infile.xml (16812 bytes)
<?xml version="1.0" encoding="UTF-8" standalone="no"?><beast beautitemplate='SNAPP' beautistatus='' namespace="beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood" required="SNAPP v1.3.0" version="2.4">
<data
id="APP_poc_thor_unlinked_snps"
name="rawdata">
<sequence id="seq_APP_H_pococki_BONE_H7191" taxon="APP_H_pococki_BONE_H719" totalcount="4" value="TATAAGACATGCAGCCCGAATTTTGAGATATTCTTTCGGGCATTCCCGAGCTGACTAGAGCCACATGTTATAATTTCATATTTATGTATTGATAACTTACCTAA?CCTTGCGTAACCAAACCACCATGCTGCCTTACCTCGCAGCGTGGGAGCCGACTGGCGTCTGACTTCTTTCGACGGGGTAGGATTTCTAGTATCAAGTAGTCGAGGAAGAAGTTTAAATCGCGGTAACGGCCACGGTTACACCCCGTTGTGGCTTATTAACCTAGGCTTTATCTCTCG?TGGTGATCCTATCTCTCGTAAAGCGCGTTCACCCCGGCACGTGGACATAATATAAGTTCGTTCCCGCGTATCTGCATCAAATATAGGT?GACTCAGAACCC?ACCGGTCCTCCTTTAAGCTTTAATCCACTAAAAAAATGTCCATTGCTCTGTTCTGGTAAGTGCG"/>
<sequence id="seq_APP_H_pococki_CENT_ALARK_H5951" taxon="APP_H_pococki_CENT_ALARK_H595" totalcount="4" value="CGT?A?ACA?G????CCGAA?TT???GATTT?CT??CG??CAT?C?C?AGTTGACTTG?G?CAC?TGTT?TAAT?T???A?T??TGT?TTGGT?CCTT?C?TAA?CC?TGCGTCAT??????T??A??CTG?T??A??TCGCA?CGTG?GA?CCGGTTG?CGTCAA?CTTC?TTCGACG?GGT???ATTTCTA?TATC??ATA?TC?A?GA?AGC?T?T???TCGCG?TAACAGC?ATGGTG???CCCCG?TGT???TTA?TAA?C?AGG?G?TA??TCTC?T???A?ATC??AT?TC?CGT??AGCGCTTTCACCCC?T?ACGTGG?C?T??T?TAAGT??GTTCC?GCGTAT?TGTAC??AATATAG?T?GACTCAAA?CC?C?CC??TCCTCCTTTA??CTT?A?TCC??T??AA?A??GTCCG??GC?CT?CTCTG??AAG???G"/>
<sequence id="seq_APP_H_pococki_CENT_BALM_H6301" taxon="APP_H_pococki_CENT_BALM_H630" totalcount="4" value="CGTAAGACATGCAACCCGAATTTTGAGATTTTCTTT?GGGCATGCTCGAGTTGACTTGAGCCACATGTTATAATTTTATATTTATGTATTAGTACCTTACCTAATTCTTGCGTCACCAAGTCTTCATGCTGCT?TACCTCGCAGCATGGGAGCCGGTTAGCGTCAAACTTCCTTCGACGGGGTAGAATTTCTAGTATCAGATAGTCGAGGAAAGCGTCTCAATCGCGGTAACAGCCATGGTGACACCCCGTTGTAGTTTATTAATCTAGGCGTTATCTCTC?TTAAAGATCCTTTCTCTCGTATCGCGCTTTCACCCCATCACGTGGGCATGATATAAGTTCGTTCC?GCATATCTGTACCAAATATAGGTAGACTCAAAACCTCGCCGGTCCTC?TTTAAGCTTTAATCCACTAA?AAAA?GTCCGTTGTTCTGCTCTGGAAA?TGCG"/>
<sequence id="seq_APP_H_pococki_CENT_HICK_H3751" taxon="APP_H_pococki_CENT_HICK_H375" totalcount="4" value="CGTAAGACATGCAGCCCGAATTTTGAGATTTTCTTTCGGGCATTCTCGAGTTGACTTGAGCCACATGTTATAATTTCATATTTATGTATTGGTACCTTGCCTAATCCTTGCGTCACCAAGTCTCCATGCTGCTCTACCTCGCAGCATGGGAGCCGGTTGGCGTCAAACTTCCTTCGACGGGGTAGGATTACAAGTATAAGATAGTCGAGGAAGGCATCTCAATCGCGGTAACGGCCATGGTTACACCCCGTTGTGGTTTATTAATCTAGGCGTTATCTCTCGTTAAAGATCCTATCTCTCGTATCGCGCTTTCACCCCATCACGTGGACATGATATAAGTTCGTTCCCGCGTATCTGTACCAAATATAGGTAGACTCAAAGCCTCACCGGTTCTCCTTTAAGCTTTAATCCACTAAAAAAACGTCCGTTGTTCTGCTCTGGAAAGTGCG"/>
<sequence id="seq_APP_H_pococki_CENT_WRGAP_H5041" taxon="APP_H_pococki_CENT_WRGAP_H504" totalcount="4" value="CATAAGACATGCAGCCCGAATTTTGAGATTTTCTTTCGGGCATTCTCGAGTTGACTTGAGCCACATGTTATAATTTTATATTTATGTATTGGTACCTTACCTAATCCTTGCGTCACCAAGTCTCCATGCTGCTTTACCTCACAGCATGGGAACCGATTGGCGTCAAACTTCCTTCGACGGGGTAGGATTTCTAGTATCAAATAGTCGAGGAAGGAGTCTCAATCGCGGTAACGGCCGTGGTTACACCCCGTTGGGGTTTATTAATCTAGGCGTTATCTCTCGTTAAAGATCCTATCTCTCGTATCGCGCTTTCACCCCATCACGTGGACATGATATAAGTTCGTTCCCGCGTATCTGTACCAAATATAGGTAGACTCAAAAGCCCACCGGTCCTCCTTTAAGCTTTAATCCACTAAAAAAGTGTCCGTTGCTCTGCTCTGAAAAGTGCG"/>
<sequence id="seq_APP_H_pococki_ELK_ELK_H4071" taxon="APP_H_pococki_ELK_ELK_H407" totalcount="4" value="CATAAGACATGCAGCCCGAATTTTGAGATTTTCTTTCGGGCATTCTCGAGTTGACTTGAGCCACATGTTATAATTTCATATTTATGTATTGGCACCATGACTAATCCTTGCGTCACCAAGTCTCCATGCTGCTTTACCTCGCAGCGCGGGAACCGATTGGCGTCAAACTTCCTTCGGCGGGGTAGGATTTTTAGTATC?AATAGTCGAGGAAAG?GTCTAAATCGCGATAACAGCCACGGTTGCGCCCCGTTATGG?TTATTAATCTAGGGGATATCTCTCAGTAATGATC?TATCTCTCGTATCGCGCTTTCACCCCAGCACGTAGACATGATACAAGTTTGTTCCTGCGTATCCGTACCAAATATAGGTTGACTCAAAACCCCACCGGTCCTCTTTTAAGATTTAAACCACTAAAAAAATGCCCGTCGCTCTGCTCTGGAAAGTGCG"/>
<sequence id="seq_APP_H_pococki_ELK_LINV_H4391" taxon="APP_H_pococki_ELK_LINV_H439" totalcount="4" value="CATAAGACATACAGCCCAAATTTTGGGATATTCTTTCGGGCATTCTCGAGTTGACTTGAGCCCCATGTTATAATTTCATATTTATGTATTGGCACCATGCCTAATCCTTGCGTCACCAAGTCTTCATGCTGCTTTACCTCGCAGCGC?GGAGCCGATTGGCGTCAAGCTTCCTTAGACGGGGTTGAATTTTTAGTATCAAATAGTCGAGG?AAAAGTCTAAATCGCGATAACAG?CACGGTGGCACCCCGTTGTGGCTTATTAATCTAGGCGTTAGCTTTC?TTAGTGATCCTATCTCTCGTATCGCGCTTTCA?C?CATCACGTGGACA?AATACAAGTTC?TTCC?GCGTATCCGTACCAAATATAGGTAGACTCAAAACCTCACCGATCCTCCTTTAAGATTTGATCCAATAAAAAAATGCCCGTTGCTCTGCTCTGGAAAGTGCG"/>
<sequence id="seq_APP_H_pococki_NE_BCFG_H4201" taxon="APP_H_pococki_NE_BCFG_H420" totalcount="4" value="CGTAAGACGTGCAGCCCGAATTTTGAGATTTTCTTTCGGGCATTCTCGAGTTGACTTGAGCCACATGTTATAATTTTATATTTATGTATTGGTACCATGCCCAATCTTTGCGT?ACCAAGTCTCCATGCTGCTCTACCTCGCAGCGTGGGAGCCGGTTGACGTCAAACTTCCTTCGACGGGG?AGGA?TTCTAGTATCAGATAGTCGAGGCAAGCGTCTAAATCTCGATAACAGCCATGGTGACACCCCGTTGTGG?TTATTAATCTAGGGGTCATCTCTTGTTAAAGATCCTATCTCTCGTATCGCGCTTTCACCCCATCACGTGGACATGATACAAGT?CGTACCT?CGTATCCGTACCAAATATAGGTAGACTCAAAACCCCACCGGTCCTCCTTTAAACTTT?ATCCACTAAAA?AACGCCCG?TGCTCTGCTCTGGAAAGTGCG"/>
<sequence id="seq_APP_H_pococki_NE_BOON_H4131" taxon="APP_H_pococki_NE_BOON_H413" totalcount="4" value="CGTAAGACGTGCAGCCCGAATTTTGAGATTTTCTTTCGGGCATTCTCGAGTTGACTTGAGCCACATGTTATAATTTTATATTTATGTATTGGTACCATGCCCAATCCTTGCGT?ACCAAGTCT?CATGTTGCTCTACCTCGCAGCGTGGGAGCCGGTTGGCGTCAAACTTCCTTCGACGGGGCAGGA??TCTAGTATCAGATAGTCGAGGCAAGCGTCTAAATCTCGATAACAGCCATGG?GACACCCCGTTGTGG?TTATTAATCTAGGCGTTATCTCTCGTTA?TGATCCTATCTCTCGT?TCGCGCTTTCACCCCATCACGTGGACATGATACAAGTTCGTACCTGCGTATCCGTACCAAATATAGGTAGACTCAAA?CCC?ACCGGTCCTCCTTTAAGCTTTGATCCACTAAAAAAA?GCCCGTTGCTCTGCTCTGGAAAGTGCG"/>
<sequence id="seq_APP_H_pococki_VA_CLIFF_H7351" taxon="APP_H_pococki_VA_CLIFF_H735" totalcount="4" value="CGTAAGACATGCAGCCCGAATTTTGAGATTTTCTTTCGGGCATTCTCGAGTTGACTTGAGTCCCATGTTATAATTTTATATTTATGTATTGGTACCTTGCCTAATCCTTGCGTCGCCAAGTCTTCATGCTGCTTTACCTCGCAGCGTGGGAGCCGGTTGGCGTCAAATTTCCTTCTATGGGGTAGGATTTCAAGTATCA?ATAGTCGAGGAAAGAGTCTATATCGCGGTAACAGCCACGGTTACACCCCGTTGTGGTTTATTAATCTAGGCGTTATCTCTTGTTAAAGATCCTATCTCTCGTATCGCACTTTCACCCCATCACGTGGGCATGATATAAGATCATTCCCGCGTATCTGTACCAAATATAGGT?GACTCAAAACCCCACCGGTCCTCTTTTAAGCTCTAATCCACTAAAAAAACGTCCA?TGCTCTGTTCTGGAAAATGCG"/>
<sequence id="seq_APP_H_pococki_WEST_DGAP_H5211" taxon="APP_H_pococki_WEST_DGAP_H521" totalcount="4" value="CGTAAGACATGCGGCCCGAATTTTGAGATTTTCTTTCGGGCATGCTCGAGTTGACTTGAGCCACATGTTATAATTTTATATTTATGTATTGGTACCTTACCTAATCCTTGCGTAACCAAATCTTCATGCTGCTTTACCTCGCAGCATGGGAGCCGATTGGCGTCAAACTTCCTTCGACGGGGTAGGATTTCTAGTATCAGGTAGTCGAGGAAAGAGTCTAAATCGCGGTAACGGCCACGGTTACACCCCGTTGTGGTTTATTAATCTAGGCGTTATCTCTCGTTAGTGATCCT?TCTCTCGTATCGCGCTTTCACCCCAGCACGTGGACAGGATATAAGTTCGTTCCCGCGTATCTGTACCAAATATAGGTAGACTCAAAACCCCACCGGTCCTCTTTTAAGCTTTAATCCACTATAAAAATGTCCGTCGCTCTGCTCTGGTAAGTGCG"/>
<sequence id="seq_APP_H_pococki_WEST_STARR_H5511" taxon="APP_H_pococki_WEST_STARR_H551" totalcount="4" value="CGTAAGACATGCA?CCCGAATTTTGAGATTTTCCTTCGGGCATTCTCGAGTTGACTTGAGCCACATGTTATAATTTTATATTTATGTATTGGTACCTTACCTAATCCTTGCGTAACCAAGTCTCCATGCTGCTTTACCTCGCAGCGTGGGAGTCGGTTGGCGTCAAACTTCCTTCGACGGGGTAAGATTTCTAGTATCAGATAGTCGAGGAAAGCGTCTAAATCGCAGTAACAGCCATGGTGACACCCCGTTGTGGTTTGTTAATCTAGGCGTTATCTCTCGTTAAAGATCCTATCTCTCGTATCGCGCTTTCACCCCATCACGTGGACATGATATAAGTTCGTTCCCGTGTATCTGTACCAAATATAAGTTGACTCAAAACCCCACCGGTCCTCCTTTAAGCTTTAATCCACTATAAAAACGTCCGTTGCTCTGCTCTGGAAAGTGCG"/>
<sequence id="seq_APP_H_thorelli_CROW_H311" taxon="APP_H_thorelli_CROW_H311" totalcount="4" value="CGTTA?TCATGCAACC?GAATTTTG?GATTCTCTC?CAGG?ATTA?CGAGTTGATTTGAGCCACATGCTATAATTT?A?ATTTGCATATCGG?ACCTTAACTAATCCTT?CGTCACCAAGTCTT?A?GCTGCT??ACCTCGCAGCGTGGGAGCCGGTTGACGTCAAACTT??TTCGACGGGGTAGGATTTT?AGTAT?AGAGAG?CGAGGAAAGCGCCTAAATCGCGATAAC?GCC?CGGT?AC?CC?CG?TGTGGTTTATTAATCTAGGGGTTATCTCT?GTTAAAGATCCTATCTC?CGGA?CGCGCTTTCACCTCAT?ACGTGGACATG?TATAAGTTC?CTCCCGCGTATCTGCACCAAATATAGGTAGACTTA?A?CCCCACCGGT?CTACTTCAAGCTTT?ATC?ACT?A?AAA?TGCCCATTGCTC?GCTCTGGACAGTGCG"/>
<sequence id="seq_APP_H_thorelli_CUMB_H802" taxon="APP_H_thorelli_CUMB_H802" totalcount="4" value="CGTTAGACATGCAACCCGAAT?TTGAGTTT?TCTC?CGGGCATTATC?AGTTGA?TTGAGCCACAT?CTATAATTTCATATTTGCATATCGGTACCTTACCTAATCCTTCCGTCACCAAGTCACCATGCTGCTCTACCTCGCAGCGTGGGA?CCGGTTGGCGTCAGACTTCCTTCGACGGGGTAG?ATTTTTAGT?TC?GAGAGTCGAGGAA?GCGCCTAAATCGCGATAACAGCC?TGGTGACACC?CGTTGTGGTTTATTAATCTAG?CGATATCT?TCGTTAAAGATCCTATCTCTCGG?ACGCGCTTTCACACC??CCCGTGGACATG?TATAAGTTTGCTCCTGCGTATCTGCACCAAATATAAGT??ACTCAAAACCCCACCGGTCCTACTTTAAGCTTTAGTCCACTAAAAAAATGC?CG?TGCTC?GCTCTGGAAAGTG?G"/>
<sequence id="seq_APP_H_thorelli_OZONE_H110" taxon="APP_H_thorelli_OZONE_H110" totalcount="4" value="CGTTAGACATGCAACC?GAATTTTGAGATTTTCTCTCAGGCATTATCGAGTTGAC?TGAGCCCCAT?CTATAATTT?ATATTTGCG?ATCGGTACCTTACCTAATCCTTGCGTCACCAAGTCTTCATGCTGCT?TACCTCGCAGCGTGGGAGCCGGTTGGCGTCAAACTTCCTGCGACGGGGT?GGATTTTTAGTATCAGAGAGTCGAGGAAAGCGCCTAAATCGCGATAACAGCC?TGGTGACACCCCGTTGTGGTTTATTAATCTAGGCGTTATCTCTCGTTAAAGATCCTATCTCTCGGATCGCGCTTTCACCCCATCACGTGGACATAATATAAGTTCGCTCCTGCGTATCTGCACCAAATATAGGTAGACTCAAAACCC?ACCG?TCCTACTTTAAGCTTTAATCCACTAA?A?AATGCCCGTTGCTCTGCTCTGGACAGTGCG"/>
</data>
<map name="Uniform" >beast.math.distributions.Uniform</map>
<map name="Exponential" >beast.math.distributions.Exponential</map>
<map name="LogNormal" >beast.math.distributions.LogNormalDistributionModel</map>
<map name="Normal" >beast.math.distributions.Normal</map>
<map name="Beta" >beast.math.distributions.Beta</map>
<map name="Gamma" >beast.math.distributions.Gamma</map>
<map name="LaplaceDistribution" >beast.math.distributions.LaplaceDistribution</map>
<map name="prior" >beast.math.distributions.Prior</map>
<map name="InverseGamma" >beast.math.distributions.InverseGamma</map>
<map name="OneOnX" >beast.math.distributions.OneOnX</map>
<run spec='beast.inference.PathSampler'
chainLength="1000000"
alpha='0.3'
rootdir='./DAPC'
burnInPercentage='0'
preBurnin="100000"
deleteOldLogs='true'
nrOfSteps='70'>
cd $(dir)
java -cp $(java.class.path) beast.app.beastapp.BeastMain $(resume/overwrite) -java -seed $(seed) beast.xml
<mcmc id="mcmc" spec="MCMC" chainLength="1000000" preBurnin="100000" storeEvery="1000">
<state id="state" storeEvery="1000">
<stateNode id="Tree.APP_poc_thor_unlinked_snps" spec="beast.util.ClusterTree" clusterType="upgma" nodetype="snap.NodeData">
<taxa id="snap.APP_poc_thor_unlinked_snps" spec="snap.Data" dataType="integerdata">
<rawdata idref="APP_poc_thor_unlinked_snps"/>
<taxonset id="poc" spec="TaxonSet">
<taxon id="APP_H_pococki_WEST_STARR_H551" spec="Taxon"/>
</taxonset>
<taxonset id="1" spec="TaxonSet">
<taxon id="APP_H_thorelli_CUMB_H802" spec="Taxon"/>
<taxon id="APP_H_thorelli_CROW_H311" spec="Taxon"/>
<taxon id="APP_H_thorelli_OZONE_H110" spec="Taxon"/>
</taxonset>
<taxonset id="4" spec="TaxonSet">
<taxon id="APP_H_pococki_NE_BCFG_H420" spec="Taxon"/>
<taxon id="APP_H_pococki_NE_BOON_H413" spec="Taxon"/>
</taxonset>
<taxonset id="3" spec="TaxonSet">
<taxon id="APP_H_pococki_ELK_ELK_H407" spec="Taxon"/>
<taxon id="APP_H_pococki_ELK_LINV_H439" spec="Taxon"/>
</taxonset>
<taxonset id="2" spec="TaxonSet">
<taxon id="APP_H_pococki_CENT_HICK_H375" spec="Taxon"/>
<taxon id="APP_H_pococki_BONE_H719" spec="Taxon"/>
<taxon id="APP_H_pococki_CENT_WRGAP_H504" spec="Taxon"/>
<taxon id="APP_H_pococki_CENT_BALM_H630" spec="Taxon"/>
<taxon id="APP_H_pococki_WEST_DGAP_H521" spec="Taxon"/>
<taxon id="APP_H_pococki_VA_CLIFF_H735" spec="Taxon"/>
<taxon id="APP_H_pococki_CENT_ALARK_H595" spec="Taxon"/>
</taxonset>
</taxa>
<parameter id="RealParameter.0" lower="0.0" name="clock.rate" upper="0.0">1.0</parameter>
</stateNode>
<parameter id="u" lower="0.0" name="stateNode">1.0</parameter>
<parameter id="v" lower="0.0" name="stateNode">1.0</parameter>
<parameter id="lambda" lower="0.0" name="stateNode">10.0</parameter>
<parameter id="coalescenceRate" name="stateNode">10.0</parameter>
</state>
<distribution id="posterior" spec="util.CompoundDistribution">
<distribution id="prior" spec="util.CompoundDistribution">
<prior id="lambdaPrior.APP_poc_thor_unlinked_snps" name="distribution" x="@lambda">
<Gamma id="Gamma.0" name="distr">
<parameter id="RealParameter.1" estimate="false" name="alpha">2.0</parameter>
<parameter id="RealParameter.2" estimate="false" name="beta">200.0</parameter>
</Gamma>
</prior>
<distribution id="snapprior.APP_poc_thor_unlinked_snps" spec="snap.likelihood.SnAPPrior" coalescenceRate="@coalescenceRate" lambda="@lambda" rateprior="gamma" tree="@Tree.APP_poc_thor_unlinked_snps">
<parameter id="alpha" estimate="false" lower="0.0" name="alpha">2.0</parameter>
<parameter id="beta" estimate="false" lower="0.0" name="beta">250.0</parameter>
<parameter id="kappa" estimate="false" lower="0.0" name="kappa">1.0</parameter>
</distribution>
<prior id="uPrior.APP_poc_thor_unlinked_snps" name="distribution" x="@u">
<OneOnX id="OneOnX.4" name="distr"/>
</prior>
<prior id="vPrior.APP_poc_thor_unlinked_snps" name="distribution" x="@v">
<OneOnX id="OneOnX.5" name="distr"/>
</prior>
</distribution>
<distribution id="likelihood" spec="util.CompoundDistribution">
<distribution id="treeLikelihood.APP_poc_thor_unlinked_snps" spec="snap.likelihood.SnAPTreeLikelihood" data="@snap.APP_poc_thor_unlinked_snps" pattern="coalescenceRate" tree="@Tree.APP_poc_thor_unlinked_snps">
<siteModel id="MutationSiteModel.APP_poc_thor_unlinked_snps" spec="SiteModel">
<parameter id="mutationRate" estimate="false" name="mutationRate">1.0</parameter>
<parameter id="shape" estimate="false" name="shape">2.0</parameter>
<parameter id="proportionInvariant" estimate="false" name="proportionInvariant">0.0</parameter>
<substModel id="MutationModel" spec="snap.likelihood.SnapSubstitutionModel" coalescenceRate="@coalescenceRate" mutationRateU="@u" mutationRateV="@v"/>
</siteModel>
</distribution>
</distribution>
</distribution>
<operator id="NodeSwapper" spec="snap.operators.NodeSwapper" tree="@Tree.APP_poc_thor_unlinked_snps" weight="0.5"/>
<operator id="NodeBudger" spec="snap.operators.NodeBudger" size="0.5" tree="@Tree.APP_poc_thor_unlinked_snps" weight="0.5"/>
<operator id="TreeScaler" spec="snap.operators.ScaleOperator" scaleFactor="0.25" tree="@Tree.APP_poc_thor_unlinked_snps" weight="0.5"/>
<operator id="GammaMover" spec="snap.operators.GammaMover" coalescenceRate="@coalescenceRate" scale="0.5" weight="8.0"/>
<operator id="RateMixer" spec="snap.operators.RateMixer" coalescenceRate="@coalescenceRate" scaleFactors="0.25" tree="@Tree.APP_poc_thor_unlinked_snps" weight="1.0"/>
<operator id="MutationMover" spec="snap.operators.MutationMover" u="@u" v="@v" weight="1.0" window="0.1"/>
<operator id="lambdaScaler" spec="snap.operators.ScaleOperator" parameter="@lambda" scaleFactor="0.75" weight="1.0"/>
<logger id="tracelog" fileName="snap.log" logEvery="1000" model="@posterior">
<log idref="posterior"/>
<log idref="likelihood"/>
<log idref="prior"/>
<log idref="u"/>
<log idref="v"/>
<log id="ThetaLogger" spec="snap.ThetaLogger" coalescenceRate="@coalescenceRate"/>
<log id="TreeHeightLogger" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.APP_poc_thor_unlinked_snps"/>
</logger>
<logger id="screenlog" logEvery="5000">
<log idref="posterior"/>
<log id="ESS.0" spec="util.ESS" arg="@posterior"/>
<log idref="likelihood"/>
<log idref="prior"/>
</logger>
<logger id="treelog" fileName="snap.trees" logEvery="5000" mode="tree">
<log id="TreeWithMetaDataLogger.APP_poc_thor_unlinked_snps" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.APP_poc_thor_unlinked_snps">
<metadata id="theta" spec="snap.RateToTheta" coalescenceRate="@coalescenceRate"/>
</log>
</logger>
</mcmc>
</run>
</beast>