<?xml version="1.0" standalone="yes"?><beast>	<!-- This XML file specifies the example phylogeny and alignment co-estimation as explained	     in the paper, "Bayesian co-estimation of phylogeny and sequence alignment", GA Lunter,	     I Miklos, AJ Drummond, JL Jensen, J Hein, BMC Bioinformatics 2005.  To run, download	     the BEAST package (AJ Drummond and A Rambaut, http://evolve.zoo.ox.ac.uk/beast.   -->	<!-- Definition of the 10 taxa, for later reference -->	<taxa id="taxa1">		<taxon id="LGB1_LUPLU"/>		<taxon id="MYG_HUMAN"/>		<taxon id="MYG_GRAGE"/>		<taxon id="MYG_CHICK"/>		<taxon id="HBA_HUMAN"/>		<taxon id="HBB_HUMAN"/>		<taxon id="HBA_CHICK"/>		<taxon id="HBB_CHICK"/>		<taxon id="HBA_CHRPI"/>		<taxon id="HBB_CHRPI"/>	</taxa>	<!-- Define the sequences, and their initial alignment -->	<alignment id="globins" dataType="amino acid">		<sequence>			<taxon idref="LGB1_LUPLU"/>			GVLTDVQVALVKSSFEEFNANIPKNTHRFFTLVLEIAPGAKDLFSFLKGSS--EVPQNNPDLQAHAGKVFKLTYEAAIQLQVNGAVASDATLKSLGSVHVSKGVVDA-HFPVVKEAILKTIKEVVGDKWSEELNTAWTIAYDELAIIIKKEMKDAA---		</sequence>		<sequence>			<taxon idref="MYG_HUMAN"/>			-GLSDGEWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGATVLTALGGILKKKG-----HHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLQSKHPGDFGADAQGAMNKALELFRKDMASNYKELGFQG		</sequence>		<sequence>			<taxon idref="MYG_GRAGE"/>			-GLSDDEWHHVLGIWAKVEPDLSAHGQEVIIRLFQVHPETQERFAKFKNLKTIDELRSSEEVKKHGTTVLTALGRILKLKN-----NHEPELKPLAESHATKHKIPVKYLEFICEIIVKVIAEKHPSDFGADSQAAMRKALELFRNDMASKYKEFGFQG		</sequence>		<sequence>			<taxon idref="MYG_CHICK"/>			-GLSDQEWQQVLTIWGKVEADIAGHGHEVLMRLFHDHPETLDRFDKFKGLKTPDQMKGSEDLKKHGATVLTQLGKILKQKG-----NHESELKPLAQTHATKHKIPVKYLEFISEVIIKVIAEKHAADFGADSQAAMKKALELFRNDMASKYKEFGFQG		</sequence>		<sequence>			<taxon idref="HBA_HUMAN"/>			-VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DLS-----HGSAQVKGHGKKVADALTNAVAHVD-----DMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR------		</sequence>		<sequence>			<taxon idref="HBB_HUMAN"/>			VHLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLD-----NLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH------		</sequence>		<sequence>			<taxon idref="HBA_CHICK"/>			-VLSAADKNNVKGIFTKIAGHAEEYGAETLERMFTTYPPTKTYFPHF-DLS-----HGSAQIKGHGKKVVAALIEAANHID-----DIAGTLSKLSDLHAHKLRVDPVNFKLLGQCFLVVVAIHHPAALTPEVHASLDKFLCAVGTVLTAKYR------		</sequence>		<sequence>			<taxon idref="HBB_CHICK"/>			VHWTAEEKQLITGLWGKV--NVAECGAEALARLLIVYPWTQRFFASFGNLSSPTAILGNPMVRAHGKKVLTSFGDAVKNLD-----NIKNTFSQLSELHCDKLHVDPENFRLLGDILIIVLAAHFSKDFTPECQAAWQKLVRVVAHALARKYH------		</sequence>		<sequence>			<taxon idref="HBA_CHRPI"/>			-VLNAGDKANVKAVWNKVAAHVEEYGAETLERMFTVYPQTKTYFPHF-DLH-----HGSAQIRTHGKKVLTALGEAVNHID-----DLASALSKLSDIHAQTLRVDPVNFKFLNHCFLVVVAIHQPSVLTPEVHVSLDKFLSAVGTVLTSKYR------		</sequence>		<sequence>			<taxon idref="HBB_CHRPI"/>			VHWTADEKQLITSLWGKV--NVEECGSEALARLLIVYPWTQRFFSTFGNLSNAEAILHNPHVHAHGKKVLTSFGEAVKNLD-----HIKQTFATLSKLHCEKLHVDPENFKLLGNVLIIVLASHFTKEFTPACQAAWQKLVSAVAHALALGYH------		</sequence>	</alignment>  	<!-- create an starting tree using the UPGMA algorithm -->	<upgmaTree id="startTree" usingDates="false">	 	<distanceMatrix correction="JC">			<alignment idref="globins"/>		</distanceMatrix>	</upgmaTree>			<treeModel id="treeModel1">		<tree idref="startTree"/>		<rootHeight>			<parameter id="root"/>		</rootHeight>		<nodeHeights internalNodes="true">			<parameter id="treeModel1.internalNodeHeights"/>		</nodeHeights>		<nodeHeights rootNode="true" internalNodes="true">			<parameter id="treeModel1.allNodeHeights"/>		</nodeHeights>	</treeModel>	 		<aminoAcidModel id="blosum62" type="blosum62"/>		<!-- The main likelihood function.  This computes the likelihood of phylogeny and alignment, 	     given evolutionary parameters, under the TKF91 model. -->	<tkf91Likelihood id="treeLikelihood1">		<alignment idref="globins"/>		<treeModel idref="treeModel1"/>		<siteModel>			<substitutionModel>				<aminoAcidModel idref="blosum62"/>			</substitutionModel>			<mutationRate> <parameter id="mu" value="1" upper="1.0" lower="1e-6"/> </mutationRate>		</siteModel>		<tkf91Model units="generations">			<lengthDistribution> <parameter id="lendistr" value="0.993243243" upper="0.9999999" lower="1e-6"/> </lengthDistribution>			<deathRate> <parameter id="deathRate" value="1.0" upper="2" lower="1e-6"/> </deathRate>		</tkf91Model>	</tkf91Likelihood>		<taxa id="alpha">		<taxon idref="HBA_HUMAN"/>		<taxon idref="HBA_CHICK"/>		<taxon idref="HBA_CHRPI"/>	</taxa>		<taxa id="beta">		<taxon idref="HBB_HUMAN"/>		<taxon idref="HBB_CHICK"/>		<taxon idref="HBB_CHRPI"/>	</taxa>		<taxa id="myo">		<taxon idref="MYG_HUMAN"/>		<taxon idref="MYG_CHICK"/>		<taxon idref="MYG_GRAGE"/>	</taxa>		<taxa id="ch_a">		<taxon idref="HBA_HUMAN"/>		<taxon idref="HBA_CHICK"/>	</taxa>		<taxa id="ch_b">		<taxon idref="HBB_HUMAN"/>		<taxon idref="HBB_CHICK"/>	</taxa>		<taxa id="ch_my">		<taxon idref="MYG_HUMAN"/>		<taxon idref="MYG_CHICK"/>	</taxa>		<taxa id="ct_a">		<taxon idref="HBA_CHICK"/>		<taxon idref="HBA_CHRPI"/>	</taxa>		<taxa id="ct_b">		<taxon idref="HBB_CHICK"/>		<taxon idref="HBB_CHRPI"/>	</taxa>		<taxa id="ct_my">		<taxon idref="MYG_GRAGE"/>		<taxon idref="MYG_CHICK"/>	</taxa>	<!-- A bunch of statistics, to investigate the topology of the tree in detail -->	<tmrcaStatistic id="ctha" name="chickTurtleHeight_A"><treeModel idref="treeModel1"/><mrca><taxa idref="ct_a"/></mrca></tmrcaStatistic>	<tmrcaStatistic id="cthb" name="chickTurtleHeight_B"><treeModel idref="treeModel1"/><mrca><taxa idref="ct_b"/></mrca></tmrcaStatistic>	<tmrcaStatistic id="cthm" name="chickTurtleHeight_M"><treeModel idref="treeModel1"/><mrca><taxa idref="ct_my"/></mrca></tmrcaStatistic>		<tmrcaStatistic id="ah" name="cthHeight_A"><treeModel idref="treeModel1"/><mrca><taxa idref="alpha"/></mrca></tmrcaStatistic>	<tmrcaStatistic id="bh" name="cthHeight_B"><treeModel idref="treeModel1"/><mrca><taxa idref="beta"/></mrca></tmrcaStatistic>	<tmrcaStatistic id="ch" name="cthHeight_M"><treeModel idref="treeModel1"/><mrca><taxa idref="myo"/></mrca></tmrcaStatistic>		<monophylyStatistic id="chickHuman_A" name="chickHumanMono_A"><treeModel idref="treeModel1"/><mrca><taxa idref="ch_a"/></mrca></monophylyStatistic>	<monophylyStatistic id="chickHuman_B" name="chickHumanMono_B"><treeModel idref="treeModel1"/><mrca><taxa idref="ch_b"/></mrca></monophylyStatistic>	<monophylyStatistic id="chickHuman_M" name="chickHumanMono_M"><treeModel idref="treeModel1"/><mrca><taxa idref="ch_my"/></mrca></monophylyStatistic>	<monophylyStatistic id="chickTurtle_A" name="chickTurtleMono_A"><treeModel idref="treeModel1"/><mrca><taxa idref="ct_a"/></mrca></monophylyStatistic>	<monophylyStatistic id="chickTurtle_B" name="chickTurtleMono_B"><treeModel idref="treeModel1"/><mrca><taxa idref="ct_b"/></mrca></monophylyStatistic>	<monophylyStatistic id="chickTurtle_M" name="chickTurtleMono_M"><treeModel idref="treeModel1"/><mrca><taxa idref="ct_my"/></mrca></monophylyStatistic>    <!-- A bunch of operators, as input to the MCMC procedure.  The most important one is alignmentChunkOperator, which proposes         a new partial alignment using a score-based alignment proposal distribution.  See paper for details -->  	<operators id="operators1">		<uniformOperator weight="2"><parameter idref="treeModel1.internalNodeHeights"/></uniformOperator>		<scaleOperator scaleFactor="0.55" adapt="false" weight="1"><parameter idref="root"/></scaleOperator>		<scaleOperator scaleFactor="0.40" adapt="false" weight="1"><parameter idref="deathRate"/></scaleOperator>		<alignmentChunkOperator weight="7" iP="0.025" exponent="1.5" gapPenalty="-10"><tkf91Likelihood idref="treeLikelihood1"/></alignmentChunkOperator>		<subtreeSlide weight="1" size="0.2" gaussian="true"><treeModel idref="treeModel1"/></subtreeSlide>		<narrowExchange weight="1"><treeModel idref="treeModel1"/></narrowExchange>		<wideExchange weight="1"><treeModel idref="treeModel1"/></wideExchange>	</operators>	<!-- The main element, specifying the MCMC run and parameter logs -->	<mcmc id="mcmc1" chainLength="1000000" verbose="false">		<treeLikelihood idref="treeLikelihood1"/>		<operators idref="operators1"/>		<log logEvery="100">			<parameter idref="lendistr"/>			<parameter idref="deathRate"/>			<parameter idref="root"/>						<statistic name="alignmentLength">				<tkf91Likelihood idref="treeLikelihood1"/>			</statistic>				<treeLikelihood idref="treeLikelihood1"/>		</log>	    <log logEvery="100" fileName="globins_10_CAB.log">			<parameter idref="lendistr"/>			<parameter idref="deathRate"/>			<parameter idref="root"/>						<statistic name="alignmentLength">				<tkf91Likelihood idref="treeLikelihood1"/>			</statistic>						<monophylyStatistic idref="chickHuman_A"/>			<monophylyStatistic idref="chickHuman_B"/>			<monophylyStatistic idref="chickHuman_M"/>			<monophylyStatistic idref="chickTurtle_A"/>			<monophylyStatistic idref="chickTurtle_B"/>			<monophylyStatistic idref="chickTurtle_M"/>			<tmrcaStatistic idref="ctha"/>			<tmrcaStatistic idref="cthb"/>			<tmrcaStatistic idref="cthm"/>			<tmrcaStatistic idref="ah"/>			<tmrcaStatistic idref="bh"/>			<tmrcaStatistic idref="ch"/>			<treeLikelihood idref="treeLikelihood1"/>		</log>		<log logEvery="100" fileName="globins_10_trees.log">			<treeModel idref="treeModel1"/>		</log>				<log logEvery="100" fileName="globins_10_operators.log">			<operators idref="operators1"/>		</log>				<log logEvery="100" fileName="globins_10_alignments.log">			<treeLikelihood idref="treeLikelihood1"/>		</log>			</mcmc>	    <!-- Output controls -->	<report>		MCMC took <property name="timer"><mcmc idref="mcmc1"/></property> seconds	</report>		<traceAnalysis fileName="globins_10.log"/></beast>