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| <?xml version="1.0" encoding="UTF-8" standalone="no"?><beast beautitemplate='Standard' beautistatus='' namespace="beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood" required="" version="2.6"> | ||
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| <data | ||
| id="test_output_0" | ||
| spec="Alignment" | ||
| name="alignment"> | ||
| <sequence id="seq_t1" spec="Sequence" taxon="t1" totalcount="4" value="acttgttgcgactgcgcctg"/> | ||
| <sequence id="seq_t2" spec="Sequence" taxon="t2" totalcount="4" value="acttattgcgactgaggccg"/> | ||
| <sequence id="seq_t3" spec="Sequence" taxon="t3" totalcount="4" value="acttaatgcgaatgagcccg"/> | ||
| <sequence id="seq_t4" spec="Sequence" taxon="t4" totalcount="4" value="aacgacccgcgatcggggat"/> | ||
| <sequence id="seq_t5" spec="Sequence" taxon="t5" totalcount="4" value="acttgttgcgactgagcctg"/> | ||
| </data> | ||
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| <map name="Uniform" >beast.math.distributions.Uniform</map> | ||
| <map name="Exponential" >beast.math.distributions.Exponential</map> | ||
| <map name="LogNormal" >beast.math.distributions.LogNormalDistributionModel</map> | ||
| <map name="Normal" >beast.math.distributions.Normal</map> | ||
| <map name="Beta" >beast.math.distributions.Beta</map> | ||
| <map name="Gamma" >beast.math.distributions.Gamma</map> | ||
| <map name="LaplaceDistribution" >beast.math.distributions.LaplaceDistribution</map> | ||
| <map name="prior" >beast.math.distributions.Prior</map> | ||
| <map name="InverseGamma" >beast.math.distributions.InverseGamma</map> | ||
| <map name="OneOnX" >beast.math.distributions.OneOnX</map> | ||
|
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| <run id="mcmc" spec="MCMC" chainLength="10000000"> | ||
| <state id="state" spec="State" storeEvery="5000"> | ||
| <tree id="Tree.t:test_output_0" spec="beast.evolution.tree.Tree" name="stateNode"> | ||
| <taxonset id="TaxonSet.test_output_0" spec="TaxonSet"> | ||
| <alignment idref="test_output_0"/> | ||
| </taxonset> | ||
| </tree> | ||
| <parameter id="birthRate.t:test_output_0" spec="parameter.RealParameter" name="stateNode">1.0</parameter> | ||
| <parameter id="ucldStdev.c:test_output_0" spec="parameter.RealParameter" lower="0.0" name="stateNode">0.1</parameter> | ||
| <stateNode id="rateCategories.c:test_output_0" spec="parameter.IntegerParameter" dimension="8">1</stateNode> | ||
| <parameter id="ucldMean.c:test_output_0" spec="parameter.RealParameter" name="stateNode">1.0</parameter> | ||
| </state> | ||
| <init id="RandomTree.t:test_output_0" spec="beast.evolution.tree.RandomTree" estimate="false" initial="@Tree.t:test_output_0" taxa="@test_output_0"> | ||
| <populationModel id="ConstantPopulation0.t:test_output_0" spec="ConstantPopulation"> | ||
| <parameter id="randomPopSize.t:test_output_0" spec="parameter.RealParameter" name="popSize">1.0</parameter> | ||
| </populationModel> | ||
| </init> | ||
| <distribution id="posterior" spec="util.CompoundDistribution"> | ||
| <distribution id="prior" spec="util.CompoundDistribution"> | ||
| <distribution id="YuleModel.t:test_output_0" spec="beast.evolution.speciation.YuleModel" birthDiffRate="@birthRate.t:test_output_0" tree="@Tree.t:test_output_0"/> | ||
| <prior id="YuleBirthRatePrior.t:test_output_0" name="distribution" x="@birthRate.t:test_output_0"> | ||
| <Uniform id="Uniform.1" name="distr" upper="Infinity"/> | ||
| </prior> | ||
| <prior id="MeanRatePrior.c:test_output_0" name="distribution" x="@ucldMean.c:test_output_0"> | ||
| <Uniform id="Uniform.3" name="distr" upper="Infinity"/> | ||
| </prior> | ||
| <prior id="ucldStdevPrior.c:test_output_0" name="distribution" x="@ucldStdev.c:test_output_0"> | ||
| <Gamma id="Gamma.0" name="distr"> | ||
| <parameter id="RealParameter.2" spec="parameter.RealParameter" estimate="false" name="alpha">0.5396</parameter> | ||
| <parameter id="RealParameter.3" spec="parameter.RealParameter" estimate="false" name="beta">0.3819</parameter> | ||
| </Gamma> | ||
| </prior> | ||
| <distribution id="all.prior" spec="beast.math.distributions.MRCAPrior" tree="@Tree.t:test_output_0"> | ||
| <taxonset id="all" spec="TaxonSet"> | ||
| <taxon id="t1" spec="Taxon"/> | ||
| <taxon id="t2" spec="Taxon"/> | ||
| <taxon id="t3" spec="Taxon"/> | ||
| <taxon id="t4" spec="Taxon"/> | ||
| <taxon id="t5" spec="Taxon"/> | ||
| </taxonset> | ||
| <OneOnX id="OneOnX.1" name="distr"/> | ||
| </distribution> | ||
| </distribution> | ||
| <distribution id="likelihood" spec="util.CompoundDistribution" useThreads="true"> | ||
| <distribution id="treeLikelihood.test_output_0" spec="ThreadedTreeLikelihood" data="@test_output_0" tree="@Tree.t:test_output_0"> | ||
| <siteModel id="SiteModel.s:test_output_0" spec="SiteModel"> | ||
| <parameter id="mutationRate.s:test_output_0" spec="parameter.RealParameter" estimate="false" name="mutationRate">1.0</parameter> | ||
| <parameter id="gammaShape.s:test_output_0" spec="parameter.RealParameter" estimate="false" name="shape">1.0</parameter> | ||
| <parameter id="proportionInvariant.s:test_output_0" spec="parameter.RealParameter" estimate="false" lower="0.0" name="proportionInvariant" upper="1.0">0.0</parameter> | ||
| <substModel id="JC69.s:test_output_0" spec="JukesCantor"/> | ||
| </siteModel> | ||
| <branchRateModel id="RelaxedClock.c:test_output_0" spec="beast.evolution.branchratemodel.UCRelaxedClockModel" clock.rate="@ucldMean.c:test_output_0" rateCategories="@rateCategories.c:test_output_0" tree="@Tree.t:test_output_0"> | ||
| <LogNormal id="LogNormalDistributionModel.c:test_output_0" S="@ucldStdev.c:test_output_0" meanInRealSpace="true" name="distr"> | ||
| <parameter id="RealParameter.1" spec="parameter.RealParameter" estimate="false" lower="0.0" name="M" upper="1.0">1.0</parameter> | ||
| </LogNormal> | ||
| </branchRateModel> | ||
| </distribution> | ||
| </distribution> | ||
| </distribution> | ||
| <operator id="YuleBirthRateScaler.t:test_output_0" spec="ScaleOperator" parameter="@birthRate.t:test_output_0" weight="3.0"/> | ||
| <operator id="YuleModelTreeScaler.t:test_output_0" spec="ScaleOperator" scaleFactor="0.5" tree="@Tree.t:test_output_0" weight="3.0"/> | ||
| <operator id="YuleModelTreeRootScaler.t:test_output_0" spec="ScaleOperator" rootOnly="true" scaleFactor="0.5" tree="@Tree.t:test_output_0" weight="3.0"/> | ||
| <operator id="YuleModelUniformOperator.t:test_output_0" spec="Uniform" tree="@Tree.t:test_output_0" weight="30.0"/> | ||
| <operator id="YuleModelSubtreeSlide.t:test_output_0" spec="SubtreeSlide" tree="@Tree.t:test_output_0" weight="15.0"/> | ||
| <operator id="YuleModelNarrow.t:test_output_0" spec="Exchange" tree="@Tree.t:test_output_0" weight="15.0"/> | ||
| <operator id="YuleModelWide.t:test_output_0" spec="Exchange" isNarrow="false" tree="@Tree.t:test_output_0" weight="3.0"/> | ||
| <operator id="YuleModelWilsonBalding.t:test_output_0" spec="WilsonBalding" tree="@Tree.t:test_output_0" weight="3.0"/> | ||
| <operator id="ucldStdevScaler.c:test_output_0" spec="ScaleOperator" parameter="@ucldStdev.c:test_output_0" scaleFactor="0.5" weight="3.0"/> | ||
| <operator id="CategoriesRandomWalk.c:test_output_0" spec="IntRandomWalkOperator" parameter="@rateCategories.c:test_output_0" weight="10.0" windowSize="1"/> | ||
| <operator id="CategoriesSwapOperator.c:test_output_0" spec="SwapOperator" intparameter="@rateCategories.c:test_output_0" weight="10.0"/> | ||
| <operator id="CategoriesUniform.c:test_output_0" spec="UniformOperator" parameter="@rateCategories.c:test_output_0" weight="10.0"/> | ||
| <operator id="ucldMeanScaler.c:test_output_0" spec="ScaleOperator" parameter="@ucldMean.c:test_output_0" scaleFactor="0.5" weight="1.0"/> | ||
| <operator id="relaxedUpDownOperator.c:test_output_0" spec="UpDownOperator" scaleFactor="0.75" weight="3.0"> | ||
| <up idref="ucldMean.c:test_output_0"/> | ||
| <down idref="Tree.t:test_output_0"/> | ||
| </operator> | ||
| <logger id="tracelog" spec="Logger" fileName="test_output_0.log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart"> | ||
| <log idref="posterior"/> | ||
| <log idref="likelihood"/> | ||
| <log idref="prior"/> | ||
| <log idref="treeLikelihood.test_output_0"/> | ||
| <log id="TreeHeight.t:test_output_0" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:test_output_0"/> | ||
| <log idref="YuleModel.t:test_output_0"/> | ||
| <log idref="birthRate.t:test_output_0"/> | ||
| <log idref="ucldStdev.c:test_output_0"/> | ||
| <log id="rate.c:test_output_0" spec="beast.evolution.branchratemodel.RateStatistic" branchratemodel="@RelaxedClock.c:test_output_0" tree="@Tree.t:test_output_0"/> | ||
| <log idref="all.prior"/> | ||
| <log idref="ucldMean.c:test_output_0"/> | ||
| </logger> | ||
| <logger id="screenlog" spec="Logger" logEvery="1000"> | ||
| <log idref="posterior"/> | ||
| <log idref="likelihood"/> | ||
| <log idref="prior"/> | ||
| </logger> | ||
| <logger id="treelog.t:test_output_0" spec="Logger" fileName="$(tree).trees" logEvery="1000" mode="tree"> | ||
| <log id="TreeWithMetaDataLogger.t:test_output_0" spec="beast.evolution.tree.TreeWithMetaDataLogger" branchratemodel="@RelaxedClock.c:test_output_0" tree="@Tree.t:test_output_0"/> | ||
| </logger> | ||
| <operatorschedule id="OperatorSchedule" spec="OperatorSchedule"/> | ||
| </run> | ||
| </beast> |