/
local-strict-constrained-TEMPLATE.xml
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/
local-strict-constrained-TEMPLATE.xml
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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.evolution.likelihood" required="" version="2.4">
<data
id="data"
name="alignment">
TEMPLATE_SEQUENCE
</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:data" name="stateNode">
<trait id="dateTrait.t:data" spec="beast.evolution.tree.TraitSet" traitname="date-backward">
E0_0=0.0,
E1_1=1.0,
E2_2=2.0,
E3_3=3.0,
E4_4=4.0,
E5_5=5.0,
E6_6=6.0,
E7_7=7.0,
E8_8=8.0,
E9_9=9.0,
E10_10=10.0,
E11_11=11.0,
E12_12=12.0,
E13_13=13.0,
E14_14=14.0,
E15_15=15.0,
E16_16=16.0,
E17_17=17.0,
E18_18=18.0,
E19_19=19.0,
H0_0=0.0,
H1_1=1.0,
H2_2=2.0,
H3_3=3.0,
H4_4=4.0,
H5_5=5.0,
H6_6=6.0,
H7_7=7.0,
H8_8=8.0,
H9_9=9.0,
H10_10=10.0,
H11_11=11.0,
H12_12=12.0,
H13_13=13.0,
H14_14=14.0,
H15_15=15.0,
H16_16=16.0,
H17_17=17.0,
H18_18=18.0,
H19_19=19.0,
B0_0=0.0,
B1_1=1.0,
B2_2=2.0,
B3_3=3.0,
B4_4=4.0,
B5_5=5.0,
B6_6=6.0,
B7_7=7.0,
B8_8=8.0,
B9_9=9.0,
B10_10=10.0,
B11_11=11.0,
B12_12=12.0,
B13_13=13.0,
B14_14=14.0,
B15_15=15.0,
B16_16=16.0,
B17_17=17.0,
B18_18=18.0,
B19_19=19.0 <taxa id="TaxonSet.data" spec="TaxonSet">
<alignment idref="data"/>
</taxa>
</trait>
<taxonset idref="TaxonSet.data"/>
</tree>
<parameter id="kappa.s:data" lower="0.0" name="stateNode">3.0</parameter>
<!-- CLOC -->
<parameter id="ucldMean.B" name="stateNode">0.015</parameter>
<parameter id="ucldMean.E" name="stateNode">0.005</parameter>
<parameter id="ucldMean.H" name="stateNode">0.01</parameter>
<parameter id="bPopSizes.t:data" dimension="5" lower="0.0" name="stateNode" upper="380000.0">10.0</parameter>
<stateNode id="bGroupSizes.t:data" spec="parameter.IntegerParameter" dimension="5" lower="1">1 1 1 49 7</stateNode>
<parameter id="freqParameter.s:data" dimension="4" lower="0.0" name="stateNode" upper="1.0">0.25</parameter>
</state>
<!--init id="RandomTree.t:data" spec="beast.evolution.tree.RandomTree" estimate="false" initial="@Tree.t:data" taxa="@data">
<populationModel id="ConstantPopulation0.t:data" spec="ConstantPopulation">
<parameter id="randomPopSize.t:data" name="popSize">1.0</parameter>
</populationModel>
</init-->
<init spec="beast.util.TreeParser" id="RandomTree.t:data" initial="@Tree.t:data" taxa="@data" IsLabelledNewick="true" newick="((((((((((((((((((((E0_0:2.0,E1_1:1.0):1.0,E2_2:1.0):1.0,E3_3:1.0):1.0,E4_4:1.0):1.0,E5_5:1.0):1.0,E6_6:1.0):1.0,E7_7:1.0):1.0,E8_8:1.0):1.0,E9_9:1.0):1.0,E10_10:1.0):1.0,E11_11:1.0):1.0,E12_12:1.0):1.0,E13_13:1.0):1.0,E14_14:1.0):1.0,E15_15:1.0):1.0,E16_16:1.0):1.0,E17_17:1.0):1.0,E18_18:1.0):1.0,E19_19:1.0):30.0,((((((((((((((((((((H0_0:2.0,H1_1:1.0):1.0,H2_2:1.0):1.0,H3_3:1.0):1.0,H4_4:1.0):1.0,H5_5:1.0):1.0,H6_6:1.0):1.0,H7_7:1.0):1.0,H8_8:1.0):1.0,H9_9:1.0):1.0,H10_10:1.0):1.0,H11_11:1.0):1.0,H12_12:1.0):1.0,H13_13:1.0):1.0,H14_14:1.0):1.0,H15_15:1.0):1.0,H16_16:1.0):1.0,H17_17:1.0):1.0,H18_18:1.0):1.0,H19_19:1.0):25.0,(((((((((((((((((((B0_0:2.0,B1_1:1.0):1.0,B2_2:1.0):1.0,B3_3:1.0):1.0,B4_4:1.0):1.0,B5_5:1.0):1.0,B6_6:1.0):1.0,B7_7:1.0):1.0,B8_8:1.0):1.0,B9_9:1.0):1.0,B10_10:1.0):1.0,B11_11:1.0):1.0,B12_12:1.0):1.0,B13_13:1.0):1.0,B14_14:1.0):1.0,B15_15:1.0):1.0,B16_16:1.0):1.0,B17_17:1.0):1.0,B18_18:1.0):1.0,B19_19:1.0):25.0):5.0);">
</init>
<distribution id="posterior" spec="util.CompoundDistribution">
<distribution id="prior" spec="util.CompoundDistribution">
<distribution id="BayesianSkyline.t:data" spec="BayesianSkyline" groupSizes="@bGroupSizes.t:data" popSizes="@bPopSizes.t:data">
<treeIntervals id="BSPTreeIntervals.t:data" spec="TreeIntervals" tree="@Tree.t:data"/>
</distribution>
<distribution id="MarkovChainedPopSizes.t:data" spec="beast.math.distributions.MarkovChainDistribution" jeffreys="true" parameter="@bPopSizes.t:data"/>
<prior id="KappaPrior.s:data" name="distribution" x="@kappa.s:data">
<LogNormal id="LogNormalDistributionModel.0" name="distr">
<parameter id="RealParameter.1" estimate="false" name="M">1.0</parameter>
<parameter id="RealParameter.2" estimate="false" name="S">1.25</parameter>
</LogNormal>
</prior>
<!-- CLOC -->
<prior id="MeanRatePrior.B" name="distribution" x="@ucldMean.B">
<Exponential id="Exponential.2B" name="distr">
<parameter id="RealParameter.7B" estimate="false" name="mean">0.003</parameter>
</Exponential>
</prior>
<prior id="MeanRatePrior.E" name="distribution" x="@ucldMean.E">
<Exponential id="Exponential.2E" name="distr">
<parameter id="RealParameter.7E" estimate="false" name="mean">0.003</parameter>
</Exponential>
</prior>
<prior id="MeanRatePrior.H" name="distribution" x="@ucldMean.H">
<Exponential id="Exponential.2H" name="distr">
<parameter id="RealParameter.7H" estimate="false" name="mean">0.003</parameter>
</Exponential>
</prior>
<distribution id="B.prior" spec="beast.math.distributions.MRCAPrior" monophyletic="true" tree="@Tree.t:data">
<taxonset id="B" spec="TaxonSet">
<taxon id="B0_0" spec="Taxon"/>
<taxon id="B10_10" spec="Taxon"/>
<taxon id="B11_11" spec="Taxon"/>
<taxon id="B12_12" spec="Taxon"/>
<taxon id="B13_13" spec="Taxon"/>
<taxon id="B14_14" spec="Taxon"/>
<taxon id="B15_15" spec="Taxon"/>
<taxon id="B16_16" spec="Taxon"/>
<taxon id="B17_17" spec="Taxon"/>
<taxon id="B18_18" spec="Taxon"/>
<taxon id="B19_19" spec="Taxon"/>
<taxon id="B1_1" spec="Taxon"/>
<taxon id="B2_2" spec="Taxon"/>
<taxon id="B3_3" spec="Taxon"/>
<taxon id="B4_4" spec="Taxon"/>
<taxon id="B5_5" spec="Taxon"/>
<taxon id="B6_6" spec="Taxon"/>
<taxon id="B7_7" spec="Taxon"/>
<taxon id="B8_8" spec="Taxon"/>
<taxon id="B9_9" spec="Taxon"/>
</taxonset>
</distribution>
<distribution id="E.prior" spec="beast.math.distributions.MRCAPrior" monophyletic="true" tree="@Tree.t:data">
<taxonset id="E" spec="TaxonSet">
<taxon id="E0_0" spec="Taxon"/>
<taxon id="E10_10" spec="Taxon"/>
<taxon id="E11_11" spec="Taxon"/>
<taxon id="E12_12" spec="Taxon"/>
<taxon id="E13_13" spec="Taxon"/>
<taxon id="E14_14" spec="Taxon"/>
<taxon id="E15_15" spec="Taxon"/>
<taxon id="E16_16" spec="Taxon"/>
<taxon id="E17_17" spec="Taxon"/>
<taxon id="E18_18" spec="Taxon"/>
<taxon id="E19_19" spec="Taxon"/>
<taxon id="E1_1" spec="Taxon"/>
<taxon id="E2_2" spec="Taxon"/>
<taxon id="E3_3" spec="Taxon"/>
<taxon id="E4_4" spec="Taxon"/>
<taxon id="E5_5" spec="Taxon"/>
<taxon id="E6_6" spec="Taxon"/>
<taxon id="E7_7" spec="Taxon"/>
<taxon id="E8_8" spec="Taxon"/>
<taxon id="E9_9" spec="Taxon"/>
</taxonset>
</distribution>
<distribution id="H.prior" spec="beast.math.distributions.MRCAPrior" monophyletic="true" tree="@Tree.t:data">
<taxonset id="H" spec="TaxonSet">
<taxon id="H0_0" spec="Taxon"/>
<taxon id="H10_10" spec="Taxon"/>
<taxon id="H11_11" spec="Taxon"/>
<taxon id="H12_12" spec="Taxon"/>
<taxon id="H13_13" spec="Taxon"/>
<taxon id="H14_14" spec="Taxon"/>
<taxon id="H15_15" spec="Taxon"/>
<taxon id="H16_16" spec="Taxon"/>
<taxon id="H17_17" spec="Taxon"/>
<taxon id="H18_18" spec="Taxon"/>
<taxon id="H19_19" spec="Taxon"/>
<taxon id="H1_1" spec="Taxon"/>
<taxon id="H2_2" spec="Taxon"/>
<taxon id="H3_3" spec="Taxon"/>
<taxon id="H4_4" spec="Taxon"/>
<taxon id="H5_5" spec="Taxon"/>
<taxon id="H6_6" spec="Taxon"/>
<taxon id="H7_7" spec="Taxon"/>
<taxon id="H8_8" spec="Taxon"/>
<taxon id="H9_9" spec="Taxon"/>
</taxonset>
</distribution>
</distribution>
<distribution id="likelihood" spec="util.CompoundDistribution" useThreads="true">
<distribution id="treeLikelihood.data" spec="ThreadedTreeLikelihood" data="@data" tree="@Tree.t:data">
<siteModel id="SiteModel.s:data" spec="SiteModel">
<parameter id="mutationRate.s:data" estimate="false" name="mutationRate">1.0</parameter>
<parameter id="gammaShape.s:data" estimate="false" name="shape">1.0</parameter>
<parameter id="proportionInvariant.s:data" estimate="false" lower="0.0" name="proportionInvariant" upper="1.0">0.0</parameter>
<substModel id="hky.s:data" spec="HKY" kappa="@kappa.s:data">
<frequencies id="estimatedFreqs.s:data" spec="Frequencies" frequencies="@freqParameter.s:data"/>
</substModel>
</siteModel>
<!-- CLOC -->
<branchRateModel spec='mf.beast.evolution.branchratemodel.FlexibleLocalClockModel' id="RelaxedClock.c:data" tree='@Tree.t:data'>
<rootClockModel id="RelaxedClock.E" clock.rate="@ucldMean.E" spec="mf.beast.evolution.branchratemodel.StrictLineageClockModel"/>
<cladeClockModel id="RelaxedClock.B" taxonset="@B" includeStem="true" clock.rate="@ucldMean.B" spec="mf.beast.evolution.branchratemodel.StrictCladeModel"/>
<cladeClockModel id="RelaxedClock.H" taxonset="@H" includeStem="true" clock.rate="@ucldMean.H" spec="mf.beast.evolution.branchratemodel.StrictCladeModel"/>
</branchRateModel>
<!--branchRateModel id="RelaxedClock.c:data" spec="beast.evolution.branchratemodel.UCRelaxedClockModel" clock.rate="@ucldMean.c:data" rateCategories="@rateCategories.c:data" tree="@Tree.t:data">
<LogNormal id="LogNormalDistributionModel.c:data" S="@ucldStdev.c:data" meanInRealSpace="true" name="distr">
<parameter id="RealParameter.3" estimate="false" lower="0.0" name="M" upper="1.0">1.0</parameter>
</LogNormal>
</branchRateModel-->
</distribution>
</distribution>
</distribution>
<operator id="KappaScaler.s:data" spec="ScaleOperator" parameter="@kappa.s:data" scaleFactor="0.5" weight="0.1"/>
<!--operator id="ucldMeanScaler.c:data" spec="ScaleOperator" parameter="@ucldMean.c:data" scaleFactor="0.5" weight="1.0"/>
<operator id="ucldStdevScaler.c:data" spec="ScaleOperator" parameter="@ucldStdev.c:data" scaleFactor="0.5" weight="3.0"/>
<operator id="CategoriesRandomWalk.c:data" spec="IntRandomWalkOperator" parameter="@rateCategories.c:data" weight="10.0" windowSize="1"/>
<operator id="CategoriesSwapOperator.c:data" spec="SwapOperator" intparameter="@rateCategories.c:data" weight="10.0"/>
<operator id="CategoriesUniform.c:data" spec="UniformOperator" parameter="@rateCategories.c:data" weight="10.0"/-->
<operator id="ucldMeanScaler.B" spec="ScaleOperator" parameter="@ucldMean.B" scaleFactor="0.5" weight="1.0"/>
<operator id="ucldMeanScaler.E" spec="ScaleOperator" parameter="@ucldMean.E" scaleFactor="0.5" weight="1.0"/>
<operator id="ucldMeanScaler.H" spec="ScaleOperator" parameter="@ucldMean.H" scaleFactor="0.5" weight="1.0"/>
<operator id="relaxedUpDownOperator.c:data" spec="UpDownOperator" scaleFactor="0.75" weight="3.0">
<!-- <up idref="ucldMean.c:data"/> -->
<up idref="ucldMean.B"/>
<up idref="ucldMean.E"/>
<up idref="ucldMean.H"/>
<down idref="Tree.t:data"/>
</operator>
<operator id="BayesianSkylineTreeScaler.t:data" spec="ScaleOperator" scaleFactor="0.5" tree="@Tree.t:data" weight="3.0"/>
<operator id="BayesianSkylineTreeRootScaler.t:data" spec="ScaleOperator" rootOnly="true" scaleFactor="0.5" tree="@Tree.t:data" weight="3.0"/>
<operator id="BayesianSkylineUniformOperator.t:data" spec="Uniform" tree="@Tree.t:data" weight="30.0"/>
<operator id="BayesianSkylineSubtreeSlide.t:data" spec="SubtreeSlide" tree="@Tree.t:data" weight="15.0"/>
<operator id="BayesianSkylineNarrow.t:data" spec="Exchange" tree="@Tree.t:data" weight="15.0"/>
<operator id="BayesianSkylineWide.t:data" spec="Exchange" isNarrow="false" tree="@Tree.t:data" weight="3.0"/>
<operator id="BayesianSkylineWilsonBalding.t:data" spec="WilsonBalding" tree="@Tree.t:data" weight="3.0"/>
<operator id="popSizesScaler.t:data" spec="ScaleOperator" parameter="@bPopSizes.t:data" scaleFactor="0.75" weight="15.0"/>
<operator id="groupSizesDelta.t:data" spec="DeltaExchangeOperator" integer="true" weight="6.0">
<intparameter idref="bGroupSizes.t:data"/>
</operator>
<operator id="FrequenciesExchanger.s:data" spec="DeltaExchangeOperator" delta="0.01" weight="0.1">
<parameter idref="freqParameter.s:data"/>
</operator>
<logger id="tracelog" fileName="data.log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
<log idref="posterior"/>
<log idref="likelihood"/>
<log idref="prior"/>
<log idref="treeLikelihood.data"/>
<log id="TreeHeight.t:data" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:data"/>
<log idref="kappa.s:data"/>
<!--
<log idref="ucldMean.c:data"/>
<log idref="ucldStdev.c:data"/>
-->
<log id="rate.c:data" spec="beast.evolution.branchratemodel.RateStatistic" branchratemodel="@RelaxedClock.c:data" tree="@Tree.t:data"/>
<log idref="B.prior"/>
<log idref="E.prior"/>
<log idref="H.prior"/>
<log idref="BayesianSkyline.t:data"/>
<log idref="bPopSizes.t:data"/>
<log idref="bGroupSizes.t:data"/>
<log idref="freqParameter.s:data"/>
<!-- CLOC -->
<parameter idref="ucldMean.E" name="log"/>
<parameter idref="ucldMean.H" name="log"/>
<parameter idref="ucldMean.B" name="log"/>
</logger>
<logger id="screenlog" logEvery="2000">
<log idref="posterior"/>
<log id="ESS.0" spec="util.ESS" arg="@posterior"/>
<log idref="likelihood"/>
<log idref="prior"/>
</logger>
<logger id="treelog.t:data" fileName="$(tree).trees" logEvery="1000" mode="tree">
<log id="TreeWithMetaDataLogger.t:data" spec="beast.evolution.tree.TreeWithMetaDataLogger" branchratemodel="@RelaxedClock.c:data" tree="@Tree.t:data"/>
</logger>
</run>
</beast>