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Standard.xml
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<beast version='2.0'
namespace='beastfx.app.beauti:beastfx.app.inputeditor:beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.branchratemodel:beast.base.evolution.speciation:beast.base.evolution.tree.coalescent:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood:beast.evolution:beast.base.inference.distribution'
templateinfo='template for standard phylogenetic analysis,<br> supporting tip-date analysis and calibrations'>
<map name='connect' reserved='true'>beastfx.app.inputeditor.BeautiConnector</map>
<map name='subtemplate' reserved='true'>beastfx.app.inputeditor.BeautiSubTemplate</map>
<map name='Uniform'>beast.base.inference.distribution.Uniform</map>
<map name='Normal'>beast.base.inference.distribution.Normal</map>
<map name='OneOnX'>beast.base.inference.distribution.OneOnX</map>
<map name='LogNormal'>beast.base.inference.distribution.LogNormalDistributionModel</map>
<map name='Exponential'>beast.base.inference.distribution.Exponential</map>
<map name='Gamma'>beast.base.inference.distribution.Gamma</map>
<map name='Beta'>beast.base.inference.distribution.Beta</map>
<map name='LaplaceDistribution'>beast.base.inference.distribution.LaplaceDistribution</map>
<map name='InverseGamma'>beast.base.inference.distribution.InverseGamma</map>
<map name='prior'>beast.base.inference.distribution.Prior</map>
<beauticonfig spec='BeautiConfig'
inputLabelMap='beast.base.inference.MCMC.operator=Operators,
beast.base.inference.MCMC.logger=Loggers,
beast.base.evolution.sitemodel.SiteModel.mutationRate =Substitution Rate,
beast.base.evolution.speciation.YuleModel.birthDiffRate=Birth Rate,
beast.base.evolution.branchratemodel.UCRelaxedClockModel.clock.rate=Mean clock rate,
beast.base.evolution.branchratemodel.StrictClockModel.clock.rate=Mean clock rate,
beast.base.evolution.branchratemodel.RandomLocalClockModel.clock.rate=Mean clock rate
'
inlinePlugins ='beast.base.inference.MCMC.distribution,
beast.base.evolution.sitemodel.SiteModel.substModel,
beast.base.evolution.tree.coalescent.ExponentialGrowth,
beast.base.evolution.tree.coalescent.ConstantPopulation,
beast.base.evolution.tree.coalescent.Coalescent,
beast.base.inference.State.stateNode'
collapsedPlugins ='beast.base.inference.MCMC.logger'
suppressPlugins = 'beast.base.inference.MCMC.operator,
beast.base.inference.MCMC.operatorschedule,
beast.base.inference.OperatorSchedule.subschedule,
beast.base.inference.OperatorSchedule.operatorPattern,
beast.base.inference.OperatorSchedule.operator,
beast.base.evolution.tree.coalescent.Coalescent.treeIntervals,
beast.base.evolution.tree.coalescent.Coalescent.tree,
beast.base.inference.MCMC.state,
beast.base.inference.MCMC.distribution,
beast.base.inference.MCMC.init,
beast.base.evolution.speciation.BirthDeathGernhard08Model.treeIntervals,
beast.base.evolution.speciation.BirthDeathGernhard08Model.tree,
beast.base.evolution.speciation.BirthDeathGernhard08Model.sampleProbability,
beast.base.evolution.speciation.YuleModel.treeIntervals,
beast.base.evolution.speciation.YuleModel.useTipDates,
beast.base.evolution.speciation.YuleModel.tree,
beast.base.evolution.tree.Tree,
beast.base.evolution.tree.Tree.trait,
beast.base.evolution.tree.Tree.taxa,
beast.base.evolution.tree.Tree.taxonset,
beast.base.evolution.tree.Tree.nodetype,
beast.base.evolution.tree.coalescent.RandomTree.trait,
beast.base.evolution.tree.coalescent.RandomTree.initial,
beast.base.evolution.tree.coalescent.RandomTree.taxa,
beast.base.evolution.tree.coalescent.RandomTree.taxonset,
beast.base.evolution.tree.coalescent.RandomTree.estimate,
beast.base.evolution.tree.coalescent.RandomTree.nodetype,
beast.base.evolution.tree.TreeParser.initial,
beast.base.evolution.tree.TreeParser.taxa,
beast.base.evolution.tree.TreeParser.taxonset,
beast.base.evolution.tree.TreeParser.trait,
beast.base.evolution.tree.TreeParser.estimate,
beast.base.evolution.tree.TreeParser.nodetype,
beast.base.evolution.tree.ClusterTree.initial,
beast.base.evolution.tree.ClusterTree.taxa,
beast.base.evolution.tree.ClusterTree.taxonset,
beast.base.evolution.tree.ClusterTree.trait,
beast.base.evolution.tree.ClusterTree.estimate,
beast.base.evolution.tree.ClusterTree.nodetype,
beast.base.evolution.tree.ClusterTree.distance,
beast.base.evolution.substitutionmodel.WAG.rates,
beast.base.evolution.substitutionmodel.WAG.frequencies,
beast.base.evolution.substitutionmodel.JTT.rates,
beast.base.evolution.substitutionmodel.JTT.frequencies,
beast.base.evolution.substitutionmodel.Blosum62.rates,
beast.base.evolution.substitutionmodel.Blosum62.frequencies,
beast.base.evolution.substitutionmodel.Dayhoff.rates,
beast.base.evolution.substitutionmodel.Dayhoff.frequencies,
beast.base.evolution.substitutionmodel.CPREV.rates,
beast.base.evolution.substitutionmodel.CPREV.frequencies,
beast.base.evolution.substitutionmodel.MTREV.rates,
beast.base.evolution.substitutionmodel.MTREV.frequencies,
beast.base.evolution.substitutionmodel.GTR.rates,
beast.base.evolution.substitutionmodel.JukesCantor.frequencies,
beast.base.inference.distribution.Prior.x,
beast.base.evolution.tree.MRCAPrior.tree,
beast.base.evolution.tree.MRCAPrior.monophyletic,
beast.base.evolution.tree.MRCAPrior.taxonset,
beast.base.evolution.branchratemodel.UCRelaxedClockModel.tree,
beast.base.evolution.branchratemodel.UCRelaxedClockModel.rateCategories,
beast.base.evolution.branchratemodel.UCRelaxedClockModel.distr,
beast.base.evolution.branchratemodel.RandomLocalClockModel.tree,
beast.base.evolution.branchratemodel.RandomLocalClockModel.meanRate,
beast.base.evolution.branchratemodel.RandomLocalClockModel.indicators,
beast.base.evolution.operator.ScaleOperator.indicator,
beast.base.inference.Operator.weight,
beast.base.inference.Logger.model,
beast.base.evolution.tree.coalescent.BayesianSkyline.treeIntervals,
beast.base.evolution.tree.coalescent.BayesianSkyline.tree,
beast.base.evolution.speciation.YuleModel.originHeight,
beast.base.inference.parameter.RealParameter.keys,
beast.base.inference.parameter.BooleanParameter.keys,
beast.base.inference.parameter.IntegerParameter.keys,
beast.base.inference.parameter.CompoundRealParameter.keys
'
hmc='BirthDeath/index/,
RandomTree/rootHeight/,
RandomTree/adjustTreeNodeHeights/,
StrictClock/clock.rate/,
FrequenciesExchanger/weightvector/,
FrequenciesExchanger/delta/,
FrequenciesExchanger/integer/,
FrequenciesExchanger/weight/,
FrequenciesExchanger/autoOptimize/,
BayesianSkyline/index/,
ConstantPopulation0/popSize/,
mcmc/numInitializationAttempts/,
mcmc/preBurnin/,
mcmc/storeEvery/,
mcmc/operatorschedule/,
mcmc/chainLength/,
mcmc/sampleFromPrior/,
tracelog/fileName/,
tracelog/sort/,
tracelog/sanitiseHeaders/,
tracelog/logEvery/,
tracelog/mode/,
ExtendedBayesianSkyline/index/,
CalibratedYuleModel/index/,
treeLikelihood/siteModel/,
treeLikelihood/branchRateModel/,
OperatorSchedule/detailedRejection/,
OperatorSchedule/autoOptimizeDelay/,
OperatorSchedule/transform/,
OperatorSchedule/weight/,
OperatorSchedule/weightIsPercentage/,
OperatorSchedule/autoOptimize/,
screenlog/fileName/,
screenlog/sort/,
screenlog/sanitiseHeaders/,
screenlog/logEvery/,
screenlog/mode/,
CoalescentExponential/index/,
NewickTree/adjustTipHeights/,
NewickTree/newick/,
NewickTree/IsLabelledNewick/,
NewickTree/adjustTreeNodeHeights/,
NewickTree/offset/,
NewickTree/threshold/,
NewickTree/scale/,
NewickTree/binarizeMultifurcations/,
NewickTree/singlechild/,
MarkovChainedPopSizes/reverse/,
MarkovChainedPopSizes/parameter/,
MarkovChainedPopSizes/uselog/,
MarkovChainedPopSizes/jeffreys/,
MarkovChainedPopSizes/shape/,
MarkovChainedPopSizes/initialMean/,
MarkovChainedPopSizes/useLogNormal/,
Standard/Operators/,
Standard/Priors/,
Standard/Clock_Model/,
Standard/MCMC/,
Standard/Partitions/,
Standard/Tip_Dates/,
Standard/Site_Model/,
Standard/Initialization/,
Standard/Starting_tree/,
birthRate/estimate/,
birthRate/dimension/,
birthRate/lower/,
birthRate/minordimension/,
birthRate/keys/,
birthRate/upper/,
treelog/fileName/,
treelog/sort/,
treelog/sanitiseHeaders/,
treelog/logEvery/,
treelog/mode/,
CoalescentConstant/index/,
YuleModel/index/,
ClusterTree/clock.rate/,
ClusterTree/adjustTreeNodeHeights/,
ClusterTree/clusterType/,
'
buttonLabelMap='beastfx.app.beauti.BeautiInitDlg.>> details=Edit parameters'
>
<!--disableMenus='Mode'-->
<panel spec='BeautiPanelConfig' panelname="Partitions" tiptext="Data Partitions"
path='distribution/distribution[id="likelihood"]/distribution/data'
hasPartitions="none" icon='2220.png.x' forceExpansion='FALSE'
type='beast.base.evolution.alignment.Alignment'
/>
<mergepoint id='aux-partitions-panels'/>
<panel spec='BeautiPanelConfig' panelname="Tip Dates" tiptext="Allows to specify data that a taxon was sampled"
path='tree'
hasPartitions="Tree" icon='2.png.x' forceExpansion='TRUE'
isVisible='true'
/>
<mergepoint id='aux-tipdates-panels'/>
<panel spec='BeautiPanelConfig' panelname="Site Model" tiptext="Site model and substitution model specifications"
path='siteModel'
hasPartitions="SiteModel" icon='3.png.x' forceExpansion='TRUE'
/>
<mergepoint id='aux-sitemodel-panels'/>
<panel spec='BeautiPanelConfig' panelname="Clock Model" tiptext="Clock model"
path='branchRateModel'
hasPartitions="ClockModel" icon='4.png.x' forceExpansion='TRUE'
/>
<mergepoint id='aux-clockmodel-panels'/>
<panel spec='BeautiPanelConfig' panelname="Initialization" tiptext="Initial state"
path='state/stateNode'
hasPartitions="none" icon='6.png.x' forceExpansion='TRUE_START_COLLAPSED'
isVisible='false'
/>
<mergepoint id='aux-initilisation-panels'/>
<panel spec='BeautiPanelConfig' panelname="Starting tree" tiptext="Starting tree"
path='init'
hasPartitions="none" icon='6.png.x' forceExpansion='TRUE'
isVisible='false'
/>
<panel spec='BeautiPanelConfig' panelname="Priors" tiptext="Other priors"
path='distribution/distribution[id="prior"]/distribution'
hasPartitions="none" icon='7.png.x' forceExpansion='TRUE_START_COLLAPSED'
type='beast.base.inference.Distribution'
/>
<mergepoint id='aux-priors-panels'/>
<panel spec='BeautiPanelConfig' panelname="Operators" tiptext="MCMC Operator details"
path='operator'
hasPartitions="none" icon='8.png.x' forceExpansion='TRUE_START_COLLAPSED'
isVisible='false' buttonStatus='ADD_ONLY'
/>
<mergepoint id='aux-operators-panels'/>
<panel spec='BeautiPanelConfig' panelname="MCMC" tiptext="MCMC parameters"
path=''
hasPartitions="none" icon='9.png.x' forceExpansion='TRUE'
/>
<mergepoint id='aux-panels'/>
<alignmentProvider id="Import Alignment" spec='BeautiAlignmentProvider' template='@StandardPartitionTemplate'/>
<partitiontemplate id='StandardPartitionTemplate' spec='BeautiSubTemplate' class='beast.base.evolution.likelihood.ThreadedTreeLikelihood' mainid='mcmc'>
<![CDATA[
<!-- site model -->
<plugin spec='SiteModel' id="SiteModel.s:$(n)" gammaCategoryCount='0'>
<!--substModel will be automatically detected /-->
<proportionInvariant spec='parameter.RealParameter' id='proportionInvariant.s:$(n)' value='0.0' lower='0' upper='1' estimate='false'/>
<mutationRate spec='parameter.RealParameter' id='mutationRate.s:$(n)' value='1.0' lower="0.0" estimate='false'/>
<shape spec='parameter.RealParameter' id='gammaShape.s:$(n)' value='1.0' lower='0.1' estimate='false'/>
</plugin>
<plugin spec='ThreadedTreeLikelihood' id="treeLikelihood.$(n)">
<data idref="data"/>
<tree idref="Tree.t:$(n)"/>
<siteModel idref="SiteModel.s:$(n)"/>
<branchRateModel spec='StrictClockModel' id='StrictClock.c:$(n)'>
<clock.rate id='clockRate.c:$(n)' spec='parameter.RealParameter' lower="0.0" value='1.0' estimate='false'/>
</branchRateModel>
</plugin>
<prior id='ClockPrior.c:$(n)' x='@clockRate.c:$(n)'><distr spec="beast.base.inference.distribution.Uniform" upper='Infinity'/></prior>
<prior id='MutationRatePrior.s:$(n)' x='@mutationRate.s:$(n)'><distr spec="OneOnX"/></prior>
<!-- tree and its properties -->
<taxonset id='TaxonSet.$(n)' spec='beast.base.evolution.alignment.TaxonSet' alignment='@$(n)' />
<plugin spec='beast.base.evolution.tree.Tree' id='Tree.t:$(n)' taxonset='@TaxonSet.$(n)'/>
<!--plugin spec='beast.base.evolution.tree.coalescent.RandomTree' id='RandomTree.t:$(n)' estimate='false' trait='@datetrait.$(n)' initial='@Tree.t:$(n)'-->
<plugin spec='beast.base.evolution.tree.coalescent.RandomTree' id='RandomTree.t:$(n)' estimate='false' initial='@Tree.t:$(n)'>
<taxa idref='data'/>
<populationModel id='ConstantPopulation0.t:$(n)' spec='ConstantPopulation'>
<popSize id='randomPopSize.t:$(n)' spec='parameter.RealParameter' value='1'/>
</populationModel>
</plugin>
<!-- default tree prior -->
<plugin spec='YuleModel' id="YuleModel.t:$(n)" tree='@Tree.t:$(n)'>
<parameter name='birthDiffRate' id="birthRate.t:$(n)" lower="0.0" value='1.0' estimate='true'/>
</plugin>
<plugin id='TreeHeight.t:$(n)' spec='beast.base.evolution.tree.TreeStatLogger' tree='@Tree.t:$(n)'/>
<logger id='treelog.t:$(n)' spec='beast.base.inference.Logger' logEvery="1000" fileName="$(filebase)-$(tree).trees" mode='tree'>
<log id='TreeWithMetaDataLogger.t:$(n)' spec='beast.base.evolution.TreeWithMetaDataLogger' tree='@Tree.t:$(n)'>
</log>
</logger>
<operator id='allTipDatesRandomWalker.t:$(n)' spec='TipDatesRandomWalker' windowSize="1" weight="0" tree="@Tree.t:$(n)"/>
<operator id="YuleModelBICEPSEpochTop.t:$(n)" spec="beast.base.evolution.operator.EpochFlexOperator" tree="@Tree.t:$(n)" weight="2.0" scaleFactor="0.1"/>
<operator id="YuleModelBICEPSEpochAll.t:$(n)" spec="beast.base.evolution.operator.EpochFlexOperator" tree="@Tree.t:$(n)" weight="2.0" scaleFactor="0.1" fromOldestTipOnly="false"/>
<operator id="YuleModelBICEPSTreeFlex.t:$(n)" spec="beast.base.evolution.operator.TreeStretchOperator" scaleFactor="0.01" tree="@Tree.t:$(n)" weight="2.0"/>
<operator id='YuleModelTreeRootScaler.t:$(n)' spec='kernel.BactrianScaleOperator' scaleFactor="0.5" weight="3" tree="@Tree.t:$(n)" rootOnly='true'/>
<operator id='YuleModelUniformOperator.t:$(n)' spec='kernel.BactrianNodeOperator' weight="30" tree="@Tree.t:$(n)"/>
<operator id='YuleModelSubtreeSlide.t:$(n)' spec='kernel.BactrianSubtreeSlide' weight="15" size="1.0" tree="@Tree.t:$(n)"/>
<operator id='YuleModelNarrow.t:$(n)' spec='Exchange' isNarrow='true' weight="15" tree="@Tree.t:$(n)"/>
<operator id='YuleModelWide.t:$(n)' spec='Exchange' isNarrow='false' weight="3" tree="@Tree.t:$(n)"/>
<operator id='YuleModelWilsonBalding.t:$(n)' spec='WilsonBalding' weight="3" tree="@Tree.t:$(n)"/>
<prior id='YuleBirthRatePrior.t:$(n)' x='@birthRate.t:$(n)'><distr spec="beast.base.inference.distribution.Uniform" lower='0' upper='Infinity'/></prior>
<prior id='GammaShapePrior.s:$(n)' x='@gammaShape.s:$(n)'><distr spec="beast.base.inference.distribution.Exponential"><mean spec="parameter.RealParameter" estimate="false" value="1.0"/></distr></prior>
<prior id='PropInvariantPrior.s:$(n)' x='@proportionInvariant.s:$(n)'><distr spec="beast.base.inference.distribution.Uniform" lower='0' upper='1'/></prior>
<operator id='YuleBirthRateScaler.t:$(n)' spec='kernel.BactrianScaleOperator' scaleFactor="0.75" weight="3" parameter="@birthRate.t:$(n)"/>
<operator id="AVMNOperator.$(n)" spec="beast.base.evolution.operator.kernel.AdaptableVarianceMultivariateNormalOperator" weight="0.1"
coefficient="1.0"
scaleFactor="1"
beta="0.05"
initial="800"
burnin="400"
every="1" allowNonsense="true">
<transformations id="AVMNSumTransform.$(n)" spec="beast.base.inference.operator.kernel.Transform$LogConstrainedSumTransform" sum="1.0">
<!-- frequencies -->
</transformations>
<transformations id="AVMNLogTransform.$(n)" spec="beast.base.inference.operator.kernel.Transform$LogTransform">
<!-- site and substitution model parameters -->
</transformations>
<transformations id="AVMNNoTransform.$(n)" spec="beast.base.inference.operator.kernel.Transform$NoTransform">
<!-- tree -->
</transformations>
</operator>
<operator id="StrictClockRateScaler.c:$(n)" spec="beast.base.evolution.operator.AdaptableOperatorSampler" weight="1.5">
<parameter idref="clockRate.c:$(n)"/>
<operator idref="AVMNOperator.$(n)"/>
<operator id='StrictClockRateScalerX.c:$(n)' spec='kernel.BactrianScaleOperator' scaleFactor="0.75" weight="3" parameter='@clockRate.c:$(n)'/>
</operator>
<operator id="strictClockUpDownOperator.c:$(n)" spec="beast.base.evolution.operator.AdaptableOperatorSampler" weight="1.5">
<parameter idref="clockRate.c:$(n)"/>
<tree idref="Tree.t:$(n)"/>
<operator idref="AVMNOperator.$(n)"/>
<operator id='strictClockUpDownOperatorX.c:$(n)' spec='kernel.BactrianUpDownOperator' scaleFactor="0.75" weight="3">
<up idref="clockRate.c:$(n)"/>
<down idref="Tree.t:$(n)"/>
</operator>
</operator>
<operator id="proportionInvariantScaler.s:$(n)" spec="beast.base.evolution.operator.AdaptableOperatorSampler" weight="0.05">
<parameter idref="proportionInvariant.s:$(n)"/>
<operator idref="AVMNOperator.$(n)"/>
<operator id='proportionInvariantScalerX.s:$(n)' spec='kernel.BactrianScaleOperator' scaleFactor="0.5" weight="0.1" parameter="@proportionInvariant.s:$(n)"/>
</operator>
<operator id="mutationRateScaler.s:$(n)" spec="beast.base.evolution.operator.AdaptableOperatorSampler" weight="0.05">
<parameter idref="mutationRate.s:$(n)"/>
<operator idref="AVMNOperator.$(n)"/>
<operator id='mutationRateScalerX.s:$(n)' spec='kernel.BactrianScaleOperator' scaleFactor="0.5" weight="0.1" parameter="@mutationRate.s:$(n)"/>
</operator>
<operator id="gammaShapeScaler.s:$(n)" spec="beast.base.evolution.operator.AdaptableOperatorSampler" weight="0.05">
<parameter idref="gammaShape.s:$(n)"/>
<operator idref="AVMNOperator.$(n)"/>
<operator id='gammaShapeScalerX.s:$(n)' spec='kernel.BactrianScaleOperator' scaleFactor="0.5" weight="0.1" parameter="@gammaShape.s:$(n)"/>
</operator>
]]>
<connect srcID='treeLikelihood.$(n)' targetID='likelihood' inputName='distribution' if="isInitializing"/>
<connect srcID='YuleModel.t:$(n)' targetID='prior' inputName='distribution' if="isInitializing"/>
<connect method="beastfx.app.inputeditor.SiteModelInputEditor.customConnector"/>
<!-- for deciding whether to connect the mean clock rate to the AVMN operator -->
<connect method="beastfx.app.inputeditor.SiteModelInputEditor.avmnConnector"/>
<connect srcID='treelog.t:$(n)' targetID='mcmc' inputName='logger' if='inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'/>
<connect srcID='RandomTree.t:$(n)' targetID='mcmc' inputName='init' if='isInitializing'/>
<connect method="beastfx.app.beauti.StateNodeInitialiserListInputEditor.customConnector"/>
<connect srcID='ClockPrior.c:$(n)' targetID='prior' inputName='distribution' if='inlikelihood(clockRate.c:$(n)) and clockRate.c:$(n)/estimate=true'/>
<!-- when FixMeanMutationRatesOperator, the prior is uniform due to the operator -->
<connect srcID='MutationRatePrior.s:$(n)' targetID='prior' inputName='distribution' if='nooperator(FixMeanMutationRatesOperator) and inlikelihood(mutationRate.s:$(n)) and mutationRate.s:$(n)/estimate=true'/>
<connect srcID='Tree.t:$(n)' targetID='state' inputName='stateNode' if='inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'/>
<connect srcID='proportionInvariant.s:$(n)' targetID='state' inputName='stateNode' if='inlikelihood(proportionInvariant.s:$(n)) and proportionInvariant.s:$(n)/estimate=true'/>
<connect srcID='mutationRate.s:$(n)' targetID='state' inputName='stateNode' if='inlikelihood(mutationRate.s:$(n)) and mutationRate.s:$(n)/estimate=true'/>
<connect srcID='gammaShape.s:$(n)' targetID='state' inputName='stateNode' if='inlikelihood(gammaShape.s:$(n)) and gammaShape.s:$(n)/estimate=true'/>
<connect srcID='clockRate.c:$(n)' targetID='state' inputName='stateNode' if='inlikelihood(clockRate.c:$(n)) and clockRate.c:$(n)/estimate=true'/>
<connect srcID='birthRate.t:$(n)' targetID='state' inputName='stateNode' if='inposterior(YuleModel.t:$(n)) and inposterior(Tree.t:$(n)) and birthRate.t:$(n)/estimate=true'/>
<connect srcID='Tree.t:$(n)' targetID='AVMNNoTransform.$(n)' inputName='f' if='inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'/>
<connect srcID='proportionInvariant.s:$(n)' targetID='AVMNLogTransform.$(n)' inputName='f' if='inlikelihood(proportionInvariant.s:$(n)) and proportionInvariant.s:$(n)/estimate=true'/>
<connect srcID='mutationRate.s:$(n)' targetID='AVMNLogTransform.$(n)' inputName='f' if='nooperator(FixMeanMutationRatesOperator) and inlikelihood(mutationRate.s:$(n)) and mutationRate.s:$(n)/estimate=true'/>
<connect srcID='gammaShape.s:$(n)' targetID='AVMNLogTransform.$(n)' inputName='f' if='inlikelihood(gammaShape.s:$(n)) and gammaShape.s:$(n)/estimate=true'/>
<connect srcID='proportionInvariantScaler.s:$(n)' targetID='mcmc' inputName='operator' if='inlikelihood(proportionInvariant.s:$(n)) and proportionInvariant.s:$(n)/estimate=true'>Scales proportion of invariant sites parameter of partition $(n)</connect>
<connect srcID='mutationRateScaler.s:$(n)' targetID='mcmc' inputName='operator' if='nooperator(FixMeanMutationRatesOperator) and inlikelihood(mutationRate.s:$(n)) and mutationRate.s:$(n)/estimate=true'>Scales mutation rate of partition s:$(n)</connect>
<connect srcID='gammaShapeScaler.s:$(n)' targetID='mcmc' inputName='operator' if='inlikelihood(gammaShape.s:$(n)) and gammaShape.s:$(n)/estimate=true'>Scales gamma shape parameter of partition s:$(n)</connect>
<connect srcID='StrictClockRateScaler.c:$(n)' targetID='mcmc' inputName='operator' if='inlikelihood(clockRate.c:$(n)) and clockRate.c:$(n)/estimate=true'>Scale clock rate of partition c:$(n)</connect>
<connect srcID='YuleBirthRateScaler.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(birthRate.t:$(n)) and birthRate.t:$(n)/estimate=true'>Scales birth rate of Yule prior for partition t:$(n)</connect>
<connect srcID='strictClockUpDownOperator.c:$(n)' targetID='mcmc' inputName='operator'
if='inlikelihood(clockRate.c:$(n)) and inlikelihood(Tree.t:$(n)) and Tree.t:$(n)/estimate=true and clockRate.c:$(n)/estimate=true'>
Scale up substitution rate c:$(n) and scale down tree t:($n)
</connect>
<connect srcID='allTipDatesRandomWalker.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true and allTipDatesRandomWalker.t:$(n)/weight!=0.0'>Estimates tip dates for tree t:$(n)</connect>
<!--
TreeScaler is replaced with more efficient BICESPS operators.
<connect srcID="YuleModelTreeScaler.t:$(n)" targetID="mcmc" inputName="operator" if="inposterior(YuleModel.t:$(n)) and Tree.t:$(n)/estimate=true" >Scales all internal nodes for tree t:$(n)</connect>
-->
<connect srcID="YuleModelTreeRootScaler.t:$(n)" targetID="mcmc" inputName="operator" if="inposterior(YuleModel.t:$(n)) and Tree.t:$(n)/estimate=true" >Scales root node for tree t:$(n)</connect>
<connect srcID="YuleModelUniformOperator.t:$(n)" targetID="mcmc" inputName="operator" if="inposterior(YuleModel.t:$(n)) and Tree.t:$(n)/estimate=true" >Draws new internal node heights uniformally for tree t:$(n)</connect>
<connect srcID="YuleModelSubtreeSlide.t:$(n)" targetID="mcmc" inputName="operator" if="inposterior(YuleModel.t:$(n)) and Tree.t:$(n)/estimate=true" >Performs subtree slide rearrangement of tree t:$(n)</connect>
<connect srcID="YuleModelNarrow.t:$(n)" targetID="mcmc" inputName="operator" if="inposterior(YuleModel.t:$(n)) and Tree.t:$(n)/estimate=true" >Narrow exchange performs local rearrangement of tree t:$(n)</connect>
<connect srcID="YuleModelWide.t:$(n)" targetID="mcmc" inputName="operator" if="inposterior(YuleModel.t:$(n)) and Tree.t:$(n)/estimate=true" >Wide exchange performs global rearrangement of tree t:$(n)</connect>
<connect srcID="YuleModelWilsonBalding.t:$(n)" targetID="mcmc" inputName="operator" if="inposterior(YuleModel.t:$(n)) and Tree.t:$(n)/estimate=true" >Performs Wilson-Balding global rearrangement of tree t:$(n)</connect>
<connect srcID='YuleModelBICEPSEpochTop.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(YuleModel.t:$(n)) and Tree.t:$(n)/estimate=true'>Epoch operator that only scale internal nodes above least recent node for tree t:$(n)</connect>
<connect srcID='YuleModelBICEPSEpochAll.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(YuleModel.t:$(n)) and Tree.t:$(n)/estimate=true'>Epoch operator that scales all internal nodes for tree t:$(n)</connect>
<connect srcID='YuleModelBICEPSTreeFlex.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(YuleModel.t:$(n)) and Tree.t:$(n)/estimate=true'>Flex operators for all internal nodes for tree t:$(n)</connect>
<connect srcID='treeLikelihood.$(n)' targetID='tracelog' inputName='log' if='inlikelihood(treeLikelihood.$(n))'/>
<connect srcID='TreeHeight.t:$(n)' targetID='tracelog' inputName='log' if='inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'/>
<connect srcID='proportionInvariant.s:$(n)' targetID='tracelog' inputName='log' if='inposterior(proportionInvariant.s:$(n)) and proportionInvariant.s:$(n)/estimate=true'/>
<connect srcID='mutationRate.s:$(n)' targetID='tracelog' inputName='log' if='inlikelihood(mutationRate.s:$(n)) and mutationRate.s:$(n)/estimate=true'/>
<connect srcID='gammaShape.s:$(n)' targetID='tracelog' inputName='log' if='inlikelihood(gammaShape.s:$(n)) and gammaShape.s:$(n)/estimate=true'/>
<connect srcID='clockRate.c:$(n)' targetID='tracelog' inputName='log' if='inlikelihood(clockRate.c:$(n)) and clockRate.c:$(n)/estimate=true'/>
<connect srcID='YuleModel.t:$(n)' targetID='tracelog' inputName='log' if='inposterior(YuleModel.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'/>
<connect srcID='birthRate.t:$(n)' targetID='tracelog' inputName='log' if='inposterior(YuleModel.t:$(n)) and birthRate.t:$(n)/estimate=true'/>
<connect srcID='GammaShapePrior.s:$(n)' targetID='prior' inputName='distribution' if='inlikelihood(gammaShape.s:$(n)) and gammaShape.s:$(n)/estimate=true'>Prior on gamma shape for partition s:$(n)</connect>
<connect srcID='PropInvariantPrior.s:$(n)' targetID='prior' inputName='distribution' if='inlikelihood(proportionInvariant.s:$(n)) and proportionInvariant.s:$(n)/estimate=true'>Prior on proportion invariant for partition s:$(n)</connect>
<connect srcID='YuleBirthRatePrior.t:$(n)' targetID='prior' inputName='distribution' if='inposterior(YuleModel.t:$(n)) and inposterior(Tree.t:$(n)) and birthRate.t:$(n)/estimate=true'>Prior on Yule birth rate for partition s:$(n)</connect>
<mergepoint id='aux-partitiontemplate'/>
</partitiontemplate>
<mergepoint id='substModelTemplates'/>
<mergepoint id='clockModelTemplates'/>
<mergepoint id='treePriorTemplates'/>
<mergepoint id='parametricDistributions'/>
<!-- Tree initialisation -->
<!-- Random tree -->
<subtemplate id='RandomTree' class='beast.base.evolution.tree.coalescent.RandomTree' mainid='RandomTree.t:$(n)'>
<![CDATA[
<tree spec='beast.base.evolution.tree.coalescent.RandomTree' id='RandomTree.t:$(n)' estimate='false' initial="@Tree.t:$(n)">
<taxa idref='data'/>
<populationModel id='ConstantPopulation0.t:$(n)' spec='ConstantPopulation'>
<popSize id='randomPopSize.t:$(n)' spec='parameter.RealParameter' value='1'/>
</populationModel>
</tree>
]]>
</subtemplate>
<!-- Cluster tree (defaults to UPGMA) -->
<subtemplate id='ClusterTree' class='beast.base.evolution.tree.ClusterTree' mainid='ClusterTree.t:$(n)'>
<![CDATA[
<tree spec='beast.base.evolution.tree.ClusterTree' id='ClusterTree.t:$(n)' initial="@Tree.t:$(n)" clusterType='upgma' estimate='false' taxa='@$(n)'/>
]]>
</subtemplate>
<!-- Newick tree -->
<subtemplate id='NewickTree' class='beast.base.evolution.tree.TreeParser' mainid='NewickTree.t:$(n)'>
<![CDATA[
<tree_ spec='beast.base.evolution.tree.TreeParser' id='NewickTree.t:$(n)' initial="@Tree.t:$(n)" estimate='false' taxa='@$(n)' newick=""/>
]]>
</subtemplate>
<subtemplate id='DefaultOperatorSchedule' class='beast.base.inference.OperatorSchedule' mainid='OperatorSchedule'
>
<![CDATA[
<operatorschedule id="OperatorSchedule" spec="beast.base.inference.OperatorSchedule"/>
]]>
</subtemplate>
<subtemplate id='MCMC' class='beast.base.inference.MCMC' mainid='mcmc'
suppressInputs='
beast.base.inference.MCMC.operator,
beast.base.inference.MCMC.operatorschedule,
beast.base.inference.MCMC.state,
beast.base.inference.MCMC.distribution,
beast.base.inference.MCMC.init
'>
<![CDATA[
<run spec="beast.base.inference.MCMC" id="mcmc" chainLength="10000000">
<operatorschedule id="OperatorSchedule" spec="OperatorSchedule"/>
<state storeEvery='5000' id='state'>
</state>
<distribution spec="CompoundDistribution" id="posterior">
<distribution spec="CompoundDistribution" id="prior">
</distribution>
<distribution spec="CompoundDistribution" id="likelihood" useThreads="true">
</distribution>
</distribution>
<logger id='tracelog' logEvery="1000" fileName="$(filebase).log" sort="smart" sanitiseHeaders='true'>
<model idref='posterior'/>
<log idref="posterior"/>
<log idref="likelihood"/>
<log idref="prior"/>
</logger>
<logger id='screenlog' logEvery="1000">
<!--model idref='posterior'/-->
<log idref="posterior"/>
<!--this ESS is computed solely based on the current BEAST run (not the chain)-->
<!--<ESS spec='ESS' name='log' arg="@posterior"/>-->
<log idref="likelihood"/>
<log idref="prior"/>
</logger>
</run>
]]>
</subtemplate>
<mergepoint id='runnables'/>
</beauticonfig>
<mergepoint id='misc'/>
<!-- framework for main model -->
<run spec="MCMC" id="mcmc" chainLength="10000000">
<operatorschedule id="OperatorSchedule" spec="OperatorSchedule"/>
<state storeEvery='5000' id='state'>
</state>
<distribution spec="CompoundDistribution" id="posterior">
<distribution spec="CompoundDistribution" id="prior">
<mergepoint id='aux-priors'/>
</distribution>
<distribution spec="CompoundDistribution" id="likelihood" useThreads="true">
<mergepoint id='aux-likelihoods'/>
</distribution>
</distribution>
<logger id='tracelog' logEvery="1000" fileName="$(filebase).log" sort="smart" sanitiseHeaders='true'>
<model idref='posterior'/>
<log idref="posterior"/>
<log idref="likelihood"/>
<log idref="prior"/>
</logger>
<logger id='screenlog' logEvery="1000">
<!--model idref='posterior'/-->
<log idref="posterior"/>
<!--this ESS is computed solely based on the current BEAST run (not the chain)-->
<!--<ESS spec='ESS' name='log' arg="@posterior"/>-->
<log idref="likelihood"/>
<log idref="prior"/>
</logger>
</run>
</beast>