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brantfaircloth/beast_subs_models.xml

Created February 17, 2011 21:56
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Alternate substitution models for BEAST and *BEAST (xml fragments)
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beast_subs_models.xml
<!-- Juke it, baby, Juke it -->
<gtrModel id="JC69">
<frequencies>
<frequencyModel dataType="nucleotide">
<frequencies>
<!-- JC69 frequencies are equal -->
<parameter id="JC69.frequencies" value="0.25 0.25 0.25 0.25"/>
</frequencies>
</frequencyModel>
</frequencies>
<rateAC>
<parameter id="JC69.ac" value="1.0" lower="0.0" upper="Infinity"/>
</rateAC>
<rateAG>
<parameter id="JC69.ag" value="1.0" lower="0.0" upper="Infinity"/>
</rateAG>
<rateAT>
<parameter id="JC69.at" value="1.0" lower="0.0" upper="Infinity"/>
</rateAT>
<rateCG>
<parameter id="JC69.cg" value="1.0" lower="0.0" upper="Infinity"/>
</rateCG>
<rateGT>
<parameter id="JC69.gt" value="1.0" lower="0.0" upper="Infinity"/>
</rateGT>
</gtrModel>
<!-- F81 -->
<gtrModel id="F81">
<frequencies>
<frequencyModel dataType="nucleotide">
<frequencies>
<!-- F81 frequencies are variable -->
<parameter id="F81.frequencies" value="0.25 0.25 0.25 0.25"/>
</frequencies>
</frequencyModel>
</frequencies>
<rateAC>
<parameter id="F81.ac" value="1.0" lower="0.0" upper="Infinity"/>
</rateAC>
<rateAG>
<parameter id="F81.ag" value="1.0" lower="0.0" upper="Infinity"/>
</rateAG>
<rateAT>
<parameter id="F81.at" value="1.0" lower="0.0" upper="Infinity"/>
</rateAT>
<rateCG>
<parameter id="F81.cg" value="1.0" lower="0.0" upper="Infinity"/>
</rateCG>
<rateGT>
<parameter id="F81.gt" value="1.0" lower="0.0" upper="Infinity"/>
</rateGT>
</gtrModel>
<!-- The K2P (K80) substitution model (Kimura, 1980) -->
<HKYModel id="K2P">
<frequencies>
<frequencyModel dataType="nucleotide">
<frequencies>
<!-- K2P frequencies are all equal -->
<parameter id="K2P.frequencies" value="0.25 0.25 0.25 0.25"/>
</frequencies>
</frequencyModel>
</frequencies>
<kappa>
<parameter id="K2P.kappa" value="1.0" lower="0.0" upper="Infinity"/>
</kappa>
</HKYModel>
<!-- The general time reversible (SYM) substitution model -->
<gtrModel id="SYM">
<frequencies>
<frequencyModel dataType="nucleotide">
<frequencies>
<!-- SYM differs from GTR in that frequencies are all equal -->
<parameter id="SYM.frequencies" value="0.25 0.25 0.25 0.25"/>
</frequencies>
</frequencyModel>
</frequencies>
<rateAC>
<parameter id="SYM.ac" value="1.0" lower="0.0" upper="Infinity"/>
</rateAC>
<rateAG>
<parameter id="SYM.ag" value="1.0" lower="0.0" upper="Infinity"/>
</rateAG>
<rateAT>
<parameter id="SYM.at" value="1.0" lower="0.0" upper="Infinity"/>
</rateAT>
<rateCG>
<parameter id="SYM.cg" value="1.0" lower="0.0" upper="Infinity"/>
</rateCG>
<rateGT>
<parameter id="SYM.gt" value="1.0" lower="0.0" upper="Infinity"/>
</rateGT>
</gtrModel>
<!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985) -->
<HKYModel id="HKY">
<frequencies>
<frequencyModel dataType="nucleotide">
<frequencies>
<!-- HKY frequencies are variable -->
<parameter id="HKY.frequencies" value="0.25 0.25 0.25 0.25"/>
</frequencies>
</frequencyModel>
</frequencies>
<kappa>
<parameter id="HKY.kappa" value="1.0" lower="0.0" upper="Infinity"/>
</kappa>
</HKYModel>
<!-- The general time reversible (GTR) substitution model -->
<gtrModel id="GTR">
<frequencies>
<frequencyModel dataType="nucleotide">
<frequencies>
<!-- GTR frequencies are variable -->
<parameter id="GTR.frequencies" value="0.25 0.25 0.25 0.25"/>
</frequencies>
</frequencyModel>
</frequencies>
<rateAC>
<parameter id="GTR.ac" value="1.0" lower="0.0" upper="Infinity"/>
</rateAC>
<rateAG>
<parameter id="GTR.ag" value="1.0" lower="0.0" upper="Infinity"/>
</rateAG>
<rateAT>
<parameter id="GTR.at" value="1.0" lower="0.0" upper="Infinity"/>
</rateAT>
<rateCG>
<parameter id="GTR.cg" value="1.0" lower="0.0" upper="Infinity"/>
</rateCG>
<rateGT>
<parameter id="GTR.gt" value="1.0" lower="0.0" upper="Infinity"/>
</rateGT>
</gtrModel>
<!-- *** DEFINE AMONG-SITE HETEROGENEITY (SITE MODELS) *** -->
<!-- JC69 site models -->
<siteModel id="siteModel_JC69">
<substitutionModel>
<gtrModel idref="JC69"/>
</substitutionModel>
</siteModel>
<siteModel id="siteModel_JC69_I">
<substitutionModel>
<gtrModel idref="JC69"/>
</substitutionModel>
<proportionInvariant>
<parameter id="siteModel_JC69_I.pInv" value="0.5" lower="0.0" upper="1.0"/>
</proportionInvariant>
</siteModel>
<!-- F81 site models -->
<siteModel id="siteModel_F81">
<substitutionModel>
<gtrModel idref="F81"/>
</substitutionModel>
</siteModel>
<siteModel id="siteModel_F81_I">
<substitutionModel>
<gtrModel idref="F81"/>
</substitutionModel>
<proportionInvariant>
<parameter id="siteModel_F81_I.pInv" value="0.5" lower="0.0" upper="1.0"/>
</proportionInvariant>
</siteModel>
<siteModel id="siteModel_F81_G">
<substitutionModel>
<gtrModel idref="F81"/>
</substitutionModel>
<gammaShape gammaCategories="4">
<parameter id="siteModel_F81_G.alpha" value="0.5" lower="0.0" upper="1000.0"/>
</gammaShape>
</siteModel>
<siteModel id="siteModel_F81_I_G">
<substitutionModel>
<gtrModel idref="F81"/>
</substitutionModel>
<proportionInvariant>
<parameter id="siteModel_F81_I.pInv" value="0.5" lower="0.0" upper="1.0"/>
</proportionInvariant>
<gammaShape gammaCategories="4">
<parameter id="siteModel_F81_G.alpha" value="0.5" lower="0.0" upper="1000.0"/>
</gammaShape>
</siteModel>
<!-- SYM (K20) site models -->
<siteModel id="siteModel_SYM">
<substitutionModel>
<HKYModel idref="SYM"/>
</substitutionModel>
</siteModel>
<siteModel id="siteModel_SYM_I">
<substitutionModel>
<HKYModel idref="SYM"/>
</substitutionModel>
<proportionInvariant>
<parameter id="siteModel_SYM_I.pInv" value="0.5" lower="0.0" upper="1.0"/>
</proportionInvariant>
</siteModel>
<siteModel id="siteModel_SYM_G">
<substitutionModel>
<HKYModel idref="SYM"/>
</substitutionModel>
<gammaShape gammaCategories="4">
<parameter id="siteModel_SYM_G.alpha" value="0.5" lower="0.0" upper="1000.0"/>
</gammaShape>
</siteModel>
<siteModel id="siteModel_SYM_I_G">
<substitutionModel>
<HKYModel idref="SYM"/>
</substitutionModel>
<proportionInvariant>
<parameter id="siteModel_SYM_I_G.pInv" value="0.5" lower="0.0" upper="1.0"/>
</proportionInvariant>
<gammaShape gammaCategories="4">
<parameter id="siteModel_SYM_I_G.alpha" value="0.5" lower="0.0" upper="1000.0"/>
</gammaShape>
</siteModel>
<!-- K2P (K20) site models -->
<siteModel id="siteModel_K2P">
<substitutionModel>
<HKYModel idref="K2P"/>
</substitutionModel>
</siteModel>
<siteModel id="siteModel_K2P_I">
<substitutionModel>
<HKYModel idref="K2P"/>
</substitutionModel>
<proportionInvariant>
<parameter id="siteModel_K2P_I.pInv" value="0.5" lower="0.0" upper="1.0"/>
</proportionInvariant>
</siteModel>
<siteModel id="siteModel_K2P_G">
<substitutionModel>
<HKYModel idref="K2P"/>
</substitutionModel>
<gammaShape gammaCategories="4">
<parameter id="siteModel_K2P_G.alpha" value="0.5" lower="0.0" upper="1000.0"/>
</gammaShape>
</siteModel>
<siteModel id="siteModel_K2P_I_G">
<substitutionModel>
<HKYModel idref="K2P"/>
</substitutionModel>
<proportionInvariant>
<parameter id="siteModel_K2P_I_G.pInv" value="0.5" lower="0.0" upper="1.0"/>
</proportionInvariant>
<gammaShape gammaCategories="4">
<parameter id="siteModel_K2P_I_G.alpha" value="0.5" lower="0.0" upper="1000.0"/>
</gammaShape>
</siteModel>
<!-- HKY site model -->
<siteModel id="siteModel_HKY">
<substitutionModel>
<HKYModel idref="HKY"/>
</substitutionModel>
</siteModel>
<siteModel id="siteModel_HKY_I">
<substitutionModel>
<HKYModel idref="HKY"/>
</substitutionModel>
<proportionInvariant>
<parameter id="siteModel_HKY_I.pInv" value="0.5" lower="0.0" upper="1.0"/>
</proportionInvariant>
</siteModel>
<siteModel id="siteModel_HKY_G">
<substitutionModel>
<HKYModel idref="HKY"/>
</substitutionModel>
<gammaShape gammaCategories="4">
<parameter id="siteModel_HKY_G.alpha" value="0.5" lower="0.0" upper="1000.0"/>
</gammaShape>
</siteModel>
<siteModel id="siteModel_HKY_I_G">
<substitutionModel>
<HKYModel idref="HKY"/>
</substitutionModel>
<proportionInvariant>
<parameter id="siteModel_HKY_I_G.pInv" value="0.5" lower="0.0" upper="1.0"/>
</proportionInvariant>
<gammaShape gammaCategories="4">
<parameter id="siteModel_HKY_I_G.alpha" value="0.5" lower="0.0" upper="1000.0"/>
</gammaShape>
</siteModel>
<!-- GTR site model -->
<siteModel id="siteModel_GTR">
<substitutionModel>
<gtrModel idref="GTR"/>
</substitutionModel>
</siteModel>
<siteModel id="siteModel_GTR_I">
<substitutionModel>
<gtrModel idref="GTR"/>
</substitutionModel>
<proportionInvariant>
<parameter id="siteModel_GTR_I.pInv" value="0.5" lower="0.0" upper="1.0"/>
</proportionInvariant>
</siteModel>
<siteModel id="siteModel_GTR_G">
<substitutionModel>
<gtrModel idref="GTR"/>
</substitutionModel>
<gammaShape gammaCategories="4">
<parameter id="siteModel_GTR_G.alpha" value="0.5" lower="0.0" upper="1000.0"/>
</gammaShape>
</siteModel>
<siteModel id="siteModel_GTR_I_G">
<substitutionModel>
<gtrModel idref="GTR"/>
</substitutionModel>
<proportionInvariant>
<parameter id="siteModel_GTR_I_G.pInv" value="0.5" lower="0.0" upper="1.0"/>
</proportionInvariant>
<gammaShape gammaCategories="4">
<parameter id="siteModel_GTR_I_G.alpha" value="0.5" lower="0.0" upper="1000.0"/>
</gammaShape>
</siteModel>
<!-- Define operators -->
<operators id="operators">
<!-- base frequency params for F81, HKY and GTR--->
<deltaExchange delta="0.01" weight="0.1">
<parameter idref="F81.frequencies"/>
</deltaExchange>
<deltaExchange delta="0.01" weight="0.1">
<parameter idref="HKY.frequencies"/>
</deltaExchange>
<deltaExchange delta="0.01" weight="0.1">
<parameter idref="GTR.frequencies"/>
</deltaExchange>
<!-- kappas for K2P and HKY-->
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="K2P.kappa"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="HKY.kappa"/>
</scaleOperator>
<!-- SYM transition/transversion params -->
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="SYM.ac"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="SYM.ag"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="SYM.at"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="SYM.cg"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="SYM.gt"/>
</scaleOperator>
<!-- GTR transition/transversion params -->
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="GTR.ac"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="GTR.ag"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="GTR.at"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="GTR.cg"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="GTR.gt"/>
</scaleOperator>
<!-- now the pInv params -->
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="siteModel_F81_I.pInv"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="siteModel_F81_I_G.pInv"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="siteModel_JC69_I.pInv"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="siteModel_SYM_I.pInv"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="siteModel_SYM_I_G.pInv"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="siteModel_K2P_I.pInv"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="siteModel_K2P_I_G.pInv"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="siteModel_HKY_I.pInv"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="siteModel_HKY_I_G.pInv"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="siteModel_GTR_I.pInv"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="siteModel_GTR_I_G.pInv"/>
</scaleOperator>
<!-- now the alpha params -->
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="siteModel_F81_G.alpha"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="siteModel_F81_I_G.alpha"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="siteModel_SYM_G.alpha"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="siteModel_SYM_I_G.alpha"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="siteModel_K2P_G.alpha"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="siteModel_K2P_I_G.alpha"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="siteModel_HKY_G.alpha"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="siteModel_HKY_I_G.alpha"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="siteModel_GTR_G.alpha"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="0.1">
<parameter idref="siteModel_GTR_I_G.alpha"/>
</scaleOperator>
</operators>
<!-- ADD TO LOG FILE SECTION -->
<parameter idref="F81.frequencies"/>
<parameter idref="HKY.frequencies"/>
<parameter idref="GTR.frequencies"/>
<!-- kappas for K2P and HKY-->
<parameter idref="K2P.kappa"/>
<parameter idref="HKY.kappa"/>
<!-- SYM transition/transversion params -->
<parameter idref="SYM.ac"/>
<parameter idref="SYM.ag"/>
<parameter idref="SYM.at"/>
<parameter idref="SYM.cg"/>
<parameter idref="SYM.gt"/>
<!-- GTR transition/transversion params -->
<parameter idref="GTR.ac"/>
<parameter idref="GTR.ag"/>
<parameter idref="GTR.at"/>
<parameter idref="GTR.cg"/>
<parameter idref="GTR.gt"/>
<!-- now the pInv params -->
<parameter idref="siteModel_F81_I.pInv"/>
<parameter idref="siteModel_F81_I_G.pInv"/>
<parameter idref="siteModel_JC69_I.pInv"/>
<parameter idref="siteModel_SYM_I.pInv"/>
<parameter idref="siteModel_SYM_I_G.pInv"/>
<parameter idref="siteModel_K2P_I.pInv"/>
<parameter idref="siteModel_K2P_I_G.pInv"/>
<parameter idref="siteModel_HKY_I.pInv"/>
<parameter idref="siteModel_HKY_I_G.pInv"/>
<parameter idref="siteModel_GTR_I.pInv"/>
<parameter idref="siteModel_GTR_I_G.pInv"/>
<!-- now the alpha params -->
<parameter idref="siteModel_F81_G.alpha"/>
<parameter idref="siteModel_F81_I_G.alpha"/>
<parameter idref="siteModel_SYM_G.alpha"/>
<parameter idref="siteModel_SYM_I_G.alpha"/>
<parameter idref="siteModel_K2P_G.alpha"/>
<parameter idref="siteModel_K2P_I_G.alpha"/>
<parameter idref="siteModel_HKY_G.alpha"/>
<parameter idref="siteModel_HKY_I_G.alpha"/>
<parameter idref="siteModel_GTR_G.alpha"/>
<parameter idref="siteModel_GTR_I_G.alpha"/>
</log>
<!-- ADD TO `Define MCMC` FILE SECTION for kappas -->
<logNormalPrior mean="1.0" stdev="1.25" offset="0.0" meanInRealSpace="false">
<parameter idref="K2P.kappa"/>
</logNormalPrior>
<logNormalPrior mean="1.0" stdev="1.25" offset="0.0" meanInRealSpace="false">
<parameter idref="HKY.kappa"/>
</logNormalPrior>
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