exponential_growth.xml

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!-- BEAST X XML Template for use with beastgen -->
<!-- BEAST X v10.5.0 / v1.10.5 format -->
<!-- This template generates a BEAST X analysis with:
     - HKY substitution model
     - Strict molecular clock
     - Exponential growth coalescent prior
     - Dated tips
-->
<beast version="1.10.5">

    <!-- Data section will be populated by beastgen from FASTA file -->
    <taxa id="taxa">
        <!-- Taxa will be populated from alignment -->
    </taxa>

    <alignment id="alignment" dataType="nucleotide">
        <!-- Sequences will be populated by beastgen from FASTA file -->
    </alignment>

    <!-- Dated tips - dates will be extracted from sequence names -->
    <tipDates>
        <taxa idref="taxa"/>
    </tipDates>

    <!-- The HKY substitution model -->
    <hkySiteModel id="siteModel">
        <frequencies>
            <frequencyModel id="freqModel" dataType="nucleotide">
                <alignment idref="alignment"/>
                <frequencies>
                    <parameter id="frequencies" value="0.25 0.25 0.25 0.25"/>
                </frequencies>
            </frequencyModel>
        </frequencies>
        <kappa>
            <parameter id="kappa" value="2.0" lower="0.0"/>
        </kappa>
    </hkySiteModel>

    <!-- Strict clock model -->
    <strictClockBranchRates id="branchRates">
        <rate>
            <parameter id="clock.rate" value="1.0" lower="0.0"/>
        </rate>
    </strictClockBranchRates>

    <!-- Exponential growth coalescent tree prior -->
    <coalescentTree id="startingTree">
        <taxa idref="taxa"/>
        <exponentialGrowth idref="exponential"/>
    </coalescentTree>

    <exponentialGrowth id="exponential" units="years">
        <populationSize>
            <parameter id="exponential.popSize" value="1.0" lower="0.0"/>
        </populationSize>
        <growthRate>
            <parameter id="exponential.growthRate" value="0.0"/>
        </growthRate>
    </exponentialGrowth>

    <!-- Tree likelihood -->
    <treeLikelihood id="treeLikelihood">
        <alignment idref="alignment"/>
        <treeModel idref="treeModel"/>
        <siteModel idref="siteModel"/>
        <strictClockBranchRates idref="branchRates"/>
    </treeLikelihood>

    <treeModel id="treeModel">
        <coalescentTree idref="startingTree"/>
        <rootHeight>
            <parameter id="treeModel.rootHeight"/>
        </rootHeight>
        <nodeHeights internalNodes="true">
            <parameter id="treeModel.internalNodeHeights"/>
        </nodeHeights>
        <nodeHeights internalNodes="true" rootNode="true">
            <parameter id="treeModel.allInternalNodeHeights"/>
        </nodeHeights>
    </treeModel>

    <!-- Coalescent prior -->
    <coalescentLikelihood id="coalescent">
        <model>
            <exponentialGrowth idref="exponential"/>
        </model>
        <populationTree>
            <treeModel idref="treeModel"/>
        </populationTree>
    </coalescentLikelihood>

    <!-- PRIORS -->
    <prior id="prior">
        <exponentialPrior mean="0.333" offset="0.0">
            <parameter idref="exponential.popSize"/>
        </exponentialPrior>
        
        <laplacePrior mean="0.0" scale="30.701135">
            <parameter idref="exponential.growthRate"/>
        </laplacePrior>
        
        <logNormalPrior mean="1.0" stdev="1.25" offset="0.0" meanInRealSpace="true">
            <parameter idref="kappa"/>
        </logNormalPrior>
        
        <uniformPrior lower="0.0" upper="1.0">
            <parameter idref="clock.rate"/>
        </uniformPrior>
    </prior>

    <!-- OPERATORS -->
    <operators id="operators" optimizationSchedule="log">
        <scaleOperator scaleFactor="0.75" weight="3">
            <parameter idref="exponential.popSize"/>
        </scaleOperator>
        
        <randomWalkOperator windowSize="1.0" weight="3">
            <parameter idref="exponential.growthRate"/>
        </randomWalkOperator>
        
        <scaleOperator scaleFactor="0.5" weight="0.1">
            <parameter idref="kappa"/>
        </scaleOperator>
        
        <deltaExchange delta="0.01" weight="0.1">
            <parameter idref="frequencies"/>
        </deltaExchange>
        
        <scaleOperator scaleFactor="0.75" weight="3">
            <parameter idref="clock.rate"/>
        </scaleOperator>
        
        <upDownOperator scaleFactor="0.75" weight="3">
            <up>
                <parameter idref="clock.rate"/>
            </up>
            <down>
                <parameter idref="treeModel.allInternalNodeHeights"/>
            </down>
        </upDownOperator>
        
        <scaleOperator scaleFactor="0.5" weight="3">
            <parameter idref="treeModel.rootHeight"/>
        </scaleOperator>
        
        <uniformOperator weight="30">
            <parameter idref="treeModel.internalNodeHeights"/>
        </uniformOperator>
        
        <subtreeSlide size="1.0" gaussian="true" weight="15">
            <treeModel idref="treeModel"/>
        </subtreeSlide>
        
        <narrowExchange weight="15">
            <treeModel idref="treeModel"/>
        </narrowExchange>
        
        <wideExchange weight="3">
            <treeModel idref="treeModel"/>
        </wideExchange>
        
        <wilsonBalding weight="3">
            <treeModel idref="treeModel"/>
        </wilsonBalding>
    </operators>

    <!-- MCMC -->
    <mcmc id="mcmc" chainLength="$(chain_length=10000000)" autoOptimize="true">
    <!-- MCMC -->
    <mcmc id="mcmc" chainLength="$(chain_length=10000000)" autoOptimize="true">
        <posterior id="posterior">
            <prior idref="prior"/>
            <likelihood id="likelihood">
                <treeLikelihood idref="treeLikelihood"/>
                <coalescentLikelihood idref="coalescent"/>
            </likelihood>
        </posterior>
        
        <operators idref="operators"/>

        <!-- write log to screen -->
        <log id="screenLog" logEvery="$(screen_every=10000)">
            <column label="Posterior" dp="4" width="12">
                <posterior idref="posterior"/>
            </column>
            <column label="Prior" dp="4" width="12">
                <prior idref="prior"/>
            </column>
            <column label="Likelihood" dp="4" width="12">
                <likelihood idref="likelihood"/>
            </column>
            <column label="rootHeight" sf="6" width="12">
                <parameter idref="treeModel.rootHeight"/>
            </column>
            <column label="clock.rate" sf="6" width="12">
                <parameter idref="clock.rate"/>
            </column>
        </log>

        <!-- write log to file -->
        <log id="fileLog" logEvery="$(log_every=1000)" fileName="beast_analysis.log" overwrite="false">
            <posterior idref="posterior"/>
            <prior idref="prior"/>
            <likelihood idref="likelihood"/>
            <parameter idref="treeModel.rootHeight"/>
            <parameter idref="exponential.popSize"/>
            <parameter idref="exponential.growthRate"/>
            <parameter idref="kappa"/>
            <parameter idref="frequencies"/>
            <parameter idref="clock.rate"/>
            <coalescentLikelihood idref="coalescent"/>
            <treeLikelihood idref="treeLikelihood"/>
            <tmrcaStatistic id="age.root" name="age(root)">
                <mrca>
                    <taxa idref="taxa"/>
                </mrca>
                <treeModel idref="treeModel"/>
            </tmrcaStatistic>
        </log>

        <!-- write tree log to file -->
        <logTree id="treeFileLog" logEvery="$(log_every=1000)" nexusFormat="true" fileName="beast_analysis.trees" sortTranslationTable="true">
            <treeModel idref="treeModel"/>
            <posterior idref="posterior"/>
        </logTree>

    </mcmc>

    <report>
        <property name="timer">
            <mcmc idref="mcmc"/>
        </property>
    </report>

</beast>