<commit_before><?xml version="1.0" ?>
<beast>
    <!-- DATA SPECIFICATION -->
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        <taxon id="Ho"/>
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        <taxon id="Dr"/>
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    <treeModel id="treeModel">
        <tree idref="shortTree"/>
        <rootHeight>
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        </rootHeight>
        <nodeHeights internalNodes="true" rootNode="false">
            <parameter id="treeModel.internalNodeHeights"/>
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        <nodeHeights internalNodes="true" rootNode="true">
            <parameter id="treeModel.allInternalNodeHeights"/>
        </nodeHeights>
    </treeModel>

    <siteModel id="siteModel">
        <substitutionModel>
            <mutationDeathModel idref="intronModel"/>
        </substitutionModel>
        <mutationRate>
            <parameter id="overallRate" lower="0.0" value="1.0"/>
        </mutationRate>
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    <alsTreeLikelihood id="bdLikelihood" useScaling="false" useAmbiguities="true" integrateGainRate="true">
        <patterns idref="shortPatterns"/>
        <treeModel idref="treeModel"/>
        <siteModel idref="siteModel"/>
        <observationProcess type="anyTip"/>
        <!-- <observationProcess type="singleTip" taxon="Ho"/>   -->
    </alsTreeLikelihood>

    <exponentialBranchLengthsPrior id="treePrior">
        <treeModel idref="treeModel"/>
    </exponentialBranchLengthsPrior>
<commit_msg>Updated testBinaryDollo.xml to use new alsSiteModel parser.<commit_after><?xml version="1.0" ?>
<beast>
    <!-- DATA SPECIFICATION -->
    <taxa id="taxa">
        <taxon id="Ar"/>
        <taxon id="Ho"/>
        <taxon id="Ca"/>
        <taxon id="Dr"/>
        <taxon id="An"/>
    </taxa>

    <extendedDataType id="bdDataType">
        <extantState code="1"/>
        <deathState code="0"/>
        <!-- Exon not present -->
        <ambiguity code="U"/>
    </extendedDataType>

    <alignment id="short">
        <dataType idref="bdDataType"/>
        <!-- Dataset from: Current Biology (2003) 13:1512–1517. -->
        <sequence>
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{'dir': 'git-commits-cleaned', 'id': '6429435', 'n_tokens_mistral': 68832, 'n_tokens_neox': 5578, 'n_words': 294}