<?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="2.4">


    <data
id="anthus_aco_sub"
name="alignment">
                    <sequence id="seq_61430_aco" taxon="61430_aco" totalcount="4" value="ACAGGTTAGAAACTACTCTGTTTTCTGGCTCCTTGTTTAATGCCCTGTCCTATTTTATTGCGAAAATTGTCTGTTTTT"/>
                    <sequence id="seq_626029_aco" taxon="626029_aco" totalcount="4" value="ACAGGTTAGAAACTACTCTGTTTTCTGGCTGCTTGTTTAATGCCCTCTCCTATTTTATTGTGACGATTGTCTGTTTTT"/>
                    <sequence id="seq_630116_aco" taxon="630116_aco" totalcount="4" value="ACAGGTTAGAAACTACTCTGTTTTCTGGCTCCTTGTTTAATGCCCTGTCCTATTTTATTGCGAAAATTGTCTGTTTTT"/>
                    <sequence id="seq_630210_aco" taxon="630210_aco" totalcount="4" value="ACAGGTTAGAAACTACTCTGTTTTCTGGCTCCTTGTTTAATGCCCTGTCCTATTTTATTGTGACAATTGTCTGTTTTT"/>
                    <sequence id="seq_B25702_aco" taxon="B25702_aco" totalcount="4" value="ACAGGTTAGAAACTACTCTGTTTTCTGGCTCCTTGTTTAATGCCCTGTCCTATTTTATTGTGACAATTGTCTGTTTTT"/>
                </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="10000">
    <state id="state" storeEvery="5000">
        <tree id="Tree.t:anthus_aco_sub" name="stateNode">
            <taxonset id="TaxonSet.anthus_aco_sub" spec="TaxonSet">
                <alignment idref="anthus_aco_sub"/>
            </taxonset>
        </tree>
        <parameter id="birthRate.t:anthus_aco_sub" name="stateNode">1.0</parameter>
        <parameter id="clockRate.c:anthus_aco_sub" name="stateNode">1.0</parameter>
    </state>

    <init id="RandomTree.t:anthus_aco_sub" spec="beast.evolution.tree.RandomTree" estimate="false" initial="@Tree.t:anthus_aco_sub" taxa="@anthus_aco_sub">
        <populationModel id="ConstantPopulation0.t:anthus_aco_sub" spec="ConstantPopulation">
            <parameter id="randomPopSize.t:anthus_aco_sub" name="popSize">1.0</parameter>
        </populationModel>
    </init>

    <distribution id="posterior" spec="util.CompoundDistribution">
        <distribution id="prior" spec="util.CompoundDistribution">
            <distribution id="YuleModel.t:anthus_aco_sub" spec="beast.evolution.speciation.YuleModel" birthDiffRate="@birthRate.t:anthus_aco_sub" tree="@Tree.t:anthus_aco_sub"/>
            <prior id="YuleBirthRatePrior.t:anthus_aco_sub" name="distribution" x="@birthRate.t:anthus_aco_sub">
                <Uniform id="Uniform.1" name="distr" upper="Infinity"/>
            </prior>
            <prior id="ClockPrior.c:anthus_aco_sub" name="distribution" x="@clockRate.c:anthus_aco_sub">
                <Uniform id="Uniform.0" name="distr" upper="Infinity"/>
            </prior>
            <distribution id="all.prior" spec="beast.math.distributions.MRCAPrior" monophyletic="true" tree="@Tree.t:anthus_aco_sub">
                <taxonset id="all" spec="TaxonSet">
                    <taxon id="626029_aco" spec="Taxon"/>
                    <taxon id="630116_aco" spec="Taxon"/>
                    <taxon id="630210_aco" spec="Taxon"/>
                    <taxon id="B25702_aco" spec="Taxon"/>
                    <taxon id="61430_aco" spec="Taxon"/>
                </taxonset>
                <Normal id="Normal.0" name="distr">
                    <parameter id="RealParameter.1" estimate="false" name="mean">0.02</parameter>
                    <parameter id="RealParameter.2" estimate="false" name="sigma">0.001</parameter>
                </Normal>
            </distribution>
        </distribution>
        <distribution id="likelihood" spec="util.CompoundDistribution" useThreads="true">
            <distribution id="treeLikelihood.anthus_aco_sub" spec="ThreadedTreeLikelihood" data="@anthus_aco_sub" tree="@Tree.t:anthus_aco_sub">
                <siteModel id="SiteModel.s:anthus_aco_sub" spec="SiteModel">
                    <parameter id="mutationRate.s:anthus_aco_sub" estimate="false" name="mutationRate">1.0</parameter>
                    <parameter id="gammaShape.s:anthus_aco_sub" estimate="false" name="shape">1.0</parameter>
                    <parameter id="proportionInvariant.s:anthus_aco_sub" estimate="false" lower="0.0" name="proportionInvariant" upper="1.0">0.0</parameter>
                    <substModel id="JC69.s:anthus_aco_sub" spec="JukesCantor"/>
                </siteModel>
                <branchRateModel id="StrictClock.c:anthus_aco_sub" spec="beast.evolution.branchratemodel.StrictClockModel" clock.rate="@clockRate.c:anthus_aco_sub"/>
            </distribution>
        </distribution>
    </distribution>

    <operator id="YuleBirthRateScaler.t:anthus_aco_sub" spec="ScaleOperator" parameter="@birthRate.t:anthus_aco_sub" scaleFactor="0.75" weight="3.0"/>

    <operator id="YuleModelTreeScaler.t:anthus_aco_sub" spec="ScaleOperator" scaleFactor="0.5" tree="@Tree.t:anthus_aco_sub" weight="3.0"/>

    <operator id="YuleModelTreeRootScaler.t:anthus_aco_sub" spec="ScaleOperator" rootOnly="true" scaleFactor="0.5" tree="@Tree.t:anthus_aco_sub" weight="3.0"/>

    <operator id="YuleModelUniformOperator.t:anthus_aco_sub" spec="Uniform" tree="@Tree.t:anthus_aco_sub" weight="30.0"/>

    <operator id="YuleModelSubtreeSlide.t:anthus_aco_sub" spec="SubtreeSlide" tree="@Tree.t:anthus_aco_sub" weight="15.0"/>

    <operator id="YuleModelNarrow.t:anthus_aco_sub" spec="Exchange" tree="@Tree.t:anthus_aco_sub" weight="15.0"/>

    <operator id="YuleModelWide.t:anthus_aco_sub" spec="Exchange" isNarrow="false" tree="@Tree.t:anthus_aco_sub" weight="3.0"/>

    <operator id="YuleModelWilsonBalding.t:anthus_aco_sub" spec="WilsonBalding" tree="@Tree.t:anthus_aco_sub" weight="3.0"/>

    <operator id="StrictClockRateScaler.c:anthus_aco_sub" spec="ScaleOperator" parameter="@clockRate.c:anthus_aco_sub" scaleFactor="0.75" weight="3.0"/>

    <operator id="strictClockUpDownOperator.c:anthus_aco_sub" spec="UpDownOperator" scaleFactor="0.75" weight="3.0">
        <up idref="clockRate.c:anthus_aco_sub"/>
        <down idref="Tree.t:anthus_aco_sub"/>
    </operator>

    <logger id="tracelog" fileName="anthus_aco_sub.log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
        <log idref="posterior"/>
        <log idref="likelihood"/>
        <log idref="prior"/>
        <log idref="treeLikelihood.anthus_aco_sub"/>
        <log id="TreeHeight.t:anthus_aco_sub" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:anthus_aco_sub"/>
        <log idref="YuleModel.t:anthus_aco_sub"/>
        <log idref="birthRate.t:anthus_aco_sub"/>
        <log idref="all.prior"/>
        <log idref="clockRate.c:anthus_aco_sub"/>
    </logger>

    <logger id="screenlog" logEvery="1000">
        <log idref="posterior"/>
        <log id="ESS.0" spec="util.ESS" arg="@posterior"/>
        <log idref="likelihood"/>
        <log idref="prior"/>
    </logger>

    <logger id="treelog.t:anthus_aco_sub" fileName="$(tree).trees" logEvery="1000" mode="tree">
        <log id="TreeWithMetaDataLogger.t:anthus_aco_sub" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:anthus_aco_sub"/>
    </logger>

</run>

</beast>
