distribution.LogNormalDistributionModel</map>
-    <map name="Gamma">beast.base.inference.distribution.Gamma</map>
-    <map name="Uniform">beast.base.inference.distribution.Uniform</map>
-    <map name="prior">beast.base.inference.distribution.Prior</map>
-    <map name="LaplaceDistribution">beast.base.inference.distribution.LaplaceDistribution</map>
-    <map name="OneOnX">beast.base.inference.distribution.OneOnX</map>
-    <map name="Normal">beast.base.inference.distribution.Normal</map>
-
-
     <run chainLength="5000000" id="mcmc" spec="MCMC">
         <state id="state" storeEvery="5000">
             <tree id="Tree.t:primate" name="stateNode">
                 <taxonset id="TaxonSet.coding" spec="TaxonSet">
-                    <alignment filter="2-457,660-896" id="coding" spec="FilteredAlignment">
+                    <alignment filter="2-457,660-896" id="coding" spec="beast.base.spec.evolution.alignment.FilteredAlignment">
                         <data idref="primate-mtDNA"/>
                     </alignment>
                 </taxonset>
             </tree>
-            <parameter id="birthRate.t:primate" name="stateNode" value="1.0"/>
-            <parameter id="rateAG.s:primate" lower="0.0" name="stateNode" value="1.0"/>
-            <parameter id="rateTransversions1.s:primate" lower="0.0" name="stateNode" value="1.0"/>
-            <parameter id="rateTransversions2.s:primate" lower="0.0" name="stateNode" value="1.0"/>
-            <parameter dimension="4" id="freqParameter.s:primate" lower="0.0" name="stateNode" upper="1.0"
-                       value="0.25"/>
+            <parameter id="birthRate.t:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+            <parameter id="rateAG.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+            <parameter id="rateTransversions1.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+            <parameter id="rateTransversions2.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+            <parameter dimension="4" id="freqParameter.s:primate" name="stateNode" value="0.25" spec="beast.base.spec.inference.parameter.SimplexParam"/>
         </state>
 
-        <init estimate="false" id="RandomTree.t:primate" initial="@Tree.t:primate"
-              spec="beast.base.evolution.tree.coalescent.RandomTree" taxa="@coding">
-            <populationModel id="ConstantPopulation0.t:primate" spec="ConstantPopulation">
-                <parameter id="randomPopSize.t:primate" name="popSize" value="1"/>
+        <init estimate="false" id="RandomTree.t:primate" initial="@Tree.t:primate" spec="beast.base.spec.evolution.tree.coalescent.RandomTree" taxa="@coding">
+            <populationModel id="ConstantPopulation0.t:primate" spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
+                <parameter id="randomPopSize.t:primate" name="popSize" value="1" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
             </populationModel>
         </init>
 
         <distribution id="posterior" spec="CompoundDistribution">
             <distribution id="prior" spec="CompoundDistribution">
-                <distribution birthDiffRate="@birthRate.t:primate" id="YuleModel.t:primate"
-                              spec="beast.base.evolution.speciation.YuleModel" tree="@Tree.t:primate"/>
-                <prior id="YuleBirthRatePrior.t:primate" name="distribution" x="@birthRate.t:primate">
-                    <Uniform id="Uniform.0" name="distr" upper="Infinity"/>
-                </prior>
-                <prior id="RateAGPrior.s:primate" name="distribution" x="@rateAG.s:primate">
-                    <LogNormal id="LogNormalDistributionModel.0" name="distr">
-                        <parameter estimate="false" id="RealParameter.0" name="M" value="0"/>
-                        <parameter estimate="false" id="RealParameter.01" lower="0.0" name="S" upper="5.0"
-                                   value="1.25"/>
-                    </LogNormal>
-                </prior>
-                <prior id="RateTransversions1Prior.s:primate" name="distribution" x="@rateTransversions1.s:primate">
-                    <LogNormal id="LogNormalDistributionModel.01" name="distr">
-                        <parameter estimate="false" id="RealParameter.02" name="M" value="0"/>
-                        <parameter estimate="false" id="RealParameter.03" lower="0.0" name="S" upper="5.0"
-                                   value="1.25"/>
-                    </LogNormal>
-                </prior>
-                <prior id="RateTransversions2Prior.s:primate" name="distribution" x="@rateTransversions2.s:primate">
-                    <LogNormal id="LogNormalDistributionModel.02" name="distr">
-                        <parameter estimate="false" id="RealParameter.04" name="M" value="0"/>
-                        <parameter estimate="false" id="RealParameter.05" lower="0.0" name="S" upper="5.0"
-                                   value="1.25"/>
-                    </LogNormal>
-                </prior>
+                <distribution birthDiffRate="@birthRate.t:primate" id="YuleModel.t:primate" spec="beast.base.spec.evolution.speciation.YuleModel" tree="@Tree.t:primate"/>
+                <distribution id="Uniform.0" spec="beast.base.spec.inference.distribution.Uniform" param="@birthRate.t:primate" upper="1.0E6"/>
+                <distribution id="LogNormalDistributionModel.0" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateAG.s:primate">
+                        <parameter estimate="false" id="RealParameter.0" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="RealParameter.01" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                    </distribution>
+                <distribution id="LogNormalDistributionModel.01" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateTransversions1.s:primate">
+                        <parameter estimate="false" id="RealParameter.02" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="RealParameter.03" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                    </distribution>
+                <distribution id="LogNormalDistributionModel.02" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateTransversions2.s:primate">
+                        <parameter estimate="false" id="RealParameter.04" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="RealParameter.05" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                    </distribution>
             </distribution>
             <distribution id="likelihood" spec="CompoundDistribution">
-                <distribution data="@coding" id="treeLikelihood.coding" spec="TreeLikelihood" tree="@Tree.t:primate">
-                    <siteModel id="SiteModel.s:primate" spec="SiteModel">
-                        <parameter estimate="false" id="mutationRate.s:primate" name="mutationRate" value="1.0"/>
-                        <parameter estimate="false" id="gammaShape.s:primate" name="shape" value="1.0"/>
-                        <parameter estimate="false" id="proportionInvariant.s:primate" lower="0.0"
-                                   name="proportionInvariant" upper="1.0" value="0.0"/>
-                        <substModel id="tim.s:primate" rateAG="@rateAG.s:primate"
-                                    rateTransversions1="@rateTransversions1.s:primate"
-                                    rateTransversions2="@rateTransversions2.s:primate"
-                                    spec="TIM">
-                            <parameter estimate="false" id="rateCT.s:primate" lower="0.0" name="rateCT" value="1.0"/>
-                            <frequencies frequencies="@freqParameter.s:primate" id="estimatedFreqs.s:primate"
-                                         spec="Frequencies"/>
+                <distribution data="@coding" id="treeLikelihood.coding" spec="beast.base.spec.evolution.likelihood.TreeLikelihood" tree="@Tree.t:primate">
+                    <siteModel id="SiteModel.s:primate" spec="beast.base.spec.evolution.sitemodel.SiteModel">
+                        <parameter estimate="false" id="mutationRate.s:primate" name="mutationRate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="gammaShape.s:primate" name="shape" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="proportionInvariant.s:primate" name="proportionInvariant" value="0.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="UnitInterval"/>
+                        <substModel id="tim.s:primate" rateAG="@rateAG.s:primate" rateTransversions1="@rateTransversions1.s:primate" rateTransversions2="@rateTransversions2.s:primate" spec="beast.base.spec.evolution.substitutionmodel.TIM">
+                            <parameter estimate="false" id="rateCT.s:primate" name="rateCT" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+                            <frequencies frequencies="@freqParameter.s:primate" id="estimatedFreqs.s:primate" spec="beast.base.spec.evolution.substitutionmodel.Frequencies"/>
                         </substModel>
                     </siteModel>
-                    <branchRateModel id="StrictClock.c:primate" spec="beast.base.evolution.branchratemodel.StrictClockModel">
-                        <parameter estimate="false" id="clockRate.c:primate" name="clock.rate" value="1.0"/>
+                    <branchRateModel id="StrictClock.c:primate" spec="beast.base.spec.evolution.branchratemodel.StrictClockModel">
+                        <parameter estimate="false" id="clockRate.c:primate" name="clock.rate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
                     </branchRateModel>
                 </distribution>
-                <distribution branchRateModel="@StrictClock.c:primate" id="treeLikelihood.noncoding"
-                              siteModel="@SiteModel.s:primate" spec="TreeLikelihood" tree="@Tree.t:primate">
-                    <data data="@primate-mtDNA" filter="1,458-659,897-898" id="noncoding" spec="FilteredAlignment"/>
+                <distribution branchRateModel="@StrictClock.c:primate" id="treeLikelihood.noncoding" siteModel="@SiteModel.s:primate" spec="beast.base.spec.evolution.likelihood.TreeLikelihood" tree="@Tree.t:primate">
+                    <data data="@primate-mtDNA" filter="1,458-659,897-898" id="noncoding" spec="beast.base.spec.evolution.alignment.FilteredAlignment"/>
                 </distribution>
             </distribution>
         </distribution>
 
-        <operator id="YuleBirthRateScaler.t:primate" parameter="@birthRate.t:primate" scaleFactor="0.75"
-                  spec="ScaleOperator" weight="3.0"/>
+        <operator id="YuleBirthRateScaler.t:primate" parameter="@birthRate.t:primate" scaleFactor="0.75" weight="3.0" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator id="treeScaler.t:primate" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:primate" weight="3.0"/>
+        <operator id="treeScaler.t:primate" scaleFactor="0.5" tree="@Tree.t:primate" weight="3.0" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
 
-        <operator id="treeRootScaler.t:primate" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator"
-                  tree="@Tree.t:primate" weight="3.0"/>
+        <operator id="treeRootScaler.t:primate" rootOnly="true" scaleFactor="0.5" tree="@Tree.t:primate" weight="3.0" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
 
-        <operator id="UniformOperator.t:primate" spec="Uniform" tree="@Tree.t:primate" weight="30.0"/>
+        <operator id="UniformOperator.t:primate" tree="@Tree.t:primate" weight="30.0" spec="beast.base.evolution.operator.Uniform"/>
 
-        <operator id="SubtreeSlide.t:primate" spec="SubtreeSlide" tree="@Tree.t:primate" weight="15.0"/>
+        <operator id="SubtreeSlide.t:primate" spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" tree="@Tree.t:primate" weight="15.0"/>
 
         <operator id="narrow.t:primate" spec="Exchange" tree="@Tree.t:primate" weight="15.0"/>
 
@@ -142,21 +95,17 @@
 
         <operator id="WilsonBalding.t:primate" spec="WilsonBalding" tree="@Tree.t:primate" weight="3.0"/>
 
-        <operator id="RateAGScaler.s:primate" parameter="@rateAG.s:primate" scaleFactor="0.5" spec="ScaleOperator"
-                  weight="0.1"/>
+        <operator id="RateAGScaler.s:primate" parameter="@rateAG.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator id="RateTransversions1Scaler.s:primate" parameter="@rateTransversions1.s:primate" scaleFactor="0.5"
-                  spec="ScaleOperator" weight="0.1"/>
+        <operator id="RateTransversions1Scaler.s:primate" parameter="@rateTransversions1.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator id="RateTransversions2Scaler.s:primate" parameter="@rateTransversions2.s:primate" scaleFactor="0.5"
-                  spec="ScaleOperator" weight="0.1"/>
+        <operator id="RateTransversions2Scaler.s:primate" parameter="@rateTransversions2.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator delta="0.01" id="FrequenciesExchanger.s:primate" spec="DeltaExchangeOperator" weight="0.1">
+        <operator delta="0.01" id="FrequenciesExchanger.s:primate" spec="beast.base.spec.inference.operator.DeltaExchangeOperator" weight="0.1">
             <parameter idref="freqParameter.s:primate"/>
         </operator>
 
-        <logger fileName="primate-mtDNA-TIM.log" id="tracelog" logEvery="5000" model="@posterior" sanitiseHeaders="true"
-                sort="smart">
+        <logger fileName="primate-mtDNA-TIM.log" id="tracelog" logEvery="5000" model="@posterior" sanitiseHeaders="true" sort="smart">
             <log idref="posterior"/>
             <log idref="likelihood"/>
             <log idref="prior"/>
@@ -173,14 +122,13 @@
 
         <logger id="screenlog" logEvery="5000">
             <log idref="posterior"/>
-            <log arg="@posterior" id="ESS.0" spec="util.ESS"/>
+            <log arg="@posterior" id="ESS.0" spec="beast.base.spec.inference.util.ESS"/>
             <log idref="likelihood"/>
             <log idref="prior"/>
         </logger>
 
         <logger fileName="$(tree).trees" id="treelog.t:primate" logEvery="5000" mode="tree">
-            <log id="TreeWithMetaDataLogger.t:primate" spec="beast.base.evolution.TreeWithMetaDataLogger"
-                 tree="@Tree.t:primate"/>
+            <log id="TreeWithMetaDataLogger.t:primate" spec="beast.base.spec.evolution.TreeWithMetaDataLogger" tree="@Tree.t:primate"/>
         </logger>
 
     </run>
diff --git a/beast-base/src/test/resources/beast.base/examples/testTN93.xml b/beast-base/src/test/resources/beast.base/examples/testTN93.xml
index 9e5a5af4..732ccf06 100644
--- a/beast-base/src/test/resources/beast.base/examples/testTN93.xml
+++ b/beast-base/src/test/resources/beast.base/examples/testTN93.xml
@@ -1,115 +1,79 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<beast beautitemplate='Standard' beautistatus=''
-       namespace="beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.alignment:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood"
-       version="2.0">
-
+<?xml version='1.0' encoding='UTF-8'?>
+<beast version="2.8"
+       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt"
+       beautitemplate="Standard"
+       beautistatus="">
 
     <data id="primate-mtDNA">
-        <sequence id="seq_Lemur_catta" taxon="Lemur_catta" totalcount="4"
-                  value="AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATTCTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGGGATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCTAGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTCATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTCCCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAACCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATTTACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAACACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATGTATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGATAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTATAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTGCATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAACAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT"/>
-        <sequence id="seq_Homo_sapiens" taxon="Homo_sapiens" totalcount="4"
-                  value="AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
-        <sequence id="seq_Pan" taxon="Pan" totalcount="4"
-                  value="AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATTCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCTCGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAAGCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TATAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCACCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCGCGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAGCTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
-        <sequence id="seq_Gorilla" taxon="Gorilla" totalcount="4"
-                  value="AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGGACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCTCGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTCCTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTCCCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAAACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCTATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CGTAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTACCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCGCATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAGCTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT"/>
-        <sequence id="seq_Pongo" taxon="Pongo" totalcount="4"
-                  value="AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGGCCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCTTGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTCTTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTCTCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAAACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTTATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAACATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGATAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAACAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCGCTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCGCATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAACCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT"/>
-        <sequence id="seq_Hylobates" taxon="Hylobates" totalcount="4"
-                  value="AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATTCTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGGGCTCCAAGCCTTACTCCCACTGATAGCCTTCTGATGACTCGCAGCAAGCCTCGCTAACCTCGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTCCTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTCCCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAAACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCTAACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAACATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CACAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAGCCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTGCCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAACCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT"/>
-        <sequence id="seq_Macaca_fuscata" taxon="Macaca_fuscata" totalcount="4"
-                  value="AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGGACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTCCTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTCTCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAAGCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAACACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT"/>
-        <sequence id="seq_M._mulatta" taxon="M._mulatta" totalcount="4"
-                  value="AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGGACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTCCTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTCCCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCTATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAACATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CGCGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT"/>
-        <sequence id="seq_M._fascicularis" taxon="M._fascicularis" totalcount="4"
-                  value="AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTTCTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGTACCATACTACTATCCCGAGGACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTCCTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTCTCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAACATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTGCCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAATATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAACAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT"/>
-        <sequence id="seq_M._sylvanus" taxon="M._sylvanus" totalcount="4"
-                  value="AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTTCTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGCATCATACTACTATCCCGAGGACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCTTGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTCCTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTCTCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAAACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCTATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAACATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TGCAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCGCTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAATATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAACAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT"/>
-        <sequence id="seq_Saimiri_sciureus" taxon="Saimiri_sciureus" totalcount="4"
-                  value="AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTCTATGCTATTCTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAATAACATTTACTCGAGGGCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCTCGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTCTTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTCACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAAACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCTTACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAACATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CGCAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGATAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAATA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAGCTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCATCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAATCAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT"/>
-        <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4"
-                  value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
+        <sequence id="seq_Lemur_catta" taxon="Lemur_catta" totalcount="4" value="AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATTCTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGGGATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCTAGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTCATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTCCCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAACCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATTTACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAACACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATGTATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGATAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTATAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTGCATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAACAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT"/>
+        <sequence id="seq_Homo_sapiens" taxon="Homo_sapiens" totalcount="4" value="AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
+        <sequence id="seq_Pan" taxon="Pan" totalcount="4" value="AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATTCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCTCGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAAGCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TATAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCACCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCGCGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAGCTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
+        <sequence id="seq_Gorilla" taxon="Gorilla" totalcount="4" value="AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGGACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCTCGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTCCTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTCCCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAAACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCTATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CGTAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTACCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCGCATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAGCTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT"/>
+        <sequence id="seq_Pongo" taxon="Pongo" totalcount="4" value="AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGGCCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCTTGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTCTTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTCTCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAAACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTTATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAACATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGATAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAACAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCGCTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCGCATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAACCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT"/>
+        <sequence id="seq_Hylobates" taxon="Hylobates" totalcount="4" value="AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATTCTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGGGCTCCAAGCCTTACTCCCACTGATAGCCTTCTGATGACTCGCAGCAAGCCTCGCTAACCTCGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTCCTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTCCCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAAACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCTAACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAACATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CACAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAGCCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTGCCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAACCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT"/>
+        <sequence id="seq_Macaca_fuscata" taxon="Macaca_fuscata" totalcount="4" value="AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGGACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTCCTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTCTCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAAGCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAACACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT"/>
+        <sequence id="seq_M._mulatta" taxon="M._mulatta" totalcount="4" value="AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGGACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTCCTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTCCCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCTATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAACATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CGCGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT"/>
+        <sequence id="seq_M._fascicularis" taxon="M._fascicularis" totalcount="4" value="AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTTCTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGTACCATACTACTATCCCGAGGACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTCCTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTCTCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAACATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTGCCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAATATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAACAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT"/>
+        <sequence id="seq_M._sylvanus" taxon="M._sylvanus" totalcount="4" value="AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTTCTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGCATCATACTACTATCCCGAGGACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCTTGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTCCTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTCTCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAAACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCTATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAACATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TGCAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCGCTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAATATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAACAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT"/>
+        <sequence id="seq_Saimiri_sciureus" taxon="Saimiri_sciureus" totalcount="4" value="AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTCTATGCTATTCTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAATAACATTTACTCGAGGGCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCTCGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTCTTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTCACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAAACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCTTACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAACATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CGCAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGATAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAATA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAGCTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCATCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAATCAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT"/>
+        <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4" value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
     </data>
 
-
-    <map name="Beta">beast.base.inference.distribution.Beta</map>
-    <map name="Exponential">beast.base.inference.distribution.Exponential</map>
-    <map name="InverseGamma">beast.base.inference.distribution.InverseGamma</map>
-    <map name="LogNormal">beast.base.inference.distribution.LogNormalDistributionModel</map>
-    <map name="Gamma">beast.base.inference.distribution.Gamma</map>
-    <map name="Uniform">beast.base.inference.distribution.Uniform</map>
-    <map name="prior">beast.base.inference.distribution.Prior</map>
-    <map name="LaplaceDistribution">beast.base.inference.distribution.LaplaceDistribution</map>
-    <map name="OneOnX">beast.base.inference.distribution.OneOnX</map>
-    <map name="Normal">beast.base.inference.distribution.Normal</map>
-
-
     <run chainLength="5000000" id="mcmc" spec="MCMC">
         <state id="state" storeEvery="5000">
             <tree id="Tree.t:primate" name="stateNode">
                 <taxonset id="TaxonSet.coding" spec="TaxonSet">
-                    <alignment filter="2-457,660-896" id="coding" spec="FilteredAlignment">
+                    <alignment filter="2-457,660-896" id="coding" spec="beast.base.spec.evolution.alignment.FilteredAlignment">
                         <data idref="primate-mtDNA"/>
                     </alignment>
                 </taxonset>
             </tree>
-            <parameter id="birthRate.t:primate" name="stateNode" value="1.0"/>
-            <parameter id="rateAG.s:primate" lower="0.0" name="stateNode" value="2.0"/>
-            <parameter id="rateCT.s:primate" lower="0.0" name="stateNode" value="2.0"/>
-            <parameter dimension="4" id="freqParameter.s:primate" lower="0.0" name="stateNode" upper="1.0"
-                       value="0.25"/>
+            <parameter id="birthRate.t:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+            <parameter id="rateAG.s:primate" name="stateNode" value="2.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+            <parameter id="rateCT.s:primate" name="stateNode" value="2.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+            <parameter dimension="4" id="freqParameter.s:primate" name="stateNode" value="0.25" spec="beast.base.spec.inference.parameter.SimplexParam"/>
         </state>
 
-        <init estimate="false" id="RandomTree.t:primate" initial="@Tree.t:primate"
-              spec="beast.base.evolution.tree.coalescent.RandomTree" taxa="@coding">
-            <populationModel id="ConstantPopulation0.t:primate" spec="ConstantPopulation">
-                <parameter id="randomPopSize.t:primate" name="popSize" value="1"/>
+        <init estimate="false" id="RandomTree.t:primate" initial="@Tree.t:primate" spec="beast.base.spec.evolution.tree.coalescent.RandomTree" taxa="@coding">
+            <populationModel id="ConstantPopulation0.t:primate" spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
+                <parameter id="randomPopSize.t:primate" name="popSize" value="1" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
             </populationModel>
         </init>
 
         <distribution id="posterior" spec="CompoundDistribution">
             <distribution id="prior" spec="CompoundDistribution">
-                <distribution birthDiffRate="@birthRate.t:primate" id="YuleModel.t:primate"
-                              spec="beast.base.evolution.speciation.YuleModel" tree="@Tree.t:primate"/>
-                <prior id="YuleBirthRatePrior.t:primate" name="distribution" x="@birthRate.t:primate">
-                    <Uniform id="Uniform.0" name="distr" upper="Infinity"/>
-                </prior>
+                <distribution birthDiffRate="@birthRate.t:primate" id="YuleModel.t:primate" spec="beast.base.spec.evolution.speciation.YuleModel" tree="@Tree.t:primate"/>
+                <distribution id="Uniform.0" spec="beast.base.spec.inference.distribution.Uniform" param="@birthRate.t:primate" upper="1.0E6"/>
             </distribution>
             <distribution id="likelihood" spec="CompoundDistribution">
-                <distribution data="@coding" id="treeLikelihood.coding" spec="TreeLikelihood" tree="@Tree.t:primate">
-                    <siteModel id="SiteModel.s:primate" spec="SiteModel">
-                        <parameter estimate="false" id="mutationRate.s:primate" name="mutationRate" value="1.0"/>
-                        <parameter estimate="false" id="gammaShape.s:primate" name="shape" value="1.0"/>
-                        <parameter estimate="false" id="proportionInvariant.s:primate" lower="0.0"
-                                   name="proportionInvariant" upper="1.0" value="0.0"/>
-                        <substModel id="tn93.s:primate" kappa1="@rateAG.s:primate" kappa2="@rateCT.s:primate"
-                                    spec="TN93">
-                            <frequencies frequencies="@freqParameter.s:primate" id="estimatedFreqs.s:primate"
-                                         spec="Frequencies"/>
+                <distribution data="@coding" id="treeLikelihood.coding" spec="beast.base.spec.evolution.likelihood.TreeLikelihood" tree="@Tree.t:primate">
+                    <siteModel id="SiteModel.s:primate" spec="beast.base.spec.evolution.sitemodel.SiteModel">
+                        <parameter estimate="false" id="mutationRate.s:primate" name="mutationRate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="gammaShape.s:primate" name="shape" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="proportionInvariant.s:primate" name="proportionInvariant" value="0.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="UnitInterval"/>
+                        <substModel id="tn93.s:primate" kappa1="@rateAG.s:primate" kappa2="@rateCT.s:primate" spec="beast.base.spec.evolution.substitutionmodel.TN93">
+                            <frequencies frequencies="@freqParameter.s:primate" id="estimatedFreqs.s:primate" spec="beast.base.spec.evolution.substitutionmodel.Frequencies"/>
                         </substModel>
                     </siteModel>
-                    <branchRateModel id="StrictClock.c:primate" spec="beast.base.evolution.branchratemodel.StrictClockModel">
-                        <parameter estimate="false" id="clockRate.c:primate" name="clock.rate" value="1.0"/>
+                    <branchRateModel id="StrictClock.c:primate" spec="beast.base.spec.evolution.branchratemodel.StrictClockModel">
+                        <parameter estimate="false" id="clockRate.c:primate" name="clock.rate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
                     </branchRateModel>
                 </distribution>
-                <distribution branchRateModel="@StrictClock.c:primate" id="treeLikelihood.noncoding"
-                              siteModel="@SiteModel.s:primate" spec="TreeLikelihood" tree="@Tree.t:primate">
-                    <data data="@primate-mtDNA" filter="1,458-659,897-898" id="noncoding" spec="FilteredAlignment"/>
+                <distribution branchRateModel="@StrictClock.c:primate" id="treeLikelihood.noncoding" siteModel="@SiteModel.s:primate" spec="beast.base.spec.evolution.likelihood.TreeLikelihood" tree="@Tree.t:primate">
+                    <data data="@primate-mtDNA" filter="1,458-659,897-898" id="noncoding" spec="beast.base.spec.evolution.alignment.FilteredAlignment"/>
                 </distribution>
             </distribution>
         </distribution>
 
-        <operator id="YuleBirthRateScaler.t:primate" parameter="@birthRate.t:primate" scaleFactor="0.75"
-                  spec="ScaleOperator" weight="3.0"/>
+        <operator id="YuleBirthRateScaler.t:primate" parameter="@birthRate.t:primate" scaleFactor="0.75" weight="3.0" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator id="treeScaler.t:primate" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:primate" weight="3.0"/>
+        <operator id="treeScaler.t:primate" scaleFactor="0.5" tree="@Tree.t:primate" weight="3.0" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
 
-        <operator id="treeRootScaler.t:primate" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator"
-                  tree="@Tree.t:primate" weight="3.0"/>
+        <operator id="treeRootScaler.t:primate" rootOnly="true" scaleFactor="0.5" tree="@Tree.t:primate" weight="3.0" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
 
-        <operator id="UniformOperator.t:primate" spec="Uniform" tree="@Tree.t:primate" weight="30.0"/>
+        <operator id="UniformOperator.t:primate" tree="@Tree.t:primate" weight="30.0" spec="beast.base.evolution.operator.Uniform"/>
 
-        <operator id="SubtreeSlide.t:primate" spec="SubtreeSlide" tree="@Tree.t:primate" weight="15.0"/>
+        <operator id="SubtreeSlide.t:primate" spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" tree="@Tree.t:primate" weight="15.0"/>
 
         <operator id="narrow.t:primate" spec="Exchange" tree="@Tree.t:primate" weight="15.0"/>
 
@@ -117,18 +81,15 @@
 
         <operator id="WilsonBalding.t:primate" spec="WilsonBalding" tree="@Tree.t:primate" weight="3.0"/>
 
-        <operator id="RateAGScaler.s:primate" parameter="@rateAG.s:primate" scaleFactor="0.5" spec="ScaleOperator"
-                  weight="0.1"/>
+        <operator id="RateAGScaler.s:primate" parameter="@rateAG.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator id="RateCTScaler.s:primate" parameter="@rateCT.s:primate" scaleFactor="0.5" spec="ScaleOperator"
-                  weight="0.1"/>
+        <operator id="RateCTScaler.s:primate" parameter="@rateCT.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator delta="0.01" id="FrequenciesExchanger.s:primate" spec="DeltaExchangeOperator" weight="0.1">
+        <operator delta="0.01" id="FrequenciesExchanger.s:primate" spec="beast.base.spec.inference.operator.DeltaExchangeOperator" weight="0.1">
             <parameter idref="freqParameter.s:primate"/>
         </operator>
 
-        <logger fileName="primate-mtDNA-tn93.log" id="tracelog" logEvery="5000" model="@posterior"
-                sanitiseHeaders="true" sort="smart">
+        <logger fileName="primate-mtDNA-tn93.log" id="tracelog" logEvery="5000" model="@posterior" sanitiseHeaders="true" sort="smart">
             <log idref="posterior"/>
             <log idref="likelihood"/>
             <log idref="prior"/>
@@ -144,7 +105,7 @@
 
         <logger id="screenlog" logEvery="5000">
             <log idref="posterior"/>
-            <log arg="@posterior" id="ESS.0" spec="util.ESS"/>
+            <log arg="@posterior" id="ESS.0" spec="beast.base.spec.inference.util.ESS"/>
             <log idref="likelihood"/>
             <log idref="prior"/>
             <parameter idref="rateAG.s:primate" name="log"/>
@@ -152,8 +113,7 @@
         </logger>
 
         <logger fileName="primate-mtDNA-tn93.trees" id="treelog.t:primate" logEvery="5000" mode="tree">
-            <log id="TreeWithMetaDataLogger.t:primate" spec="beast.base.evolution.TreeWithMetaDataLogger"
-                 tree="@Tree.t:primate"/>
+            <log id="TreeWithMetaDataLogger.t:primate" spec="beast.base.spec.evolution.TreeWithMetaDataLogger" tree="@Tree.t:primate"/>
         </logger>
 
     </run>
diff --git a/beast-base/src/test/resources/beast.base/examples/testTVM.xml b/beast-base/src/test/resources/beast.base/examples/testTVM.xml
index 56147dcc..07030e1b 100644
--- a/beast-base/src/test/resources/beast.base/examples/testTVM.xml
+++ b/beast-base/src/test/resources/beast.base/examples/testTVM.xml
@@ -1,146 +1,99 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<beast beautitemplate='Standard' beautistatus=''
-       namespace="beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.alignment:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood"
-       version="2.0">
+<?xml version='1.0' encoding='UTF-8'?>
+<beast version="2.8"
+       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt"
+       beautitemplate="Standard"
+       beautistatus="">
 
     <data id="primate-mtDNA">
-        <sequence id="seq_Lemur_catta" taxon="Lemur_catta" totalcount="4"
-                  value="AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATTCTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGGGATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCTAGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTCATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTCCCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAACCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATTTACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAACACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATGTATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGATAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTATAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTGCATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAACAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT"/>
-        <sequence id="seq_Homo_sapiens" taxon="Homo_sapiens" totalcount="4"
-                  value="AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
-        <sequence id="seq_Pan" taxon="Pan" totalcount="4"
-                  value="AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATTCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCTCGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAAGCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TATAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCACCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCGCGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAGCTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
-        <sequence id="seq_Gorilla" taxon="Gorilla" totalcount="4"
-                  value="AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGGACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCTCGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTCCTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTCCCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAAACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCTATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CGTAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTACCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCGCATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAGCTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT"/>
-        <sequence id="seq_Pongo" taxon="Pongo" totalcount="4"
-                  value="AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGGCCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCTTGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTCTTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTCTCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAAACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTTATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAACATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGATAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAACAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCGCTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCGCATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAACCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT"/>
-        <sequence id="seq_Hylobates" taxon="Hylobates" totalcount="4"
-                  value="AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATTCTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGGGCTCCAAGCCTTACTCCCACTGATAGCCTTCTGATGACTCGCAGCAAGCCTCGCTAACCTCGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTCCTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTCCCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAAACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCTAACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAACATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CACAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAGCCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTGCCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAACCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT"/>
-        <sequence id="seq_Macaca_fuscata" taxon="Macaca_fuscata" totalcount="4"
-                  value="AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGGACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTCCTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTCTCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAAGCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAACACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT"/>
-        <sequence id="seq_M._mulatta" taxon="M._mulatta" totalcount="4"
-                  value="AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGGACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTCCTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTCCCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCTATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAACATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CGCGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT"/>
-        <sequence id="seq_M._fascicularis" taxon="M._fascicularis" totalcount="4"
-                  value="AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTTCTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGTACCATACTACTATCCCGAGGACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTCCTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTCTCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAACATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTGCCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAATATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAACAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT"/>
-        <sequence id="seq_M._sylvanus" taxon="M._sylvanus" totalcount="4"
-                  value="AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTTCTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGCATCATACTACTATCCCGAGGACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCTTGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTCCTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTCTCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAAACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCTATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAACATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TGCAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCGCTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAATATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAACAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT"/>
-        <sequence id="seq_Saimiri_sciureus" taxon="Saimiri_sciureus" totalcount="4"
-                  value="AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTCTATGCTATTCTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAATAACATTTACTCGAGGGCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCTCGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTCTTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTCACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAAACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCTTACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAACATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CGCAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGATAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAATA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAGCTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCATCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAATCAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT"/>
-        <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4"
-                  value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
+        <sequence id="seq_Lemur_catta" taxon="Lemur_catta" totalcount="4" value="AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATTCTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGGGATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCTAGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTCATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTCCCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAACCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATTTACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAACACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATGTATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGATAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTATAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTGCATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAACAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT"/>
+        <sequence id="seq_Homo_sapiens" taxon="Homo_sapiens" totalcount="4" value="AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
+        <sequence id="seq_Pan" taxon="Pan" totalcount="4" value="AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATTCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCTCGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAAGCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TATAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCACCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCGCGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAGCTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT"/>
+        <sequence id="seq_Gorilla" taxon="Gorilla" totalcount="4" value="AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGGACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCTCGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTCCTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTCCCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAAACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCTATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CGTAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTACCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCGCATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAGCTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT"/>
+        <sequence id="seq_Pongo" taxon="Pongo" totalcount="4" value="AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGGCCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCTTGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTCTTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTCTCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAAACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTTATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAACATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGATAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAACAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCGCTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCGCATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAACCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT"/>
+        <sequence id="seq_Hylobates" taxon="Hylobates" totalcount="4" value="AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATTCTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGGGCTCCAAGCCTTACTCCCACTGATAGCCTTCTGATGACTCGCAGCAAGCCTCGCTAACCTCGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTCCTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTCCCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAAACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCTAACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAACATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CACAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAGCCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTGCCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAACCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT"/>
+        <sequence id="seq_Macaca_fuscata" taxon="Macaca_fuscata" totalcount="4" value="AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGGACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTCCTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTCTCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAAGCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAACACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT"/>
+        <sequence id="seq_M._mulatta" taxon="M._mulatta" totalcount="4" value="AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGGACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTCCTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTCCCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCTATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAACATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CGCGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT"/>
+        <sequence id="seq_M._fascicularis" taxon="M._fascicularis" totalcount="4" value="AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTTCTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGTACCATACTACTATCCCGAGGACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTCCTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTCTCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAACATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTGCCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAATATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAACAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT"/>
+        <sequence id="seq_M._sylvanus" taxon="M._sylvanus" totalcount="4" value="AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTTCTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGCATCATACTACTATCCCGAGGACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCTTGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTCCTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTCTCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAAACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCTATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAACATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TGCAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCGCTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAATATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAACAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT"/>
+        <sequence id="seq_Saimiri_sciureus" taxon="Saimiri_sciureus" totalcount="4" value="AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTCTATGCTATTCTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAATAACATTTACTCGAGGGCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCTCGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTCTTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTCACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAAACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCTTACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAACATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CGCAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGATAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAATA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAGCTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCATCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAATCAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT"/>
+        <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4" value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
     </data>
 
-
-    <map name="Beta">beast.base.inference.distribution.Beta</map>
-    <map name="Exponential">beast.base.inference.distribution.Exponential</map>
-    <map name="InverseGamma">beast.base.inference.distribution.InverseGamma</map>
-    <map name="LogNormal">beast.base.inference.distribution.LogNormalDistributionModel</map>
-    <map name="Gamma">beast.base.inference.distribution.Gamma</map>
-    <map name="Uniform">beast.base.inference.distribution.Uniform</map>
-    <map name="prior">beast.base.inference.distribution.Prior</map>
-    <map name="LaplaceDistribution">beast.base.inference.distribution.LaplaceDistribution</map>
-    <map name="OneOnX">beast.base.inference.distribution.OneOnX</map>
-    <map name="Normal">beast.base.inference.distribution.Normal</map>
-
-
     <run chainLength="5000000" id="mcmc" spec="MCMC">
         <state id="state" storeEvery="5000">
             <tree id="Tree.t:primate" name="stateNode">
                 <taxonset id="TaxonSet.coding" spec="TaxonSet">
-                    <alignment filter="2-457,660-896" id="coding" spec="FilteredAlignment">
+                    <alignment filter="2-457,660-896" id="coding" spec="beast.base.spec.evolution.alignment.FilteredAlignment">
                         <data idref="primate-mtDNA"/>
                     </alignment>
                 </taxonset>
             </tree>
-            <parameter id="birthRate.t:primate" name="stateNode" value="1.0"/>
-            <parameter id="rateGT.s:primate" lower="0.0" name="stateNode" value="1.0"/>
-            <parameter id="rateTransitions.s:primate" lower="0.0" name="stateNode" value="1.0"/>
-            <parameter id="rateAT.s:primate" lower="0.0" name="stateNode" value="1.0"/>
-            <parameter id="rateCG.s:primate" lower="0.0" name="stateNode" value="1.0"/>
-            <parameter dimension="4" id="freqParameter.s:primate" lower="0.0" name="stateNode" upper="1.0"
-                       value="0.25"/>
+            <parameter id="birthRate.t:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+            <parameter id="rateGT.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+            <parameter id="rateTransitions.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+            <parameter id="rateAT.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+            <parameter id="rateCG.s:primate" name="stateNode" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+            <parameter dimension="4" id="freqParameter.s:primate" name="stateNode" value="0.25" spec="beast.base.spec.inference.parameter.SimplexParam"/>
         </state>
 
-        <init estimate="false" id="RandomTree.t:primate" initial="@Tree.t:primate"
-              spec="beast.base.evolution.tree.coalescent.RandomTree" taxa="@coding">
-            <populationModel id="ConstantPopulation0.t:primate" spec="ConstantPopulation">
-                <parameter id="randomPopSize.t:primate" name="popSize" value="1"/>
+        <init estimate="false" id="RandomTree.t:primate" initial="@Tree.t:primate" spec="beast.base.spec.evolution.tree.coalescent.RandomTree" taxa="@coding">
+            <populationModel id="ConstantPopulation0.t:primate" spec="beast.base.spec.evolution.tree.coalescent.ConstantPopulation">
+                <parameter id="randomPopSize.t:primate" name="popSize" value="1" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
             </populationModel>
         </init>
 
         <distribution id="posterior" spec="CompoundDistribution">
             <distribution id="prior" spec="CompoundDistribution">
-                <distribution birthDiffRate="@birthRate.t:primate" id="YuleModel.t:primate"
-                              spec="beast.base.evolution.speciation.YuleModel" tree="@Tree.t:primate"/>
-                <prior id="YuleBirthRatePrior.t:primate" name="distribution" x="@birthRate.t:primate">
-                    <Uniform id="Uniform.0" name="distr" upper="Infinity"/>
-                </prior>
-                <prior id="RateGTPrior.s:primate" name="distribution" x="@rateGT.s:primate">
-                    <LogNormal id="LogNormalDistributionModel.0" name="distr">
-                        <parameter estimate="false" id="RealParameter.0" name="M" value="0"/>
-                        <parameter estimate="false" id="RealParameter.01" lower="0.0" name="S" upper="5.0"
-                                   value="1.25"/>
-                    </LogNormal>
-                </prior>
-                <prior id="RateTransitionsPrior.s:primate" name="distribution" x="@rateTransitions.s:primate">
-                    <LogNormal id="LogNormalDistributionModel.01" name="distr">
-                        <parameter estimate="false" id="RealParameter.02" name="M" value="0"/>
-                        <parameter estimate="false" id="RealParameter.03" lower="0.0" name="S" upper="5.0"
-                                   value="1.25"/>
-                    </LogNormal>
-                </prior>
-                <prior id="RateATPrior.s:primate" name="distribution" x="@rateAT.s:primate">
-                    <LogNormal id="LogNormalDistributionModel.02" name="distr">
-                        <parameter estimate="false" id="RealParameter.04" name="M" value="0"/>
-                        <parameter estimate="false" id="RealParameter.05" lower="0.0" name="S" upper="5.0"
-                                   value="1.25"/>
-                    </LogNormal>
-                </prior>
-                <prior id="RateCGPrior.s:primate" name="distribution" x="@rateCG.s:primate">
-                    <LogNormal id="LogNormalDistributionModel.03" name="distr">
-                        <parameter estimate="false" id="RealParameter.06" name="M" value="0"/>
-                        <parameter estimate="false" id="RealParameter.07" lower="0.0" name="S" upper="5.0"
-                                   value="1.25"/>
-                    </LogNormal>
-                </prior>
+                <distribution birthDiffRate="@birthRate.t:primate" id="YuleModel.t:primate" spec="beast.base.spec.evolution.speciation.YuleModel" tree="@Tree.t:primate"/>
+                <distribution id="Uniform.0" spec="beast.base.spec.inference.distribution.Uniform" param="@birthRate.t:primate" upper="1.0E6"/>
+                <distribution id="LogNormalDistributionModel.0" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateGT.s:primate">
+                        <parameter estimate="false" id="RealParameter.0" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="RealParameter.01" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                    </distribution>
+                <distribution id="LogNormalDistributionModel.01" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateTransitions.s:primate">
+                        <parameter estimate="false" id="RealParameter.02" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="RealParameter.03" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                    </distribution>
+                <distribution id="LogNormalDistributionModel.02" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateAT.s:primate">
+                        <parameter estimate="false" id="RealParameter.04" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="RealParameter.05" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                    </distribution>
+                <distribution id="LogNormalDistributionModel.03" spec="beast.base.spec.inference.distribution.LogNormal" param="@rateCG.s:primate">
+                        <parameter estimate="false" id="RealParameter.06" name="M" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="RealParameter.07" name="S" value="1.25" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                    </distribution>
             </distribution>
 
             <distribution id="likelihood" spec="CompoundDistribution">
-                <distribution data="@coding" id="treeLikelihood.coding" spec="TreeLikelihood" tree="@Tree.t:primate">
-                    <siteModel id="SiteModel.s:primate" spec="SiteModel">
-                        <parameter estimate="false" id="mutationRate.s:primate" name="mutationRate" value="1.0"/>
-                        <parameter estimate="false" id="gammaShape.s:primate" name="shape" value="1.0"/>
-                        <parameter estimate="false" id="proportionInvariant.s:primate" lower="0.0"
-                                   name="proportionInvariant" upper="1.0" value="0.0"/>
-                        <substModel id="tvm.s:primate" rateGT="@rateGT.s:primate" rateTransitions="@rateTransitions.s:primate"
-                                    rateAT="@rateAT.s:primate" rateCG="@rateCG.s:primate" spec="TVM">
-                            <parameter estimate="false" id="rateAC.s:primate" lower="0.0" name="rateAC" value="1.0"/>
-                            <frequencies frequencies="@freqParameter.s:primate" id="estimatedFreqs.s:primate"
-                                         spec="Frequencies"/>
+                <distribution data="@coding" id="treeLikelihood.coding" spec="beast.base.spec.evolution.likelihood.TreeLikelihood" tree="@Tree.t:primate">
+                    <siteModel id="SiteModel.s:primate" spec="beast.base.spec.evolution.sitemodel.SiteModel">
+                        <parameter estimate="false" id="mutationRate.s:primate" name="mutationRate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="gammaShape.s:primate" name="shape" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+                        <parameter estimate="false" id="proportionInvariant.s:primate" name="proportionInvariant" value="0.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="UnitInterval"/>
+                        <substModel id="tvm.s:primate" rateGT="@rateGT.s:primate" rateTransitions="@rateTransitions.s:primate" rateAT="@rateAT.s:primate" rateCG="@rateCG.s:primate" spec="beast.base.spec.evolution.substitutionmodel.TVM">
+                            <parameter estimate="false" id="rateAC.s:primate" name="rateAC" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="PositiveReal"/>
+                            <frequencies frequencies="@freqParameter.s:primate" id="estimatedFreqs.s:primate" spec="beast.base.spec.evolution.substitutionmodel.Frequencies"/>
                         </substModel>
                     </siteModel>
-                    <branchRateModel id="StrictClock.c:primate" spec="beast.base.evolution.branchratemodel.StrictClockModel">
-                        <parameter estimate="false" id="clockRate.c:primate" name="clock.rate" value="1.0"/>
+                    <branchRateModel id="StrictClock.c:primate" spec="beast.base.spec.evolution.branchratemodel.StrictClockModel">
+                        <parameter estimate="false" id="clockRate.c:primate" name="clock.rate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
                     </branchRateModel>
                 </distribution>
-                <distribution branchRateModel="@StrictClock.c:primate" id="treeLikelihood.noncoding"
-                              siteModel="@SiteModel.s:primate" spec="TreeLikelihood" tree="@Tree.t:primate">
-                    <data data="@primate-mtDNA" filter="1,458-659,897-898" id="noncoding" spec="FilteredAlignment"/>
+                <distribution branchRateModel="@StrictClock.c:primate" id="treeLikelihood.noncoding" siteModel="@SiteModel.s:primate" spec="beast.base.spec.evolution.likelihood.TreeLikelihood" tree="@Tree.t:primate">
+                    <data data="@primate-mtDNA" filter="1,458-659,897-898" id="noncoding" spec="beast.base.spec.evolution.alignment.FilteredAlignment"/>
                 </distribution>
             </distribution>
         </distribution>
 
-        <operator id="YuleBirthRateScaler.t:primate" parameter="@birthRate.t:primate" scaleFactor="0.75"
-                  spec="ScaleOperator" weight="3.0"/>
+        <operator id="YuleBirthRateScaler.t:primate" parameter="@birthRate.t:primate" scaleFactor="0.75" weight="3.0" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator id="treeScaler.t:primate" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:primate" weight="3.0"/>
+        <operator id="treeScaler.t:primate" scaleFactor="0.5" tree="@Tree.t:primate" weight="3.0" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
 
-        <operator id="treeRootScaler.t:primate" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator"
-                  tree="@Tree.t:primate" weight="3.0"/>
+        <operator id="treeRootScaler.t:primate" rootOnly="true" scaleFactor="0.5" tree="@Tree.t:primate" weight="3.0" spec="beast.base.spec.evolution.operator.ScaleTreeOperator"/>
 
-        <operator id="UniformOperator.t:primate" spec="Uniform" tree="@Tree.t:primate" weight="30.0"/>
+        <operator id="UniformOperator.t:primate" tree="@Tree.t:primate" weight="30.0" spec="beast.base.evolution.operator.Uniform"/>
 
-        <operator id="SubtreeSlide.t:primate" spec="SubtreeSlide" tree="@Tree.t:primate" weight="15.0"/>
+        <operator id="SubtreeSlide.t:primate" spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" tree="@Tree.t:primate" weight="15.0"/>
 
         <operator id="narrow.t:primate" spec="Exchange" tree="@Tree.t:primate" weight="15.0"/>
 
@@ -148,24 +101,19 @@
 
         <operator id="WilsonBalding.t:primate" spec="WilsonBalding" tree="@Tree.t:primate" weight="3.0"/>
 
-        <operator id="RateGTScaler.s:primate" parameter="@rateGT.s:primate" scaleFactor="0.5" spec="ScaleOperator"
-                  weight="0.1"/>
+        <operator id="RateGTScaler.s:primate" parameter="@rateGT.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator id="RateATScaler.s:primate" parameter="@rateAT.s:primate" scaleFactor="0.5" spec="ScaleOperator"
-                  weight="0.1"/>
+        <operator id="RateATScaler.s:primate" parameter="@rateAT.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator id="RateCGScaler.s:primate" parameter="@rateCG.s:primate" scaleFactor="0.5" spec="ScaleOperator"
-                  weight="0.1"/>
+        <operator id="RateCGScaler.s:primate" parameter="@rateCG.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator id="RateTransitionsScaler.s:primate" parameter="@rateTransitions.s:primate" scaleFactor="0.5" spec="ScaleOperator"
-                  weight="0.1"/>
+        <operator id="RateTransitionsScaler.s:primate" parameter="@rateTransitions.s:primate" scaleFactor="0.5" weight="0.1" spec="beast.base.spec.inference.operator.ScaleOperator"/>
 
-        <operator delta="0.01" id="FrequenciesExchanger.s:primate" spec="DeltaExchangeOperator" weight="0.1">
+        <operator delta="0.01" id="FrequenciesExchanger.s:primate" spec="beast.base.spec.inference.operator.DeltaExchangeOperator" weight="0.1">
             <parameter idref="freqParameter.s:primate"/>
         </operator>
 
-        <logger fileName="primate-mtDNA-TVM.log" id="tracelog" logEvery="5000" model="@posterior" sanitiseHeaders="true"
-                sort="smart">
+        <logger fileName="primate-mtDNA-TVM.log" id="tracelog" logEvery="5000" model="@posterior" sanitiseHeaders="true" sort="smart">
             <log idref="posterior"/>
             <log idref="likelihood"/>
             <log idref="prior"/>
@@ -183,14 +131,13 @@
 
         <logger id="screenlog" logEvery="5000">
             <log idref="posterior"/>
-            <log arg="@posterior" id="ESS.0" spec="util.ESS"/>
+            <log arg="@posterior" id="ESS.0" spec="beast.base.spec.inference.util.ESS"/>
             <log idref="likelihood"/>
             <log idref="prior"/>
         </logger>
 
         <logger fileName="$(tree).trees" id="treelog.t:primate" logEvery="5000" mode="tree">
-            <log id="TreeWithMetaDataLogger.t:primate" spec="beast.base.evolution.TreeWithMetaDataLogger"
-                 tree="@Tree.t:primate"/>
+            <log id="TreeWithMetaDataLogger.t:primate" spec="beast.base.spec.evolution.TreeWithMetaDataLogger" tree="@Tree.t:primate"/>
         </logger>
 
     </run>
diff --git a/beast-base/src/test/resources/beast.base/examples/testYuleOneSite.xml b/beast-base/src/test/resources/beast.base/examples/testYuleOneSite.xml
index 465f1bcc..92e4b88f 100644
--- a/beast-base/src/test/resources/beast.base/examples/testYuleOneSite.xml
+++ b/beast-base/src/test/resources/beast.base/examples/testYuleOneSite.xml
@@ -1,7 +1,7 @@
-<?xml version="1.0" standalone="yes"?>
+<?xml version='1.0' encoding='UTF-8'?>
 <!-- test Yule birth model and Birth Death model per Gernhard 2008-->
-<beast version='2.0'
-       namespace='beast.base.evolution.speciation:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood'>
+<beast version="2.8"
+       namespace="beast.core:beast.core.util:beast.evolution.alignment:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.tree.coalescent:beast.base.core:beast.base.evolution.alignment:beast.base.evolution.likelihood:beast.base.evolution.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.inference:beast.base.inference.operator:beast.base.inference.util:beast.pkgmgmt">
 
     <data id="alignment" dataType="nucleotide">
         <sequence taxon="A">A</sequence>
@@ -12,78 +12,77 @@
     
     <!-- A prior on the distribution node heights defined given                  -->
     <!-- a Yule speciation process (a pure birth process).                       -->
-    <input spec='YuleModel' id="yule">
-        <parameter name='birthDiffRate' idref="birthRate"/>
-	<tree spec='beast.base.evolution.tree.TreeParser' id='tree' IsLabelledNewick='true' taxa='@alignment'
-	        newick='((A:1.0,B:1.0):1.0,(C:1.0,D:1.0):1.0);'/>
+    <input spec="beast.base.spec.evolution.speciation.YuleModel" id="yule">
+        <parameter name="birthDiffRate" idref="birthRate"/>
+	<tree spec="beast.base.evolution.tree.TreeParser" id="tree" IsLabelledNewick="true" taxa="@alignment" newick="((A:1.0,B:1.0):1.0,(C:1.0,D:1.0):1.0);"/>
     </input>
 
-    <input spec='BirthDeathGernhard08Model' id="yulelike" type='unscaled' tree='@tree'>
-        <parameter name='birthDiffRate' idref="birthRate"/>
-	    <parameter name='relativeDeathRate' idref='relativeDeathRate'/>
+    <input spec="beast.base.spec.evolution.speciation.BirthDeathGernhard08Model" id="yulelike" type="unscaled" tree="@tree">
+        <parameter name="birthDiffRate" idref="birthRate"/>
+	    <parameter name="relativeDeathRate" idref="relativeDeathRate"/>
     </input>
 
     <!-- site model                                                              -->
-    <input spec='SiteModel' id="siteModel" gammaCategoryCount='1'>
-	<substModel spec='HKY' id='hky'>
-	    <kappa id='hky.kappa' spec='parameter.RealParameter' value='1.0'/>
-	    <frequencies id='freqs' spec='Frequencies'>
-	       <data idref='alignment'/>
+    <input spec="beast.base.spec.evolution.sitemodel.SiteModel" id="siteModel" gammaCategoryCount="1">
+	<substModel spec="beast.base.spec.evolution.substitutionmodel.HKY" id="hky">
+	    <kappa id="hky.kappa" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+	    <frequencies id="freqs" spec="beast.base.spec.evolution.substitutionmodel.Frequencies">
+	       <data idref="alignment"/>
 	    </frequencies>
 	</substModel>
     </input>
 
-    <parameter id="birthRate" value="1.0" lower="0.0" upper="100.0"/>
-    <parameter id='relativeDeathRate' value='0'/>
+    <parameter id="birthRate" value="1.0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
+    <parameter id="relativeDeathRate" value="0" spec="beast.base.spec.inference.parameter.RealScalarParam" domain="Real"/>
 
     <!-- initial yule prior = -6.0, yule-like prior = -2.8219461696520542 -->
     <!-- expected yule prior = 1/(n.lambda)\sum_{k=1}^{n-1}k/(n-k) where lambda = birth rate, n = number of taxa
 	with lambda=1, n=-4 we expect 1/4(1/3+2/2+3/1)=1.155555555
  -->
-    <run spec='MCMC' chainLength="10">
+    <run spec="MCMC" chainLength="10">
 	<state>
-	    <stateNode idref='tree'/>
-	    <stateNode idref='birthRate'/>
-	    <stateNode id='tree-test-single-child-parsing' IsLabelledNewick='true' spec='beast.base.evolution.tree.TreeParser' singlechild='true' newick='((A:1.0):2,C:3);' >
-			<taxonset spec='beast.base.evolution.alignment.TaxonSet'>
-				<taxon spec='beast.base.evolution.alignment.Taxon' id='A'/>
-				<taxon spec='beast.base.evolution.alignment.Taxon' id='C'/>
+	    <stateNode idref="tree"/>
+	    <stateNode idref="birthRate"/>
+	    <stateNode id="tree-test-single-child-parsing" IsLabelledNewick="true" spec="beast.base.evolution.tree.TreeParser" singlechild="true" newick="((A:1.0):2,C:3);">
+			<taxonset spec="beast.base.evolution.alignment.TaxonSet">
+				<taxon spec="beast.base.evolution.alignment.Taxon" id="A"/>
+				<taxon spec="beast.base.evolution.alignment.Taxon" id="C"/>
 			</taxonset>
 		</stateNode>
 	</state>
 
-	<distribution spec='CompoundDistribution'>
-	        <distribution id="yule.prior" idref='yule'/>
+	<distribution spec="CompoundDistribution">
+	        <distribution id="yule.prior" idref="yule"/>
 <!--
 		<distribution spec='TreeLikelihood' id="treeLikelihood" data='@alignment' tree='@tree' siteModel='@siteModel'/>
 -->
-	        <distribution id="yulelike.prior" idref='yulelike'/>
+	        <distribution id="yulelike.prior" idref="yulelike"/>
 	</distribution>
 
-        <operator spec='SubtreeSlide' weight="5" gaussian="true" size="1.0" tree="@tree"/>
+        <operator spec="beast.base.evolution.operator.kernel.BactrianSubtreeSlide" weight="5" size="1.0" tree="@tree"/>
 <!--
         <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" tree="@tree"/>
 -->
-        <operator spec='Uniform' weight="10" tree="@tree"/>
-        <operator id='narrow' spec='Exchange' isNarrow='true' weight="1" tree="@tree"/>
-        <operator id='wide' spec='Exchange' isNarrow='false' weight="1" tree="@tree"/>
-        <operator spec='WilsonBalding' weight="1" tree="@tree"/>
+        <operator weight="10" tree="@tree" spec="beast.base.evolution.operator.Uniform"/>
+        <operator id="narrow" spec="Exchange" isNarrow="true" weight="1" tree="@tree"/>
+        <operator id="wide" spec="Exchange" isNarrow="false" weight="1" tree="@tree"/>
+        <operator spec="WilsonBalding" weight="1" tree="@tree"/>
 <!--
         <operator spec='ScaleOperator' scaleFactor="0.75" weight="3">
             <parameter idref="birthRate"/>
         </operator>
 -->
-	<logger logEvery='100'>
-	    <log idref='yule.prior'/>
+	<logger logEvery="100">
+	    <log idref="yule.prior"/>
 	    <!--log idref='treeLikelihood'/-->
-	    <log idref='yulelike.prior'/>
-            <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree'/>
+	    <log idref="yulelike.prior"/>
+            <log spec="beast.base.evolution.tree.TreeStatLogger" tree="@tree"/>
 	</logger>
-	<logger logEvery='100' fileName='$(seed).log'>
-	    <log idref='yule.prior'/>
+	<logger logEvery="100" fileName="$(seed).log">
+	    <log idref="yule.prior"/>
 	    <!--log idref='treeLikelihood'/-->
 	    <!--log idref='yulelike.prior'/-->
-            <log spec='beast.base.evolution.tree.TreeStatLogger' tree='@tree'/>
+            <log spec="beast.base.evolution.tree.TreeStatLogger" tree="@tree"/>
 	</logger>
     </run>
 
diff --git a/beast-fx/src/test/java/test/beastfx/integration/ResumeTest.java b/beast-fx/src/test/java/test/beastfx/integration/ResumeTest.java
index f048f046..9f16fbee 100644
--- a/beast-fx/src/test/java/test/beastfx/integration/ResumeTest.java
+++ b/beast-fx/src/test/java/test/beastfx/integration/ResumeTest.java
@@ -15,9 +15,9 @@
 public class ResumeTest  {
 
     final static String XML_FILE = "testHKY.xml";
-    // Classpath path to the spec example, copied from beast-base test resources
+    // Classpath path to the example, copied from beast-base test resources
     // by Maven's generate-test-resources phase (see beast-fx/pom.xml).
-    final static String XML_CLASSPATH = "beast.base/examples/spec/" + XML_FILE;
+    final static String XML_CLASSPATH = "beast.base/examples/" + XML_FILE;
 
 	{
 		ExampleXmlParsingTest.setUpTestDir();
diff --git a/release/Linux/README.md b/release/Linux/README.md
index 85fc2e7a..9b76e5ed 100644
--- a/release/Linux/README.md
+++ b/release/Linux/README.md
@@ -49,8 +49,7 @@ BEAST.v<version>/
   bin/              shell launchers (beast, beauti, treeannotator,
                     logcombiner, applauncher, packagemanager,
                     loganalyser, densitree)
-  examples/         sample XML files + nexus/
-    spec/           beast3 spec XMLs
+  examples/         beast3 XML files + nexus/ + fasta/
   jre/              bundled Zulu JRE+FX 25 (target platform)
   lib/              boot-layer JARs (beast-pkgmgmt + deps, DensiTree.jar)
   lib/packages/     beast-base and beast-fx package ZIPs — seeded into
@@ -134,9 +133,9 @@ Or as a workflow step (requires `contents: write` permission):
    `release/Linux/linuxbin/` into `bin/` and made executable. Each script
    resolves `BUNDLE_HOME` symlink-safely, sets `JAVA_HOME=$BUNDLE_HOME/jre`,
    and invokes `jre/bin/java` with `--module-path lib/`.
-8. **Copy examples** — XML files and `nexus/` from
-   `beast-base/src/test/resources/beast.base/examples/`;
-   `spec/*.xml` files go into `examples/spec/`.
+8. **Copy examples** — beast3 XML files, `nexus/`, and `fasta/` from
+   `beast-base/src/test/resources/beast.base/examples/` into `examples/`.
+   `beast2vs1/` and `legacy/` subdirectories are excluded from the release.
 9. **Copy version.xml and docs** — `version.xml`, `README.txt`, `LICENSE.txt`.
 10. **Verify bundle** — checks required files, JAR count, beast-base/beast-fx
     absent from `lib/`, package ZIPs present in `lib/packages/`, bin/
diff --git a/release/Linux/assemble-bundle.sh b/release/Linux/assemble-bundle.sh
index 3c0e901e..15b7ac23 100755
--- a/release/Linux/assemble-bundle.sh
+++ b/release/Linux/assemble-bundle.sh
@@ -163,13 +163,13 @@ echo "==> Step 6: Extracting examples from $(basename "$BASE_PKG_ZIP")..."
 # Extract the full zip to a temp dir then copy examples/ — avoids unzip glob
 # portability issues where 'examples/*' may not match subdirs on some platforms.
 # Which subdirs are included/excluded is controlled by the include patterns in
-# beast-base/src/assembly/package.xml (e.g. spec/*.xml excludes spec/beast2vs1/).
+# beast-base/src/assembly/package.xml (beast2vs1/ and legacy/ are excluded).
 EXAMPLES_TMP=$(mktemp -d)
 unzip -o -q "$BASE_PKG_ZIP" -d "$EXAMPLES_TMP"
 cp -r "$EXAMPLES_TMP/examples/." "$BUNDLE/examples/"
 rm -rf "$EXAMPLES_TMP"
 EXAMPLE_COUNT=$(find "$BUNDLE/examples" -name "*.xml" | wc -l | tr -d ' ')
-echo "    Extracted ${EXAMPLE_COUNT} example XML files (incl. spec/)"
+echo "    Extracted ${EXAMPLE_COUNT} example XML files"
 
 # ── Step 7: Copy version.xml and docs ────────────────────────────────────────
 echo ""
@@ -190,7 +190,7 @@ _fail() { echo "  [FAIL] $*"; FAIL=$((FAIL + 1)); }
 
 for f in bin/beast bin/beauti bin/treeannotator bin/logcombiner \
           bin/applauncher bin/packagemanager bin/loganalyser \
-          jre/bin/java lib version.xml examples/spec; do
+          jre/bin/java lib version.xml examples; do
     [ -e "$BUNDLE/$f" ] && _ok "$f present" || _fail "$f MISSING"
 done
 
@@ -233,10 +233,10 @@ _FX_SO=$(find "$BUNDLE/jre/lib" -name "libjavafx*.so" 2>/dev/null | head -1)
 find "$BUNDLE/jre/lib" -name "libjavafx*.dylib" 2>/dev/null | grep -q . \
     && _fail "JavaFX .dylib files found in jre/lib/ — wrong platform bundled"
 
-SPEC_COUNT=$(find "$BUNDLE/examples/spec" -name "*.xml" 2>/dev/null | wc -l | tr -d ' ')
+SPEC_COUNT=$(find "$BUNDLE/examples" -maxdepth 1 -name "*.xml" 2>/dev/null | wc -l | tr -d ' ')
 [ "$SPEC_COUNT" -gt 0 ] \
-    && _ok "examples/spec/ has ${SPEC_COUNT} XML files" \
-    || _fail "examples/spec/ is empty — no XML files copied"
+    && _ok "examples/ has ${SPEC_COUNT} beast3 XML files" \
+    || _fail "examples/ is empty — no XML files copied"
 
 if [ "$FAIL" -gt 0 ]; then
     echo "==> FAILED: ${FAIL} check(s) failed, ${PASS} passed — aborting."
diff --git a/release/Mac/README.md b/release/Mac/README.md
index 8ca8e830..1915757c 100644
--- a/release/Mac/README.md
+++ b/release/Mac/README.md
@@ -68,7 +68,7 @@ release/Mac/
 │   │   ├── AppLauncher.app   ← shell-script wrapper
 │   │   ├── DensiTree.app     ← standalone JAR wrapper (if present)
 │   │   ├── bin/              ← command-line launcher scripts
-│   │   ├── examples/         ← sample XML files + nexus/ + spec/
+│   │   ├── examples/         ← beast3 XML files + nexus/ + fasta/
 │   │   ├── README.txt
 │   │   └── LICENSE.txt
 │   ├── .background/          ← install.png for DMG Finder window
@@ -197,8 +197,8 @@ Non-bundle content is added **after** signing, so it cannot affect any bundle
 seal (it lives alongside `.app` bundles, not inside them):
 
 - `bin/` — copied from `release/Mac/macbin`, made executable.
-- `examples/` — top-level XML files, `nexus/` and `spec/` subdirectories from
-  `beast-base/src/test/resources/beast.base/examples`.
+- `examples/` — beast3 XML files, `nexus/`, and `fasta/` from
+  `beast-base/src/test/resources/beast.base/examples`. `beast2vs1/` and `legacy/` are excluded.
 - `README.txt` and `LICENSE.txt` from `release/common/`.
 
 **DMG creation (two-phase):**
diff --git a/release/Mac/build-sign-dmg.sh b/release/Mac/build-sign-dmg.sh
index 812c886e..b71340e4 100755
--- a/release/Mac/build-sign-dmg.sh
+++ b/release/Mac/build-sign-dmg.sh
@@ -17,7 +17,7 @@
 # version.xml must NOT be copied to Contents/ root — Apple's codesign resource
 # rules reject plain files directly in Contents/.
 #
-# Also includes bin/ (command-line launchers) and examples/ (sample XML files, incl. spec/).
+# Also includes bin/ (command-line launchers) and examples/ (sample beast3 XML files).
 #
 # Usage:
 #   cd release/Mac && ./build-sign-dmg.sh
diff --git a/release/Windows/assemble-bundle.sh b/release/Windows/assemble-bundle.sh
index 8d37cee4..e8f0f6d9 100644
--- a/release/Windows/assemble-bundle.sh
+++ b/release/Windows/assemble-bundle.sh
@@ -255,13 +255,13 @@ echo "==> Step 7: Extracting examples from $(basename "$BASE_PKG_ZIP")..."
 # Extract the full zip to a temp dir then copy examples/ — avoids unzip glob
 # portability issues where 'examples/*' may not match subdirs on some platforms.
 # Which subdirs are included/excluded is controlled by the include patterns in
-# beast-base/src/assembly/package.xml (e.g. spec/*.xml excludes spec/beast2vs1/).
+# beast-base/src/assembly/package.xml (beast2vs1/ and legacy/ are excluded).
 EXAMPLES_TMP=$(mktemp -d)
 unzip -o -q "$BASE_PKG_ZIP" -d "$EXAMPLES_TMP"
 cp -r "$EXAMPLES_TMP/examples/." "$BUNDLE/examples/"
 rm -rf "$EXAMPLES_TMP"
 EXAMPLE_COUNT=$(find "$BUNDLE/examples" -name "*.xml" | wc -l | tr -d ' ')
-echo "    Extracted ${EXAMPLE_COUNT} example XML files (incl. spec/)"
+echo "    Extracted ${EXAMPLE_COUNT} example XML files"
 
 # ── Step 8: Copy version.xml and docs ────────────────────────────────────────
 echo ""
@@ -282,7 +282,7 @@ _fail() { echo "  [FAIL] $*"; FAIL=$((FAIL + 1)); }
 
 for f in beast.exe beauti.exe treeannotator.exe logcombiner.exe \
           loganalyser.exe applauncher.exe packagemanager.exe \
-          runtime/bin/java.exe app version.xml examples/spec; do
+          runtime/bin/java.exe app version.xml examples; do
     [ -e "$BUNDLE/$f" ] && _ok "$f present" || _fail "$f MISSING"
 done
 
@@ -309,10 +309,10 @@ PKG_COUNT=$(find "$BUNDLE/app/packages" -name "*.zip" 2>/dev/null | wc -l | tr -
     && _ok "app/packages/ has ${PKG_COUNT} core package zip(s)" \
     || _fail "app/packages/ has too few package zips: ${PKG_COUNT} (expected ≥2)"
 
-SPEC_COUNT=$(find "$BUNDLE/examples/spec" -name "*.xml" 2>/dev/null | wc -l | tr -d ' ')
+SPEC_COUNT=$(find "$BUNDLE/examples" -maxdepth 1 -name "*.xml" 2>/dev/null | wc -l | tr -d ' ')
 [ "$SPEC_COUNT" -gt 0 ] \
-    && _ok "examples/spec/ has ${SPEC_COUNT} XML files" \
-    || _fail "examples/spec/ is empty — no XML files copied"
+    && _ok "examples/ has ${SPEC_COUNT} beast3 XML files" \
+    || _fail "examples/ is empty — no XML files copied"
 
 if $DENSITREE_FOUND; then
     [ -f "$BUNDLE/app/DensiTree.jar" ] \
diff --git a/scripts/spec-namespace-test-resources.md b/scripts/spec-namespace-test-resources.md
index 4eaf3b53..6cbbaa6c 100644
--- a/scripts/spec-namespace-test-resources.md
+++ b/scripts/spec-namespace-test-resources.md
@@ -41,7 +41,7 @@ module exclusively owns its JPMS module name, no two modules can collide.
 src/test/resources/examples/   →   src/test/resources/beast.base/examples/
 ```
 
-All contents (XMLs, subdirectories `nexus/`, `beast2vs1/`, `spec/`, `fasta/`,
+All contents (XMLs, subdirectories `nexus/`, `beast2vs1/`, `fasta/`,
 `benchmark/`, `parameterised/`, `starbeastinit/`, `testDirichlet/`) move
 unchanged.
 
@@ -53,7 +53,7 @@ unchanged.
 | `test/beast/util/NexusParserTest.java:160` | `"/examples/nexus/Primates.nex"` | `"/beast.base/examples/nexus/Primates.nex"` |
 | `test/beast/integration/XMLProducerTest.java:37` | `"/examples/nexus"` | `"/beast.base/examples/nexus"` |
 | `test/beast/beast2vs1/TestFramework.java:28` | `"/examples/beast2vs1/"` | `"/beast.base/examples/beast2vs1/"` |
-| `beast/base/spec/beast2vs1/TestFramework.java:35` | `"/examples/spec/beast2vs1/"` | `"/beast.base/examples/spec/beast2vs1/"` |
+| `beast/base/spec/beast2vs1/TestFramework.java:35` | `"/examples/spec/beast2vs1/"` | `"/beast.base/examples/beast2vs1/"` |
 
 ### beast-fx