<?xml version="1.0" standalone="yes"?>

<!-- Generated by BEAUTi v1.6.0pre                                           -->
<!--       by Alexei J. Drummond and Andrew Rambaut                          -->
<!--       Department of Computer Science, University of Auckland and        -->
<!--       Institute of Evolutionary Biology, University of Edinburgh        -->
<!--       http://beast.bio.ed.ac.uk/                                        -->
<beast>

	<!-- The list of taxa analyse (can also include dates/ages).                 -->
	<!-- ntax=62                                                                 -->
	<taxa id="taxa">
		<taxon id="Acinonyx jubatus "/>
		<taxon id="Ailuropoda melanoleuca "/>
		<taxon id="Ailurus fulgens "/>
		<taxon id="Alopex lagopus "/>
		<taxon id="Arctocephalus australis "/>
		<taxon id="Arctocephalus forsteri "/>
		<taxon id="Arctocephalus pusillus "/>
		<taxon id="Arctocephalus townsendi "/>
		<taxon id="Callorhinus ursinus "/>
		<taxon id="Canis latrans "/>
		<taxon id="Canis lupus "/>
		<taxon id="Cystophora cristata "/>
		<taxon id="Enhydra lutris "/>
		<taxon id="Erignathus barbatus "/>
		<taxon id="Eumetopias jubatus "/>
		<taxon id="Felis silvestris "/>
		<taxon id="Gulo gulo "/>
		<taxon id="Halichoerus grypus "/>
		<taxon id="Helarctos malayanus "/>
		<taxon id="Herpestes auropunctatus "/>
		<taxon id="Hydrurga leptonyx "/>
		<taxon id="Leptonychotes weddellii "/>
		<taxon id="Lobodon carcinophaga "/>
		<taxon id="Lontra canadensis "/>
		<taxon id="Lynx canadensis "/>
		<taxon id="Martes americana "/>
		<taxon id="Martes melampus "/>
		<taxon id="Meles meles "/>
		<taxon id="Melursus ursinus "/>
		<taxon id="Mephitis mephitis "/>
		<taxon id="Mirounga angustirostris "/>
		<taxon id="Mirounga leonina "/>
		<taxon id="Monachus monachus "/>
		<taxon id="Monachus schauinslandi "/>
		<taxon id="Mustela vison "/>
		<taxon id="Neofelis nebulosa "/>
		<taxon id="Neophoca cinerea "/>
		<taxon id="Odobenus rosmarus "/>
		<taxon id="Ommatophoca rossii "/>
		<taxon id="Otaria byronia "/>
		<taxon id="Panthera pardus "/>
		<taxon id="Panthera tigris "/>
		<taxon id="Phoca caspica "/>
		<taxon id="Phoca fasciata "/>
		<taxon id="Phoca groenlandica "/>
		<taxon id="Phoca hispida "/>
		<taxon id="Phoca largha "/>
		<taxon id="Phoca sibirica "/>
		<taxon id="Phoca vitulina "/>
		<taxon id="Phocarctos hookeri "/>
		<taxon id="Procyon lotor "/>
		<taxon id="Puma concolor "/>
		<taxon id="Spilogale putorius "/>
		<taxon id="Taxidea taxus "/>
		<taxon id="Tremarctos ornatus "/>
		<taxon id="Uncia uncia "/>
		<taxon id="Ursus americanus "/>
		<taxon id="Ursus arctos "/>
		<taxon id="Ursus maritimus "/>
		<taxon id="Ursus thibetanus "/>
		<taxon id="Vulpes vulpes "/>
		<taxon id="Zalophus californianus "/>
	</taxa>

	<!-- The sequence alignment (each sequence refers to a taxon above).         -->
	<!-- ntax=62 nchar=10869                                                     -->
	<alignment id="alignment" dataType="nucleotide">
		<sequence>
			<taxon idref="Acinonyx jubatus "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Ailuropoda melanoleuca "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Ailurus fulgens "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Alopex lagopus "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Arctocephalus australis "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Arctocephalus forsteri "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Arctocephalus pusillus "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Arctocephalus townsendi "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Callorhinus ursinus "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Canis latrans "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Canis lupus "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Cystophora cristata "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Enhydra lutris "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Erignathus barbatus "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Eumetopias jubatus "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Felis silvestris "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Gulo gulo "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Halichoerus grypus "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Helarctos malayanus "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Herpestes auropunctatus "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Hydrurga leptonyx "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Leptonychotes weddellii "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Lobodon carcinophaga "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Lontra canadensis "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Lynx canadensis "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Martes americana "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Martes melampus "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Meles meles "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Melursus ursinus "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Mephitis mephitis "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Mirounga angustirostris "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Mirounga leonina "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Monachus monachus "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Monachus schauinslandi "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Mustela vison "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Neofelis nebulosa "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Neophoca cinerea "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Odobenus rosmarus "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Ommatophoca rossii "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Otaria byronia "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Panthera pardus "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Panthera tigris "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Phoca caspica "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Phoca fasciata "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Phoca groenlandica "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Phoca hispida "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Phoca largha "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Phoca sibirica "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Phoca vitulina "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Phocarctos hookeri "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Procyon lotor "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Puma concolor "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Spilogale putorius "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Taxidea taxus "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Tremarctos ornatus "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Uncia uncia "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Ursus americanus "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Ursus arctos "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Ursus maritimus "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Ursus thibetanus "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Vulpes vulpes "/>
[encoded data, 10893 characters]
		</sequence>
		<sequence>
			<taxon idref="Zalophus californianus "/>
[encoded data, 10893 characters]
		</sequence>
	</alignment>

	<!-- The unique patterns from 1 to end                                       -->
	<!-- npatterns=5565                                                          -->
	<patterns id="patterns" from="1">
		<alignment idref="alignment"/>
	</patterns>

	<!-- A prior on the distribution node heights defined given                  -->
	<!-- a Yule speciation process (a pure birth process).                       -->
	<yuleModel id="yule" units="substitutions">
		<birthRate>
			<parameter id="yule.birthRate" value="1.0" lower="0.0" upper="Infinity"/>
		</birthRate>
	</yuleModel>

	<!-- This is a simple constant population size coalescent model              -->
	<!-- that is used to generate an initial tree for the chain.                 -->
	<constantSize id="initialDemo" units="substitutions">
		<populationSize>
			<parameter id="initialDemo.popSize" value="100.0"/>
		</populationSize>
	</constantSize>

	<!-- Generate a random starting tree under the coalescent process            -->

	<!-- No calibration                                                          -->
	<coalescentTree id="startingTree" rootHeight="0.2">
		<taxa idref="taxa"/>
		<constantSize idref="initialDemo"/>
	</coalescentTree>

	<!-- Generate a tree model                                                   -->
	<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>

	<!-- Generate a speciation likelihood for Yule or Birth Death                -->
	<speciationLikelihood id="speciation">
		<model>
			<yuleModel idref="yule"/>
		</model>
		<speciesTree>
			<treeModel idref="treeModel"/>
		</speciesTree>
	</speciationLikelihood>

	<!-- The strict clock (Uniform rates across branches)                        -->
	<strictClockBranchRates id="branchRates">
		<rate>
			<parameter id="clock.rate" value="1.0"/>
		</rate>
	</strictClockBranchRates>

	<!-- The general time reversible (GTR) substitution model                    -->
	<gtrModel id="gtr">
		<frequencies>
			<frequencyModel dataType="nucleotide">
				<frequencies>
					<parameter id="frequencies" value="0.25 0.25 0.25 0.25"/>
				</frequencies>
			</frequencyModel>
		</frequencies>
		<rateAC>
			<parameter id="ac" value="1.0" lower="0.0" upper="Infinity"/>
		</rateAC>
		<rateAG>
			<parameter id="ag" value="1.0" lower="0.0" upper="Infinity"/>
		</rateAG>
		<rateAT>
			<parameter id="at" value="1.0" lower="0.0" upper="Infinity"/>
		</rateAT>
		<rateCG>
			<parameter id="cg" value="1.0" lower="0.0" upper="Infinity"/>
		</rateCG>
		<rateGT>
			<parameter id="gt" value="1.0" lower="0.0" upper="Infinity"/>
		</rateGT>
	</gtrModel>

	<!-- site model                                                              -->
	<siteModel id="siteModel">
		<substitutionModel>
			<gtrModel idref="gtr"/>
		</substitutionModel>
		<gammaShape gammaCategories="4">
			<parameter id="alpha" value="0.5" lower="0.0" upper="1000.0"/>
		</gammaShape>
	</siteModel>
	<treeLikelihood id="treeLikelihood" useAmbiguities="false">
		<patterns idref="patterns"/>
		<treeModel idref="treeModel"/>
		<siteModel idref="siteModel"/>
		<strictClockBranchRates idref="branchRates"/>
	</treeLikelihood>

	<!-- Define operators                                                        -->
	<operators id="operators">
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="ac"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="ag"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="at"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="cg"/>
		</scaleOperator>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="gt"/>
		</scaleOperator>
		<deltaExchange delta="0.01" weight="0.1">
			<parameter idref="frequencies"/>
		</deltaExchange>
		<scaleOperator scaleFactor="0.75" weight="0.1">
			<parameter idref="alpha"/>
		</scaleOperator>
		<subtreeSlide size="0.02" 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>
		<scaleOperator scaleFactor="0.75" weight="3">
			<parameter idref="treeModel.rootHeight"/>
		</scaleOperator>
		<uniformOperator weight="30">
			<parameter idref="treeModel.internalNodeHeights"/>
		</uniformOperator>
		<scaleOperator scaleFactor="0.75" weight="3">
			<parameter idref="yule.birthRate"/>
		</scaleOperator>
		<upDownOperator scaleFactor="0.75" weight="3">
			<up>
			</up>
			<down>
				<parameter idref="treeModel.allInternalNodeHeights"/>
			</down>
		</upDownOperator>
	</operators>

	<!-- Define MCMC                                                             -->
	<mcmc id="mcmc" chainLength="1000000" autoOptimize="true" fullEvaluation="0">
		<posterior id="posterior">
			<prior id="prior">
				<gammaPrior shape="0.05" scale="10.0" offset="0.0">
					<parameter idref="ac"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="20.0" offset="0.0">
					<parameter idref="ag"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="10.0" offset="0.0">
					<parameter idref="at"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="10.0" offset="0.0">
					<parameter idref="cg"/>
				</gammaPrior>
				<gammaPrior shape="0.05" scale="10.0" offset="0.0">
					<parameter idref="gt"/>
				</gammaPrior>
				<speciationLikelihood idref="speciation"/>
			</prior>
			<likelihood id="likelihood">
				<treeLikelihood idref="treeLikelihood"/>
			</likelihood>
		</posterior>
		<operators idref="operators"/>

		<!-- write log to screen                                                     -->
		<log id="screenLog" logEvery="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="10000" fileName="benchmark2.log" overwrite="false">
			<posterior idref="posterior"/>
			<prior idref="prior"/>
			<likelihood idref="likelihood"/>
			<parameter idref="treeModel.rootHeight"/>
			<parameter idref="yule.birthRate"/>
			<parameter idref="ac"/>
			<parameter idref="ag"/>
			<parameter idref="at"/>
			<parameter idref="cg"/>
			<parameter idref="gt"/>
			<parameter idref="frequencies"/>
			<parameter idref="alpha"/>
			<parameter idref="clock.rate"/>
			<treeLikelihood idref="treeLikelihood"/>
			<speciationLikelihood idref="speciation"/>
		</log>

		<logTree id="treeFileLog" logEvery="1000" nexusFormat="true" fileName="benchmark2.trees" sortTranslationTable="true">
			<treeModel idref="treeModel"/>
			<strictClockBranchRates idref="branchRates"/>
			<posterior idref="posterior"/>
		</logTree>
		-->
	</mcmc>
	<report>
		<property name="timer">
			<mcmc idref="mcmc"/>
		</property>
	</report>
    <report>
        <posterior idref="posterior"/>
    </report>
</beast>
