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Copy pathtestSimpleMutableAlignment.xml
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47 lines (39 loc) · 2.95 KB
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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.base.evolution.alignment:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood" required="BEAST.base v2.7.7" version="2.7">
<data id="dna" spec="mutablealignment.MutableAlignment">
<sequence id="seq_Cow" spec="Sequence" taxon="Cow" totalcount="4" value="AAAAA"/>
<sequence id="seq_Carp" spec="Sequence" taxon="Carp" totalcount="4" value="GGGGG"/>
<sequence id="seq_Chicken" spec="Sequence" taxon="Chicken" totalcount="4" value="CCCCC"/>
</data>
<run id="mcmc" spec="MCMC" chainLength="10000000">
<state id="state" spec="State" storeEvery="5000">
<stateNode idref="Tree"/>
<stateNode idref="dna"/>
</state>
<init id="NewickTree" spec="beast.base.evolution.tree.TreeParser" IsLabelledNewick="true" estimate="false" initial="@Tree" newick="((Cow:0.1,Carp:0.1):0.1,Chicken:0.2)" taxa="@dna"/>
<distribution id="posterior" spec="CompoundDistribution">
<distribution id="treeLikelihood.dna" spec="mutablealignment.MATreeLikelihood" data="@dna">
<tree id="Tree" spec="beast.base.evolution.tree.Tree">
<taxonset id="TaxonSet.dna" spec="TaxonSet">
<taxon spec="Taxon" id="Cow"/>
<taxon spec="Taxon" id="Carp"/>
<taxon spec="Taxon" id="Chicken"/>
</taxonset>
</tree>
<siteModel id="SiteModel" spec="SiteModel" mutationRate="1.0" shape="1.0" proportionInvariant="0.0">
<substModel id="hky" spec="HKY" kappa="2.0">
<frequencies id="equalFreqs" spec="Frequencies" estimate="false" frequencies="0.25 0.25 0.25 0.25"/>
</substModel>
</siteModel>
</distribution>
</distribution>
<operator spec="mutablealignment.MutableAlignmentOperator" mutableAlignment="@dna" weight="1.0"/>
<logger id="tracelog" spec="Logger" fileName="$(filebase).log" logEvery="1" model="@posterior" sanitiseHeaders="true" sort="smart">
<log idref="posterior"/>
<log idref="treeLikelihood.dna"/>
<log spec="mutablealignment.MutableAlignmentLogger" alignment="@dna"/>
</logger>
<logger id="screenlog" spec="Logger" logEvery="1000">
<log idref="posterior"/>
</logger>
</run>
</beast>