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<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>
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<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="100000" storeEvery="1000">
<state id="state" storeEvery="1000">
<stateNode id="Tree.TestForSNAPP" spec="beast.util.ClusterTree" clusterType="upgma" nodetype="snap.NodeData">
<taxa id="snap.TestForSNAPP" spec="snap.Data" dataType="integerdata">
<rawdata idref="TestForSNAPP"/>
<taxonset id="Sub" spec="TaxonSet">
<taxon id="Sub_P6_11P_Sagehen_Fsubaenescens" spec="Taxon"/>
<taxon id="Sub_P6_14P_Sagehen_Fsubaenescens" spec="Taxon"/>
<taxon id="Sub_P10_8P_Sagehen_Fsubaenescens" spec="Taxon"/>
<taxon id="Sub_Pol549_1P_Sagehen_Fsubaenescens" spec="Taxon"/>
</taxonset>
<taxonset id="Argentea" spec="TaxonSet">
<taxon id="Argentea_NDT718_P_nearRedbridgeCamp" spec="Taxon"/>
<taxon id="Argentea_P2_6P_Sagehen_Fargente" spec="Taxon"/>
<taxon id="Argentea_P4_12P_Sagehen_Fargentea" spec="Taxon"/>
<taxon id="Argentea_P7_5P_Sagehen_Fargentea" spec="Taxon"/>
</taxonset>
<taxonset id="AccretaB" spec="TaxonSet">
<taxon id="AccretaB_NDT736_2P_nearBloomfieldCamp" spec="Taxon"/>
<taxon id="AccretaB_Pol550c_Sagehen_FaccretaB" spec="Taxon"/>
<taxon id="AccretaB_Pol782_1P_Sagehen_FaccretaB" spec="Taxon"/>
<taxon id="AccretaB_PSW06720_P_CampSpaulding" spec="Taxon"/>
</taxonset>
<taxonset id="AccretaA" spec="TaxonSet">
<taxon id="AccretaA_P5_4P_Ssagehen_FaccretaA" spec="Taxon"/>
<taxon id="AccretaA_Pol499_1P_Sagehen_FaccretaA" spec="Taxon"/>
<taxon id="AccretaA_PSW15985_1Pmale_BCL_FaccretaA" spec="Taxon"/>
<taxon id="AccretaA_RWG001_2P_JuneLake" 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">0.01</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.TestForSNAPP" name="distribution" x="@lambda">
<Gamma id="Gamma.1" name="distr">
<parameter id="RealParameter.3" estimate="false" name="alpha">2.0</parameter>
<parameter id="RealParameter.4" estimate="false" name="beta">1000.0</parameter>
</Gamma>
</prior>
<distribution id="snapprior.TestForSNAPP" spec="snap.likelihood.SnAPPrior" coalescenceRate="@coalescenceRate" lambda="@lambda" rateprior="gamma" tree="@Tree.TestForSNAPP">
<parameter id="alpha" estimate="false" lower="0.0" name="alpha">1.0</parameter>
<parameter id="beta" estimate="false" lower="0.0" name="beta">909.0</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.TestForSNAPP" spec="snap.likelihood.SnAPTreeLikelihood" data="@snap.TestForSNAPP" pattern="coalescenceRate" tree="@Tree.TestForSNAPP">
<siteModel id="MutationSiteModel.TestForSNAPP" 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.TestForSNAPP" weight="0.5"/>
<operator id="NodeBudger" spec="snap.operators.NodeBudger" size="0.5" tree="@Tree.TestForSNAPP" weight="0.5"/>
<operator id="TreeScaler" spec="snap.operators.ScaleOperator" scaleFactor="0.25" tree="@Tree.TestForSNAPP" 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.TestForSNAPP" weight="1.0"/>
<operator id="lambdaScaler" spec="snap.operators.ScaleOperator" parameter="@lambda" scaleFactor="0.75" weight="1.0"/>
<logger id="tracelog" fileName="RUN2.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.TestForSNAPP"/>
</logger>
<logger id="screenlog" logEvery="100">
<log idref="posterior"/>
<log id="ESS.0" spec="util.ESS" arg="@posterior"/>
<log idref="likelihood"/>
<log idref="prior"/>
</logger>
<logger id="treelog" fileName="RUN2.trees" logEvery="100" mode="tree">
<log id="TreeWithMetaDataLogger.TestForSNAPP" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.TestForSNAPP">
<metadata id="theta" spec="snap.RateToTheta" coalescenceRate="@coalescenceRate"/>
</log>
</logger>
</run>
</beast>