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Flu_ANP32A.xml
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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="BEAST v2.5.2" version="2.5">
<data id="2_avian_ANP32A-X1_nt_sequences_NoPrimers" name="alignment">
<sequence id="seq_BLACKBIRD_X1" taxon="BLACKBIRD_X1" totalcount="4" value="----------------AAGGAAGCGCCGGATTCCGACGCCGAGGGATACGTGGAGGGGCTGGATGACGAGGAGGAGGATGAGGAT--------GCTTTAT-------CCC---TAGTGAAAGACCGGGACGACAAGGAAGCGCCGGATTCCGACGCCGAGGGATA"/>
<sequence id="seq_CHICKEN_X1" taxon="CHICKEN_X1" totalcount="4" value="----------------AAAGAAGCACCAGACTCTGATGCAGAGGGCTACGTGGAGGGCTTAGACGATGAGGAGGAAGATGAAGAT--------GTCTTAT-------CTC---TAGTGAAAGATCGGGATGACAAAGAAGCACCGGACTCTGATGCAGAGGGCTA"/>
<sequence id="seq_DUCK_X1" taxon="DUCK_X1" totalcount="4" value="CTATGACCGGGACGACAAAGAAGCGCCGGACTCTGACGCAGAGGGCTACGTGGAGGGCCTAGACGACGAGGAGGAGGATGAAGAT--------GTCTTAT-------CTC---TAGTGAAAGATCGGGACGACAAAGAAGCGCCGGA------------------"/>
<sequence id="seq_GOOSE_X1" taxon="GOOSE_X1" totalcount="4" value="----------------AAAGAAGCGCCGGACTCTGACGCGGAGGGCTACGTGGAGGGCCTAGACGACGAGGAGGAGGATGAAGAT--------GTCTTAT-------CTC---TAGTGAAAGATCGGGACGACAAAGAAGCGCCGGACTCTGACGCGGAGGGCTA"/>
<sequence id="seq_GULL_X1" taxon="GULL_X1" totalcount="4" value="----------------AAAGAAGCACCGGACTCTGATGCAGAGGGCTACGTGGAGGGCTTAGACGACGAGGAAGAAGATGAAGAT--------GTCTTAT-------CTC---TAGTGAAAGATCGGGATGACAAAGAAGCGCCGGACTCTGATGCAGAGGGCTA"/>
<sequence id="seq_HUMAN" taxon="HUMAN" totalcount="4" value="--------GGGACGACAAGGAGGCCCCTGACTCGGATGCTGAGGGCTACGTGGAGGGCCTGGATGATGAGGAGGAGGATGAGGATGAGGAGGAGTATGATGAAGATGCTCAGGTAGTGGAAGACGAGGAGGACGAGGATG-------------------------"/>
<sequence id="seq_MAGPIE_X1" taxon="MAGPIE_X1" totalcount="4" value="----------------AAGGAAGCGCCGGATTCCGACGCCGAGGGATACGTGGAGGGCCTGGATGACGAGGAGGAGGATGAGGAT--------GTTTTAT-------CCC---TAGTGAAAGACCGGGATGACAAGGAAGCGCCGGATTCTGACGCCGAGGGATA"/>
<sequence id="seq_MALLARD_X1" taxon="MALLARD_X1" totalcount="4" value="CTACGACCGGGACGACAAAGAAGCGCCGGACTCTGACGCAGAGGGCTACGTGGAGGGCCTAGACGACGAGGAGGAGGATGAAGAT--------GTCTTAT-------CTC---TAGTGAAAGATCGGGACGACAAAGAAGCGCCGGA------------------"/>
<sequence id="seq_QUAIL_X1" taxon="QUAIL_X1" totalcount="4" value="----------GATGACAAAGAAGCACCAGACTCTGATGCAGAGGGCTACGTGGAGGGCTTAGACGACGAGGAGGAAGATGAAGAT--------GTCTTAT-------CTC---TAGTGAAAGATCGGGATGACAAAGAAGCACCGGACTCTGATGCA--------"/>
<sequence id="seq_SWALLOW_X1" taxon="SWALLOW_X1" totalcount="4" value="----------------AAGGAAGCGCCGGATTCCGACGCCGAGGGATACGTGGAGGGGCTGGACGACGAGGAGGAGGATGAGGAC--------GTTTTAT-------CCC---TAGTGAAAGACCGGGACGACAAGGAAGCGCCGGATTCCGACGCCGAGGGATA"/>
<sequence id="seq_SWAN_X1" taxon="SWAN_X1" totalcount="4" value="----------------AAAGAAGCGCCGGACTCTGACGCAGAGGGCTACGTGGAGGGCCTAGACGACGAGGAGGAAGATGAAGAT--------GTCTTAT-------CTC---TAGTGAAAGATCGGGACGACAAAGAAGCGCCGGACTCTGACGCAGAGGGCTA"/>
<sequence id="seq_TURKEY_X1" taxon="TURKEY_X1" totalcount="4" value="----------------AAAGAAGCACCAGACTCTGATGCAGAGGGCTACGTGGAGGGCTTAGACGATGAGGAGGAAGATGAAGAT--------GTCTTAT-------CTC---TAGTGAAAGATCGGGATGACAAAGAAGCACCGGACTCTGATGCAGAGGGCTA"/>
</data>
<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>
<run id="mcmc" spec="MCMC" chainLength="10000000">
<state id="state" storeEvery="5000">
<tree id="Tree.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers" name="stateNode">
<taxonset id="TaxonSet.2_avian_ANP32A-X1_nt_sequences_NoPrimers" spec="TaxonSet">
<alignment idref="2_avian_ANP32A-X1_nt_sequences_NoPrimers"/>
</taxonset>
</tree>
<parameter id="birthRate.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers" name="stateNode">1.0</parameter>
<parameter id="kappa.s:2_avian_ANP32A-X1_nt_sequences_NoPrimers" lower="0.0" name="stateNode">2.0</parameter>
<parameter id="freqParameter.s:2_avian_ANP32A-X1_nt_sequences_NoPrimers" dimension="4" lower="0.0" name="stateNode" upper="1.0">0.25</parameter>
</state>
<init id="RandomTree.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers" spec="beast.evolution.tree.RandomTree" estimate="false" initial="@Tree.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers" taxa="@2_avian_ANP32A-X1_nt_sequences_NoPrimers">
<populationModel id="ConstantPopulation0.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers" spec="ConstantPopulation">
<parameter id="randomPopSize.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers" name="popSize">1.0</parameter>
</populationModel>
</init>
<distribution id="posterior" spec="util.CompoundDistribution">
<distribution id="prior" spec="util.CompoundDistribution">
<distribution id="YuleModel.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers" spec="beast.evolution.speciation.YuleModel" birthDiffRate="@birthRate.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers" tree="@Tree.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers"/>
<prior id="YuleBirthRatePrior.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers" name="distribution" x="@birthRate.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers">
<Uniform id="Uniform.1" name="distr" upper="Infinity"/>
</prior>
<prior id="KappaPrior.s:2_avian_ANP32A-X1_nt_sequences_NoPrimers" name="distribution" x="@kappa.s:2_avian_ANP32A-X1_nt_sequences_NoPrimers">
<LogNormal id="LogNormalDistributionModel.0" name="distr">
<parameter id="RealParameter.1" estimate="false" name="M">1.0</parameter>
<parameter id="RealParameter.2" estimate="false" name="S">1.25</parameter>
</LogNormal>
</prior>
</distribution>
<distribution id="likelihood" spec="util.CompoundDistribution" useThreads="true">
<distribution id="treeLikelihood.2_avian_ANP32A-X1_nt_sequences_NoPrimers" spec="ThreadedTreeLikelihood" data="@2_avian_ANP32A-X1_nt_sequences_NoPrimers" tree="@Tree.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers">
<siteModel id="SiteModel.s:2_avian_ANP32A-X1_nt_sequences_NoPrimers" spec="SiteModel">
<parameter id="mutationRate.s:2_avian_ANP32A-X1_nt_sequences_NoPrimers" estimate="false" name="mutationRate">1.0</parameter>
<parameter id="gammaShape.s:2_avian_ANP32A-X1_nt_sequences_NoPrimers" estimate="false" name="shape">1.0</parameter>
<parameter id="proportionInvariant.s:2_avian_ANP32A-X1_nt_sequences_NoPrimers" estimate="false" lower="0.0" name="proportionInvariant" upper="1.0">0.0</parameter>
<substModel id="hky.s:2_avian_ANP32A-X1_nt_sequences_NoPrimers" spec="HKY" kappa="@kappa.s:2_avian_ANP32A-X1_nt_sequences_NoPrimers">
<frequencies id="estimatedFreqs.s:2_avian_ANP32A-X1_nt_sequences_NoPrimers" spec="Frequencies" frequencies="@freqParameter.s:2_avian_ANP32A-X1_nt_sequences_NoPrimers"/>
</substModel>
</siteModel>
<branchRateModel id="StrictClock.c:2_avian_ANP32A-X1_nt_sequences_NoPrimers" spec="beast.evolution.branchratemodel.StrictClockModel">
<parameter id="clockRate.c:2_avian_ANP32A-X1_nt_sequences_NoPrimers" estimate="false" name="clock.rate">1.0</parameter>
</branchRateModel>
</distribution>
</distribution>
</distribution>
<operator id="YuleBirthRateScaler.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers" spec="ScaleOperator" parameter="@birthRate.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers" scaleFactor="0.75" weight="3.0"/>
<operator id="YuleModelTreeScaler.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers" spec="ScaleOperator" scaleFactor="0.5" tree="@Tree.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers" weight="3.0"/>
<operator id="YuleModelTreeRootScaler.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers" spec="ScaleOperator" rootOnly="true" scaleFactor="0.5" tree="@Tree.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers" weight="3.0"/>
<operator id="YuleModelUniformOperator.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers" spec="Uniform" tree="@Tree.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers" weight="30.0"/>
<operator id="YuleModelSubtreeSlide.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers" spec="SubtreeSlide" tree="@Tree.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers" weight="15.0"/>
<operator id="YuleModelNarrow.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers" spec="Exchange" tree="@Tree.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers" weight="15.0"/>
<operator id="YuleModelWide.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers" spec="Exchange" isNarrow="false" tree="@Tree.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers" weight="3.0"/>
<operator id="YuleModelWilsonBalding.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers" spec="WilsonBalding" tree="@Tree.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers" weight="3.0"/>
<operator id="KappaScaler.s:2_avian_ANP32A-X1_nt_sequences_NoPrimers" spec="ScaleOperator" parameter="@kappa.s:2_avian_ANP32A-X1_nt_sequences_NoPrimers" scaleFactor="0.5" weight="0.1"/>
<operator id="FrequenciesExchanger.s:2_avian_ANP32A-X1_nt_sequences_NoPrimers" spec="DeltaExchangeOperator" delta="0.01" weight="0.1">
<parameter idref="freqParameter.s:2_avian_ANP32A-X1_nt_sequences_NoPrimers"/>
</operator>
<logger id="tracelog" fileName="2_avian_ANP32A-X1_nt_sequences_NoPrimers.log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
<log idref="posterior"/>
<log idref="likelihood"/>
<log idref="prior"/>
<log idref="treeLikelihood.2_avian_ANP32A-X1_nt_sequences_NoPrimers"/>
<log id="TreeHeight.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers"/>
<log idref="YuleModel.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers"/>
<log idref="birthRate.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers"/>
<log idref="kappa.s:2_avian_ANP32A-X1_nt_sequences_NoPrimers"/>
<log idref="freqParameter.s:2_avian_ANP32A-X1_nt_sequences_NoPrimers"/>
</logger>
<logger id="screenlog" logEvery="1000">
<log idref="posterior"/>
<log idref="likelihood"/>
<log idref="prior"/>
</logger>
<logger id="treelog.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers" fileName="$(tree).trees" logEvery="1000" mode="tree">
<log id="TreeWithMetaDataLogger.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:2_avian_ANP32A-X1_nt_sequences_NoPrimers"/>
</logger>
</run>
</beast>