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testCalibration.xml
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<beast version='2.0'
namespace='beast.evolution: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 -->
<!-- npatterns=69 -->
<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>
<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'/>
<constraint idref='mrcaPrior2'/>
<constraint idref='mrcaPrior1'/>
</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 spec='beast.base.evolution.tree.Tree' id='tree'>
<taxonset spec='TaxonSet' alignment='@alignment'/>
</stateNode>
</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>
<distribution id='mrcaPrior1' spec='beast.base.evolution.tree.MRCAPrior' tree='@tree' monophyletic='true'>
<taxonset spec='TaxonSet' id='allButSiamang'>
<!--
-->
<taxon spec='Taxon' idref='human'/>
<taxon spec='Taxon' id='bonobo'/>
<taxon spec='Taxon' idref='chimp'/>
<taxon spec='Taxon' id='gorilla'/>
<taxon spec='Taxon' id='orangutan'/>
</taxonset>
<distr idref='normalDistr'/>
</distribution>
<distribution id='mrcaPrior2' spec='beast.base.evolution.tree.MRCAPrior' tree='@tree' monophyletic='true'>
<taxonset spec='TaxonSet' id='human,chimp'>
<taxon spec='Taxon' id='human'/>
<taxon spec='Taxon' id='chimp'/>
</taxonset>
<distr id='normalDistr' spec='beast.base.inference.distribution.Normal'>
<parameter name='mean' value='6.0'/>
<parameter name='sigma' 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'>
<parameter name="popSize" idref="popSize"/>
</populationModel>
</distribution>
</distribution>
<distribution spec='TreeLikelihood' id="likelihood" data='@alignment' tree='@tree'>
<siteModel id="siteModel" spec='SiteModel'>
<substModel spec='HKY' id="hky">
<parameter name='kappa' idref='hky.kappa'/>
<frequencies id='freqs' spec='Frequencies' frequencies='@hky.frequencies'/>
</substModel>
</siteModel>
</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 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"/>
<logger logEvery="1000" fileName="test.$(seed).log">
<model idref='posterior'/>
<log idref="posterior"/>
<log idref="prior"/>
<log spec='beast.base.evolution.tree.TreeHeightLogger' tree='@tree'/>
<log spec='beast.base.evolution.tree.MRCAPrior' tree='@tree' id='HumanChimpMRCA' taxonset='@human,chimp' />
<log idref="popSize"/>
<log idref="hky.kappa"/>
<log idref="hky.frequencies"/>
<log idref="likelihood"/>
<log idref="coalescent"/>
</logger>
<logger logEvery="1000" fileName="test.$(seed).trees">
<log idref="tree"/>
</logger>
<logger logEvery="100000">
<model idref='posterior'/>
<log idref="posterior"/>
<log idref="prior"/>
<log spec='beast.base.evolution.tree.TreeHeightLogger' tree='@tree'/>
<log idref='HumanChimpMRCA'/>
<log idref="popSize"/>
<log idref="hky.kappa"/>
<log idref="hky.frequencies"/>
<log idref="likelihood"/>
<log idref="coalescent"/>
</logger>
</run>
</beast>