2_4.xml

<?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="test_output_0"
name="alignment">
                    <sequence id="seq_t1" taxon="t1" totalcount="4" value="acttgttgcgactgcgcctg"/>
                    <sequence id="seq_t2" taxon="t2" totalcount="4" value="acttattgcgactgaggccg"/>
                    <sequence id="seq_t3" taxon="t3" totalcount="4" value="acttaatgcgaatgagcccg"/>
                    <sequence id="seq_t4" taxon="t4" totalcount="4" value="aacgacccgcgatcggggat"/>
                    <sequence id="seq_t5" taxon="t5" totalcount="4" value="acttgttgcgactgagcctg"/>
                </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:test_output_0" name="stateNode">
            <taxonset id="TaxonSet.test_output_0" spec="TaxonSet">
                <alignment idref="test_output_0"/>
            </taxonset>
        </tree>
        <parameter id="birthRate.t:test_output_0" 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" 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>
        </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" estimate="false" name="mutationRate">1.0</parameter>
                    <parameter id="gammaShape.s:test_output_0" estimate="false" name="shape">1.0</parameter>
                    <parameter id="proportionInvariant.s:test_output_0" 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="StrictClock.c:test_output_0" spec="beast.evolution.branchratemodel.StrictClockModel">
                    <parameter id="clockRate.c:test_output_0" estimate="false" name="clock.rate">1.0</parameter>
                </branchRateModel>
            </distribution>
        </distribution>
    </distribution>

    <operator id="YuleBirthRateScaler.t:test_output_0" spec="ScaleOperator" parameter="@birthRate.t:test_output_0" scaleFactor="0.75" 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"/>

    <logger id="tracelog" 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"/>
    </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:test_output_0" fileName="$(tree).trees" logEvery="1000" mode="tree">
        <log id="TreeWithMetaDataLogger.t:test_output_0" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:test_output_0"/>
    </logger>

</run>

</beast>