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Merged
walterxie merged 1 commit into from
Jun 18, 2026
Merged

add bitflip.xml for beast3 #90 #101

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23 changes: 23 additions & 0 deletions beast-base/src/test/resources/beast.base/examples/spec/bitflip.xml
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<?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>
2 changes: 1 addition & 1 deletion beast-base/src/test/resources/beast.base/examples/spec/testGTR.xml
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<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">
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2 changes: 1 addition & 1 deletion beast-base/src/test/resources/beast.base/examples/spec/testHKY.xml
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</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">
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2 changes: 1 addition & 1 deletion beast-base/src/test/resources/beast.base/examples/spec/testJukesCantor.xml
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</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">
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2 changes: 1 addition & 1 deletion beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShort.xml
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</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">
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2 changes: 1 addition & 1 deletion beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShortUncertain.xml
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</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">
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2 changes: 1 addition & 1 deletion beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShortUncertain2.xml
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</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">
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2 changes: 1 addition & 1 deletion beast-base/src/test/resources/beast.base/examples/spec/testJukesCantorShortUncertain2MLE.xml
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</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">
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2 changes: 1 addition & 1 deletion beast-base/src/test/resources/beast.base/examples/spec/testOpSubSchedule.xml
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</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">
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2 changes: 1 addition & 1 deletion beast-base/src/test/resources/beast.base/examples/spec/testPlates.xml
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Expand Up @@ -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"/>
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2 changes: 1 addition & 1 deletion beast-base/src/test/resources/beast.base/examples/spec/testRNA.xml
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<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">
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2 changes: 1 addition & 1 deletion beast-base/src/test/resources/beast.base/examples/spec/testRestrictedGTR.xml
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<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">
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2 changes: 1 addition & 1 deletion beast-base/src/test/resources/beast.base/examples/spec/testSYM.xml
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<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">
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2 changes: 1 addition & 1 deletion beast-base/src/test/resources/beast.base/examples/spec/testTIM.xml
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<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">
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2 changes: 1 addition & 1 deletion beast-base/src/test/resources/beast.base/examples/spec/testTN93.xml
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<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">
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2 changes: 1 addition & 1 deletion beast-base/src/test/resources/beast.base/examples/spec/testTVM.xml
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<sequence id="seq_Tarsius_syrichta" taxon="Tarsius_syrichta" totalcount="4" value="AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"/>
</data>

<run chainLength="$(chainLength=5000000)" id="mcmc" spec="MCMC">
<run chainLength="5000000" id="mcmc" spec="MCMC">
<state id="state" storeEvery="5000">
<tree id="Tree.t:primate" name="stateNode">
<taxonset id="TaxonSet.coding" spec="TaxonSet">
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2 changes: 1 addition & 1 deletion beast-base/src/test/resources/beast.base/examples/spec/testYuleOneSite.xml
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<!-- expected yule prior = 1/(n.lambda)\sum_{k=1}^{n-1}k/(n-k) where lambda = birth rate, n = number of taxa
with lambda=1, n=-4 we expect 1/4(1/3+2/2+3/1)=1.155555555
-->
<run spec="MCMC" chainLength="$(chainLength=10)">
<run spec="MCMC" chainLength="10">
<state>
<stateNode idref="tree"/>
<stateNode idref="birthRate"/>
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