/
testSRD06.xml
127 lines (106 loc) · 19.5 KB
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testSRD06.xml
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<?xml version="1.0" encoding="UTF-8" standalone="no"?><beast namespace="beast.core:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood" version="2.0">
<!-- SRD06 model: split sequences in first together with seconds and thirds of all sites -->
<data dataType="nucleotide" id="Primates">
<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"/>
</data>
<data data="@Primates" dataType="nucleotide" filter="1::3,2::3" id="firstAndSecondSites" name="taxa" spec="beast.evolution.alignment.FilteredAlignment"/>
<data data="@Primates" dataType="nucleotide" filter="3::3" id="thirdSites" name="taxa" spec="beast.evolution.alignment.FilteredAlignment"/>
<distribution id="posterior" spec="util.CompoundDistribution">
<distribution id="prior" spec="util.CompoundDistribution">
<distribution id="firstAndSecondSites.coalescent" populationModel="@firstAndSecondSites.ConstantPopulation" spec="Coalescent">
<treeIntervals id="treeIntervals" spec="TreeIntervals" tree="@tree"/>
</distribution>
<distribution id="firstAndSecondSites.kappa.prior" spec="beast.math.distributions.Prior" x="@firstAndSecondSites.hky.kappa">
<distr id="OneOnX0" offset="0.0" spec="beast.math.distributions.OneOnX"/>
</distribution>
<distribution id="thirdSites.kappa.prior" spec="beast.math.distributions.Prior" x="@thirdSites.hky.kappa">
<distr id="OneOnX1" offset="0.0" spec="beast.math.distributions.OneOnX"/>
</distribution>
</distribution>
<distribution id="likelihood" spec="util.CompoundDistribution">
<distribution data="@firstAndSecondSites" id="treeLikelihood" spec="TreeLikelihood" tree="@tree" useAmbiguities="false">
<siteModel gammaCategoryCount="0" id="firstAndSecondSites.siteModel" spec="SiteModel">
<parameter dimension="1" estimate="false" id="firstAndSecondSites.mutationRate" name="mutationRate" value="1.0"/>
<parameter dimension="1" estimate="false" id="firstAndSecondSites.gammaShape" name="shape" value="1.0"/>
<parameter dimension="1" estimate="false" id="firstAndSecondSites.proportionInvariant" lower="0.0" name="proportionInvariant" upper="1.0" value="0.0"/>
<substModel id="firstAndSecondSites.hky" kappa="@firstAndSecondSites.hky.kappa" spec="HKY">
<frequencies estimate="true" frequencies="@firstAndSecondSites.freqParameter" id="firstAndSecondSites.freqs" spec="Frequencies"/>
</substModel>
</siteModel>
<branchRateModel id="firstAndSecondSites.StrictClockModel" spec="beast.evolution.branchratemodel.StrictClockModel">
<parameter dimension="1" estimate="false" id="firstAndSecondSites.clockRate" name="clock.rate" value="1.0"/>
</branchRateModel>
</distribution>
<distribution branchRateModel="@firstAndSecondSites.StrictClockModel" data="@thirdSites" id="thirdSites.treeLikelihood" spec="TreeLikelihood" tree="@tree" useAmbiguities="false">
<siteModel gammaCategoryCount="0" id="thirdSites.siteModel" spec="SiteModel">
<parameter dimension="1" estimate="false" id="thirdSites.mutationRate" name="mutationRate" value="1.0"/>
<parameter dimension="1" estimate="false" id="thirdSites.gammaShape" name="shape" value="1.0"/>
<parameter dimension="1" estimate="false" id="thirdSites.proportionInvariant" lower="0.0" name="proportionInvariant" upper="1.0" value="0.0"/>
<substModel id="thirdSites.hky" kappa="@thirdSites.hky.kappa" spec="HKY">
<frequencies estimate="true" frequencies="@thirdSites.freqParameter" id="thirdSites.freqs" spec="Frequencies"/>
</substModel>
</siteModel>
</distribution>
</distribution>
</distribution>
<run chainLength="10000000" id="mcmc" preBurnin="0" spec="MCMC" storeEvery="-1">
<init estimate="false" id="firstAndSecondSites.RandomTree" initial="@tree" spec="beast.evolution.tree.RandomTree">
<data idref="firstAndSecondSites" name="taxa"/>
<populationModel id="firstAndSecondSites.ConstantPopulation" spec="ConstantPopulation">
<parameter dimension="1" estimate="false" id="firstAndSecondSites.popSize" name="popSize" value="1.0"/>
</populationModel>
</init>
<state id="State0" storeEvery="100000">
<tree estimate="true" id="tree" name="stateNode"/>
<parameter dimension="4" estimate="true" id="thirdSites.freqParameter" name="stateNode" value="0.25"/>
<parameter dimension="1" estimate="true" id="thirdSites.hky.kappa" lower="0.0" name="stateNode" value="1.0"/>
<parameter dimension="1" estimate="true" id="firstAndSecondSites.hky.kappa" lower="0.0" name="stateNode" value="1.0"/>
<parameter dimension="1" estimate="true" id="RealParameter7" name="stateNode" value="0.333"/>
<parameter dimension="1" estimate="true" id="RealParameter6" name="stateNode" value="0.333"/>
<parameter dimension="4" estimate="true" id="firstAndSecondSites.freqParameter" name="stateNode" value="0.25"/>
</state>
<distribution idref="posterior"/>
<operator autoOptimize="true" delta="0.01" id="firstAndSecondSites.FrequenciesExchanger" integer="false" parameter="@firstAndSecondSites.freqParameter" spec="DeltaExchangeOperator" weight="0.1"/>
<operator autoOptimize="true" delta="0.01" id="thirdSites.FrequenciesExchanger" integer="false" parameter="@thirdSites.freqParameter" spec="DeltaExchangeOperator" weight="0.1"/>
<operator id="WilsonBalding0" spec="WilsonBalding" tree="@tree" weight="1.0"/>
<operator degreesOfFreedom="1" id="thirdSites.kappaScaler" parameter="@thirdSites.hky.kappa" scaleAll="false" scaleAllIndependently="false" scaleFactor="0.5" spec="ScaleOperator" weight="1.0"/>
<operator degreesOfFreedom="1" id="treeScaler" scaleAll="false" scaleAllIndependently="false" scaleFactor="0.5" spec="ScaleOperator" tree="@tree" weight="1.0"/>
<operator id="firstAndSecondSites.wide" isNarrow="false" spec="Exchange" tree="@tree" weight="1.0"/>
<operator id="Uniform0" spec="Uniform" tree="@tree" weight="10.0"/>
<operator id="firstAndSecondSites.narrow" isNarrow="true" spec="Exchange" tree="@tree" weight="1.0"/>
<operator degreesOfFreedom="1" id="firstAndSecondSites.kappaScaler" parameter="@firstAndSecondSites.hky.kappa" scaleAll="false" scaleAllIndependently="false" scaleFactor="0.5" spec="ScaleOperator" weight="1.0"/>
<operator gaussian="true" id="SubtreeSlide0" size="1.0" spec="SubtreeSlide" tree="@tree" weight="5.0"/>
<logger fileName="beast_$(seed).log" id="tracelog" logEvery="10000" mode="autodetect" model="@posterior">
<distribution idref="likelihood" name="log"/>
<parameter idref="firstAndSecondSites.hky.kappa" name="log"/>
<log id="TreeHeightLogger0" spec="beast.evolution.tree.TreeHeightLogger" tree="@tree"/>
<parameter idref="firstAndSecondSites.freqParameter" name="log"/>
<parameter idref="thirdSites.hky.kappa" name="log"/>
<parameter idref="thirdSites.freqParameter" name="log"/>
</logger>
<logger fileName="beast_.$(seed).trees" id=".treelog" logEvery="10000" mode="autodetect">
<tree idref="tree" name="log"/>
</logger>
<logger id="screenlog" logEvery="10000" mode="autodetect" model="@posterior">
<log idref="posterior"/>
<distribution idref="treeLikelihood" name="log"/>
<distribution idref="thirdSites.treeLikelihood" name="log"/>
<log arg="@likelihood" id="ESS0" spec="util.ESS"/>
<parameter idref="firstAndSecondSites.hky.kappa" name="log"/>
<log arg="@firstAndSecondSites.hky.kappa" id="ESS1" spec="util.ESS"/>
<parameter idref="thirdSites.hky.kappa" name="log"/>
<log arg="@thirdSites.hky.kappa" id="ESS2" spec="util.ESS"/>
</logger>
</run>
</beast>