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
new file mode 100644
index 0000000..383b77f
--- /dev/null
+++ b/beast-base/src/test/resources/beast.base/examples/spec/bitflip.xml
@@ -0,0 +1,23 @@
+<?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
index ddfb352..50899ee 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/testGTR.xml
+++ b/beast-base/src/test/resources/beast.base/examples/spec/testGTR.xml
@@ -19,7 +19,7 @@
         <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4" value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
     </data>
 
-    <run chainLength="$(chainLength=5000000)" id="mcmc" spec="MCMC">
+    <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">
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/testHKY.xml b/beast-base/src/test/resources/beast.base/examples/spec/testHKY.xml
index 213b607..a6a83b2 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/testHKY.xml
+++ b/beast-base/src/test/resources/beast.base/examples/spec/testHKY.xml
@@ -62,7 +62,7 @@
         </populationModel>
     </tree>
 
-    <run spec="MCMC" id="mcmc" chainLength="$(chainLength=5000000)" preBurnin="50000">
+    <run spec="MCMC" id="mcmc" chainLength="5000000" preBurnin="50000">
 
         <init idref="coalescentSimulator"/>
         <distribution spec="CompoundDistribution" id="posterior">
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantor.xml b/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantor.xml
index bdcb8ae..559ba59 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantor.xml
+++ b/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantor.xml
@@ -51,7 +51,7 @@
         </populationModel>
     </tree>
 
-    <run spec="MCMC" id="mcmc" chainLength="$(chainLength=5000000)" preBurnin="50000">
+    <run spec="MCMC" id="mcmc" chainLength="5000000" preBurnin="50000">
 
         <init idref="coalescentSimulator"/>
         <distribution spec="CompoundDistribution" id="posterior">
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShort.xml b/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShort.xml
index bbd2d24..ca09b44 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShort.xml
+++ b/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShort.xml
@@ -50,7 +50,7 @@
         </populationModel>
     </tree>
 
-    <run spec="MCMC" id="mcmc" chainLength="$(chainLength=5000000)" preBurnin="50000">
+    <run spec="MCMC" id="mcmc" chainLength="5000000" preBurnin="50000">
 
         <init idref="coalescentSimulator"/>
         <distribution spec="CompoundDistribution" id="posterior">
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShortUncertain.xml b/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShortUncertain.xml
index 38b7e34..ed12c1b 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShortUncertain.xml
+++ b/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShortUncertain.xml
@@ -61,7 +61,7 @@
         </populationModel>
     </tree>
 
-    <run spec="MCMC" id="mcmc" chainLength="$(chainLength=5000000)" preBurnin="50000">
+    <run spec="MCMC" id="mcmc" chainLength="5000000" preBurnin="50000">
 
         <init idref="coalescentSimulator"/>
         <distribution spec="CompoundDistribution" id="posterior">
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShortUncertain2.xml b/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShortUncertain2.xml
index 9b86ef9..3f45e0d 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShortUncertain2.xml
+++ b/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShortUncertain2.xml
@@ -62,7 +62,7 @@
         </populationModel>
     </tree>
 
-    <run spec="MCMC" id="mcmc" chainLength="$(chainLength=5000000)" preBurnin="50000">
+    <run spec="MCMC" id="mcmc" chainLength="5000000" preBurnin="50000">
 
         <init idref="coalescentSimulator"/>
         <distribution spec="CompoundDistribution" id="posterior">
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShortUncertain2MLE.xml b/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShortUncertain2MLE.xml
index 1e7d936..5384997 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShortUncertain2MLE.xml
+++ b/beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShortUncertain2MLE.xml
@@ -53,7 +53,7 @@
         </populationModel>
     </tree>
 
-    <run spec="MCMC" id="mcmc" chainLength="$(chainLength=5000000)" preBurnin="50000">
+    <run spec="MCMC" id="mcmc" chainLength="5000000" preBurnin="50000">
 
         <init idref="coalescentSimulator"/>
         <distribution spec="CompoundDistribution" id="posterior">
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/testOpSubSchedule.xml b/beast-base/src/test/resources/beast.base/examples/spec/testOpSubSchedule.xml
index bbca0c4..f828101 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/testOpSubSchedule.xml
+++ b/beast-base/src/test/resources/beast.base/examples/spec/testOpSubSchedule.xml
@@ -62,7 +62,7 @@
         </populationModel>
     </tree>
 
-    <run spec="MCMC" id="mcmc" chainLength="$(chainLength=1000000)" preBurnin="50000">
+    <run spec="MCMC" id="mcmc" chainLength="1000000" preBurnin="50000">
 
         <init idref="coalescentSimulator"/>
         <distribution spec="CompoundDistribution" id="posterior">
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/testPlates.xml b/beast-base/src/test/resources/beast.base/examples/spec/testPlates.xml
index b5332a0..b5a0da1 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/testPlates.xml
+++ b/beast-base/src/test/resources/beast.base/examples/spec/testPlates.xml
@@ -73,7 +73,7 @@
 
     <tree spec="beast.base.spec.evolution.tree.ClusterTree" id="tree" clusterType="upgma" taxa="@alignment.p1"/>
 
-    <run spec="MCMC" id="mcmc" chainLength="$(chainLength=10000000)">
+    <run spec="MCMC" id="mcmc" chainLength="10000000">
         <state storeEvery="100000">
             <stateNode idref="hky.kappa.p1"/>
             <stateNode idref="hky.kappa.p2"/>
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
index ede943b..9d7f701 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/testRNA.xml
+++ b/beast-base/src/test/resources/beast.base/examples/spec/testRNA.xml
@@ -21,7 +21,7 @@
         <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4" value="AAGUUUCAUUGGAGCCACCACUCUUAUAAUUGCCCAUGGCCUCACCUCCUCCCUAUUAUUUUGCCUAGCAAAUACAAACUACGAACGAGUCCACAGUCGAACAAUAGCACUAGCCCGUGGCCUUCAAACCCUAUUACCUCUUGCAGCAACAUGAUGACUCCUCGCCAGCUUAACCAACCUGGCCCUUCCCCCAACAAUUAAUUUAAUCGGUGAACUGUCCGUAAUAAUAGCAGCAUUUUCAUGGUCACACCUAACUAUUAUCUUAGUAGGCCUUAACACCCUUAUCACCGCCCUAUAUUCCCUAUAUAUACUAAUCAUAACUCAACGAGGAAAAUACACAUAUCAUAUCAACAAUAUCAUGCCCCCUUUCACCCGAGAAAAUACAUUAAUAAUCAUACACCUAUUUCCCUUAAUCCUACUAUCUACCAACCCCAAAGUAAUUAUAGGAACCAUGUACUGUAAAUAUAGUUUAAACAAAACAUUAGAUUGUGAGUCUAAUAAUAGAAGCCCAAAGAUUUCUUAUUUACCAAGAAAGUA-UGCAAGAACUGCUAACUCAUGCCUCCAUAUAUAACAAUGUGGCUUUCUU-ACUUUUAAAGGAUAGAAGUAAUCCAUCGGUCUUAGGAACCGAAAA-AUUGGUGCAACUCCAAAUAAAAGUAAUAAAUUUAUUUUCAUCCUCCAUUUUACUAUCACUUACACUCUUAAUUACCCCAUUUAUUAUUACAACAACUAAAAAAUAUGAAACACAUGCAUACCCUUACUACGUAAAAAACUCUAUCGCCUGCGCAUUUAUAACAAGCCUAGUCCCAAUGCUCAUAUUUCUAUACACAAAUCAAGAAAUAAUCAUUUCCAACUGACAUUGAAUAACGAUUCAUACUAUCAAAUUAUGCCUAAGCUU"/>
     </data>
 
-    <run chainLength="$(chainLength=5000000)" id="mcmc" spec="MCMC">
+    <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">
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
index 1d9bc1a..f14f49d 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/testRestrictedGTR.xml
+++ b/beast-base/src/test/resources/beast.base/examples/spec/testRestrictedGTR.xml
@@ -19,7 +19,7 @@
         <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4" value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
     </data>
 
-    <run chainLength="$(chainLength=5000000)" id="mcmc" spec="MCMC">
+    <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">
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
index db79bde..3198b41 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/testSYM.xml
+++ b/beast-base/src/test/resources/beast.base/examples/spec/testSYM.xml
@@ -19,7 +19,7 @@
         <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4" value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
     </data>
 
-    <run chainLength="$(chainLength=5000000)" id="mcmc" spec="MCMC">
+    <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">
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
index b6902e8..e9882e7 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/testTIM.xml
+++ b/beast-base/src/test/resources/beast.base/examples/spec/testTIM.xml
@@ -19,7 +19,7 @@
         <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4" value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
     </data>
 
-    <run chainLength="$(chainLength=5000000)" id="mcmc" spec="MCMC">
+    <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">
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
index 248e70e..732ccf0 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/testTN93.xml
+++ b/beast-base/src/test/resources/beast.base/examples/spec/testTN93.xml
@@ -19,7 +19,7 @@
         <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4" value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
     </data>
 
-    <run chainLength="$(chainLength=5000000)" id="mcmc" spec="MCMC">
+    <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">
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
index aed7633..07030e1 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/testTVM.xml
+++ b/beast-base/src/test/resources/beast.base/examples/spec/testTVM.xml
@@ -19,7 +19,7 @@
         <sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4" value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
     </data>
 
-    <run chainLength="$(chainLength=5000000)" id="mcmc" spec="MCMC">
+    <run chainLength="5000000" id="mcmc" spec="MCMC">
         <state id="state" storeEvery="5000">
             <tree id="Tree.t:primate" name="stateNode">
                 <taxonset id="TaxonSet.coding" spec="TaxonSet">
diff --git a/beast-base/src/test/resources/beast.base/examples/spec/testYuleOneSite.xml b/beast-base/src/test/resources/beast.base/examples/spec/testYuleOneSite.xml
index 839d8cf..92e4b88 100644
--- a/beast-base/src/test/resources/beast.base/examples/spec/testYuleOneSite.xml
+++ b/beast-base/src/test/resources/beast.base/examples/spec/testYuleOneSite.xml
@@ -39,7 +39,7 @@
     <!-- expected yule prior = 1/(n.lambda)\sum_{k=1}^{n-1}k/(n-k) where lambda = birth rate, n = number of taxa
 	with lambda=1, n=-4 we expect 1/4(1/3+2/2+3/1)=1.155555555
  -->
-    <run spec="MCMC" chainLength="$(chainLength=10)">
+    <run spec="MCMC" chainLength="10">
 	<state>
 	    <stateNode idref="tree"/>
 	    <stateNode idref="birthRate"/>