test_1.xml (8411 bytes)
<?xml version="1.0" encoding="UTF-8" standalone="no"?><beast beautitemplate='SNAPP' 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:SNAPP v1.4.2" version="2.5">
<data id="o6" dataType="integer" name="rawdata">
<sequence id="seq_10" taxon="10" totalcount="3" value="000000100000100010002200000020000000000200"/>
<sequence id="seq_11A" taxon="11A" totalcount="3" value="001000100000000000002200000020000000002000"/>
<sequence id="seq_12C" taxon="12C" totalcount="3" value="000000000000000000002200000020000000000200"/>
<sequence id="seq_13A" taxon="13A" totalcount="3" value="000000000000000000001200000020000000002000"/>
<sequence id="seq_18" taxon="18" totalcount="3" value="000000000000000000000200000020000000002000"/>
<sequence id="seq_3" taxon="3" totalcount="3" value="010000000000000000002200000020000000000200"/>
<sequence id="seq_4" taxon="4" totalcount="3" value="000000000000002000000220000020000000000000"/>
<sequence id="seq_7-3_B" taxon="7-3_B" totalcount="3" value="000000001000000000200000000001002000000000"/>
<sequence id="seq_7-3_C" taxon="7-3_C" totalcount="3" value="000000000000000000000000000000000000000000"/>
<sequence id="seq_8" taxon="8" totalcount="3" value="000020000000000000000000000000000000000000"/>
</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="100000000" storeEvery="1000">
<state id="state" storeEvery="1000">
<stateNode id="Tree.o6" spec="beast.util.ClusterTree" clusterType="upgma" nodetype="snap.NodeData">
<taxa id="snap.o6" spec="snap.Data" dataType="integerdata">
<rawdata idref="o6"/>
<taxonset id="tax1" spec="TaxonSet">
<taxon id="8" spec="Taxon"/>
</taxonset>
<taxonset id="tax2" spec="TaxonSet">
<taxon id="10" spec="Taxon"/>
</taxonset>
<taxonset id="tax3" spec="TaxonSet">
<taxon id="12C" spec="Taxon"/>
</taxonset>
<taxonset id="tax4" spec="TaxonSet">
<taxon id="13A" spec="Taxon"/>
</taxonset>
<taxonset id="tax5" spec="TaxonSet">
<taxon id="18" spec="Taxon"/>
</taxonset>
<taxonset id="tax6" spec="TaxonSet">
<taxon id="3" spec="Taxon"/>
</taxonset>
<taxonset id="tax7" spec="TaxonSet">
<taxon id="4" spec="Taxon"/>
</taxonset>
<taxonset id="tax8" spec="TaxonSet">
<taxon id="7-3_B" spec="Taxon"/>
</taxonset>
<taxonset id="tax9" spec="TaxonSet">
<taxon id="7-3_C" spec="Taxon"/>
</taxonset>
<taxonset id="tax10" spec="TaxonSet">
<taxon id="11A" spec="Taxon"/>
</taxonset>
</taxa>
<parameter id="RealParameter.0" lower="0.0" name="clock.rate" upper="0.0">1.0</parameter>
</stateNode>
<parameter id="lambda" lower="0.0" name="stateNode">10.0</parameter>
<parameter id="coalescenceRate" name="stateNode">10.0</parameter>
</state>
<distribution id="posterior" spec="util.CompoundDistribution">
<distribution id="prior" spec="util.CompoundDistribution">
<prior id="lambdaPrior.o6" name="distribution" x="@lambda">
<Gamma id="Gamma.0" name="distr">
<parameter id="RealParameter.1" estimate="false" name="alpha">2.0</parameter>
<parameter id="RealParameter.2" estimate="false" name="beta">200.0</parameter>
</Gamma>
</prior>
<distribution id="snapprior.o6" spec="snap.likelihood.SnAPPrior" coalescenceRate="@coalescenceRate" lambda="@lambda" rateprior="gamma" tree="@Tree.o6">
<parameter id="alpha" estimate="false" lower="0.0" name="alpha">2.0</parameter>
<parameter id="beta" estimate="false" lower="0.0" name="beta">250.0</parameter>
<parameter id="kappa" estimate="false" lower="0.0" name="kappa">1.0</parameter>
</distribution>
</distribution>
<distribution id="likelihood" spec="util.CompoundDistribution">
<distribution id="treeLikelihood.o6" spec="snap.likelihood.SnAPTreeLikelihood" data="@snap.o6" non-polymorphic="false" pattern="coalescenceRate" tree="@Tree.o6">
<siteModel id="MutationSiteModel.o6" spec="SiteModel">
<parameter id="mutationRate" estimate="false" name="mutationRate">1.0</parameter>
<parameter id="shape" estimate="false" name="shape">2.0</parameter>
<parameter id="proportionInvariant" estimate="false" name="proportionInvariant">0.0</parameter>
<substModel id="MutationModel" spec="snap.likelihood.SnapSubstitutionModel" coalescenceRate="@coalescenceRate">
<parameter id="u" estimate="false" lower="0.0" name="mutationRateU">1.0</parameter>
<parameter id="v" lower="0.0" name="mutationRateV">1.0</parameter>
</substModel>
</siteModel>
</distribution>
</distribution>
</distribution>
<operator id="NodeSwapper" spec="snap.operators.NodeSwapper" tree="@Tree.o6" weight="0.5"/>
<operator id="NodeBudger" spec="snap.operators.NodeBudger" size="0.5" tree="@Tree.o6" weight="0.5"/>
<operator id="TreeScaler" spec="snap.operators.ScaleOperator" scaleFactor="0.25" tree="@Tree.o6" weight="0.5"/>
<operator id="GammaMover" spec="snap.operators.GammaMover" coalescenceRate="@coalescenceRate" scale="0.5" weight="8.0"/>
<operator id="RateMixer" spec="snap.operators.RateMixer" coalescenceRate="@coalescenceRate" scaleFactors="0.25" tree="@Tree.o6" weight="1.0"/>
<operator id="lambdaScaler" spec="snap.operators.ScaleOperator" parameter="@lambda" scaleFactor="0.75" weight="1.0"/>
<logger id="tracelog" fileName="snap.log" logEvery="1000" model="@posterior">
<log idref="posterior"/>
<log idref="likelihood"/>
<log idref="prior"/>
<log id="ThetaLogger" spec="snap.ThetaLogger" coalescenceRate="@coalescenceRate"/>
<log id="TreeHeightLogger" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.o6"/>
</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" fileName="snap.trees" logEvery="1000" mode="tree">
<log id="TreeWithMetaDataLogger.o6" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.o6">
<metadata id="theta" spec="snap.RateToTheta" coalescenceRate="@coalescenceRate"/>
</log>
</logger>
</run>
</beast>