Stripped-down BEAUti template

gistfile1.txt

<beast version='2.0'
       namespace='beast.app.beauti:beast.core:beast.evolution.branchratemodel:beast.evolution.speciation:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood:beast.evolution:beast.math.distributions'
       templateinfo='template for structured coalescent analyses'>

       <map name='connect' reserved='true'>beast.app.beauti.BeautiConnector</map>
       <map name='subtemplate' reserved='true'>beast.app.beauti.BeautiSubTemplate</map>

       <beauticonfig spec='BeautiConfig'>

        <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.evolution.alignment.Alignment'
            />
        <panel spec='BeautiPanelConfig' panelname="Site Model" tiptext="Site model and substitution model specifications"
            path='siteModel'
            hasPartitions="SiteModel" icon='3.png.x' forceExpansion='TRUE'
            />

                <panel spec='BeautiPanelConfig' panelname="MCMC" tiptext="MCMC parameters"
            path=''
            hasPartitions="none" icon='9.png.x' forceExpansion='TRUE'
            />

                <alignmentProvider id="Add Alignment" spec='BeautiAlignmentProvider' template='@StandardPartitionTemplate'/>

        <partitiontemplate id='StandardPartitionTemplate' spec='BeautiSubTemplate' class='beast.evolution.likelihood.TreeLikelihood' mainid='mcmc'>
<![CDATA[

            <!-- site model                                                              -->
            <plugin spec='SiteModel' id="SiteModel.s:$(n)" gammaCategoryCount='0'>
                <!--substModel will be automatically detected /-->
                <substModel spec='JukesCantor'/>
                <proportionInvariant spec='parameter.RealParameter' id='proportionInvariant.s:$(n)' value='0.0' lower='0' upper='1' estimate='false'/>
                <mutationRate        spec='parameter.RealParameter' id='mutationRate.s:$(n)' value='1.0'        estimate='false'/>
                <shape               spec='parameter.RealParameter' id='gammaShape.s:$(n)' value='1.0'         estimate='false'/>
            </plugin>

            <plugin spec='TreeLikelihood' 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' value='1.0' estimate='false'/>
                </branchRateModel>
            </plugin>

            <!-- tree and its properties -->
            <plugin spec='beast.evolution.tree.RandomTree' id='Tree.t:$(n)' estimate='true'>
                <taxa spec='Alignment' idref='data'/>
                <populationModel id='ConstantPopulation0.t:$(n)' spec='ConstantPopulation'>
                        <popSize id='randomPopSize.t:$(n)' spec='parameter.RealParameter' value='1'/>
                    </populationModel>
            </plugin>

]]>
            <connect srcID='treeLikelihood.$(n)'            targetID='likelihood' inputName='distribution' if="isInitializing"/>
                        <connect method="beast.app.beauti.SiteModelInputEditor.customConnector"/>
            <connect srcID='Tree.t:$(n)'                targetID='mcmc' inputName='init'   if='inposterior(Tree.t:$(n))'/>

            <connect srcID='Tree.t:$(n)'                      targetID='state' inputName='stateNode' if='inposterior(Tree.t:$(n))'/>
        </partitiontemplate>

    </beauticonfig>


<!--
<operator spec='DeltaExchangeOperator' id='FixMeanRatesOperator' weight='2' delta='0.75'/>
-->

<!-- framework for main model -->

    <run spec="MCMC" id="mcmc" chainLength="10000000">

        <state storeEvery='5000' id='state'>
        </state>

        <distribution spec="CompoundDistribution" id="posterior">
            <distribution spec="CompoundDistribution" id="prior">
            </distribution>
            <distribution spec="CompoundDistribution" id="likelihood">
            </distribution>
        </distribution>

        <logger id='tracelog' logEvery="1000" fileName="$(filebase).log">
            <log idref="posterior"/>
            <log idref="likelihood"/>
            <log idref="prior"/>
        </logger>

        <logger id='screenlog' logEvery="1000">
                <!--model idref='posterior'/-->
            <log idref="posterior"/>
            <ESS spec='ESS' name='log' arg="@posterior"/>
            <log idref="likelihood"/>
            <log idref="prior"/>
        </logger>
    </run>

</beast>