<?xml version="1.0" standalone="yes"?>
<!-- $Id: testLikelihood.xml,v 1.2 2005/07/11 23:22:40 rambaut Exp $ -->
<!-- Tests the tree likelihood -->

<beast>

	<!-- The list of taxa analyse (can also include dates/ages).                 -->
	<!-- ntax=6                                                                  -->
	<taxa id="taxa1">
		<taxon id="human"/>
		<taxon id="chimp"/>
		<taxon id="bonobo"/>
		<taxon id="gorilla"/>
		<taxon id="orangutan"/>
		<taxon id="siamang"/>
	</taxa>

	<!-- The sequence alignment (each sequence refers to a taxon above).         -->
	<!-- ntax=6 nchar=768                                                        -->
	<alignment id="alignment1" dataType="nucleotide">
		<sequence>
			<taxon idref="human"/>
			AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCCTTATTTCTACTAGGACTATGAGAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTG-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCGGAGCTTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGGCCTCCATGACTTTTTCAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAATTATAGGCT-AAATCCTATATATCTTA-CACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACACCTCTTTACAGTGA
		</sequence>
		<sequence>
			<taxon idref="chimp"/>
			AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTCAAATCCCCTTATTTCTACTAGGACTATAAGAATCGAACTCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTAAGCACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCTCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AACCCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCGACACCTCTTTACAGTGA
		</sequence>
		<sequence>
			<taxon idref="bonobo"/>
			AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTTAAATCCCCTTATTTCTACTAGGACTATGAGAGTCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCTCTCAGTAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAGC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTTGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCCCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCAACACCTCTTTACAGTGA
		</sequence>
		<sequence>
			<taxon idref="gorilla"/>
			AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGAGGTTTAAACCCCCTTATTTCTACTAGGACTATGAGAATTGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTGTCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTCACATCCTTCCCGTACTAAGAAATTTAGGTTAAACATAGACCAAGAGCCTTCAAAGCCCTTAGTAAGTTA-CAACACTTAATTTCTGTAAGGACTGCAAAACCCTACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCAATGGGACTCAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAT-TCACCTCGGAGCTTGGTAAAAAGAGGCCCAGCCTCTGTCTTTAGATTTACAGTCCAATGCCTTA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGACCTTCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAGGTTAAATTACGGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCGTTAACCTTTTAAGTTAAAGATTAAGAGTATCGGCACCTCTTTGCAGTGA
		</sequence>
		<sequence>
			<taxon idref="orangutan"/>
			AGAAATATGTCTGACAAAAGAGTTACTTTGATAGAGTAAAAAATAGAGGTCTAAATCCCCTTATTTCTACTAGGACTATGGGAATTGAACCCACCCCTGAGAATCCAAAATTCTCCGTGCCACCCATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTA--CACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTCA-CAGCACTTAATTTCTGTAAGGACTGCAAAACCCCACTTTGCATCAACTGAGCGCAAATCAGCCACTTTAATTAAGCTAAGCCCTCCTAGACCGATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAT-TGGCTTCAGTCCAAAGCCCCGGCAGGCCTTAAAGCTGCTCCTTCGAATTTGCAATTCAACATGACAA-TCACCTCAGGGCTTGGTAAAAAGAGGTCTGACCCCTGTTCTTAGATTTACAGCCTAATGCCTTAACTCGGCCATTTTACCGCAAAAAAGGAAGGAATCGAACCTCCTAAAGCTGGTTTCAAGCCAACCCCATAACCCCCATGACTTTTTCAAAAGGTACTAGAAAAACCATTTCGTAACTTTGTCAAAGTTAAATTACAGGTC-AGACCCTGTGTATCTTA-CATTGCAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACCAGCCTCTCTTTGCAATGA
		</sequence>
		<sequence>
			<taxon idref="siamang"/>
			AGAAATACGTCTGACGAAAGAGTTACTTTGATAGAGTAAATAACAGGGGTTTAAATCCCCTTATTTCTACTAGAACCATAGGAGTCGAACCCATCCTTGAGAATCCAAAACTCTCCGTGCCACCCGTCGCACCCTGTTCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCATACTAAGAAATTTAGGTTAAACACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTAACAAAACTTAATTTCTGCAAGGGCTGCAAAACCCTACTTTGCATCAACCGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCGATGGGACTTAAACCCATAAAAATTTAGTTAACAGCTAAACACCCTAAACAACCTGGCTTCAATCTAAAGCCCCGGCAGA-GTTGAAGCTGCTTCTTTGAACTTGCAATTCAACGTGAAAAATCACTTCGGAGCTTGGCAAAAAGAGGTTTCACCTCTGTCCTTAGATTTACAGTCTAATGCTTTA-CTCAGCCACTTTACCACAAAAAAGGAAGGAATCGAACCCTCTAAAACCGGTTTCAAGCCAGCCCCATAACCTTTATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATCACAGGTCCAAACCCCGTATATCTTATCACTGTAGAGCTAGACCAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACTACCGCCTCTTTACAGTGA
		</sequence>
	</alignment>

	<!-- The unique patterns                                                     -->
	<!-- npatterns=69                                                            -->
	<patterns id="patterns1" from="1">
		<alignment idref="alignment1"/>
	</patterns>

	<tree id="treeML" units="years" usingDates="false">
		<node height="0.099582">
			<node height="0.069125">
				<node height="0.036038">
					<node height="0.024003">
						<node height="0.000000">
							<taxon idref="human"/>
						</node>
						<node height="0.010772">
							<node height="0.000000">
								<taxon idref="chimp"/>
							</node>
							<node height="0.000000">
								<taxon idref="bonobo"/>
							</node>
						</node>
					</node>
					<node height="0.000000">
						<taxon idref="gorilla"/>
					</node>
				</node>
				<node height="0.000000">
					<taxon idref="orangutan"/>
				</node>
			</node>
			<node height="0.000000">
				<taxon idref="siamang"/>
			</node>
		</node>
	</tree>

	<treeModel id="treeModel1">
		<tree idref="treeML"/>
		<rootHeight>
			<parameter id="treeModel1.rootHeight"/>
		</rootHeight>
		<nodeHeights internalNodes="true">
			<parameter id="treeModel1.internalNodeHeights"/>
		</nodeHeights>
		<nodeHeights internalNodes="true" rootNode="true">
			<parameter id="treeModel1.allInternalNodeHeights"/>
		</nodeHeights>
	</treeModel>


    <report>
        Newick Tree: <tree idref="treeML"/>

    </report>

    <!-- GTR -->

	<gtrModel id="gtr">
		<frequencies>
			<frequencyModel dataType="nucleotide">
				<alignment idref="alignment1"/>
				<frequencies>
					<parameter id="gtr.frequencies" dimension="4"/>
				</frequencies>
			</frequencyModel>
		</frequencies>
		<rateAC>
			<parameter id="gtr.ac" value="1.0" lower="1.0E-8" upper="Infinity"/>
		</rateAC>
		<rateAG>
			<parameter id="gtr.ag" value="1.0" lower="1.0E-8" upper="Infinity"/>
		</rateAG>
		<rateAT>
			<parameter id="gtr.at" value="1.0" lower="1.0E-8" upper="Infinity"/>
		</rateAT>
		<rateCG>
			<parameter id="gtr.cg" value="1.0" lower="1.0E-8" upper="Infinity"/>
		</rateCG>
		<rateGT>
			<parameter id="gtr.gt" value="1.0" lower="1.0E-8" upper="Infinity"/>
		</rateGT>
	</gtrModel>

    <siteModel id="siteModel7">
		<substitutionModel>
			<gtrModel idref="gtr"/>
		</substitutionModel>
        <mutationRate>
			<parameter id="siteModel7.mu" value="1.0" lower="0.0"/>
		</mutationRate>
    </siteModel>

	<OTFPCTreeLikelihood id="OTFPCTreeLikelihood7">
		<patterns idref="patterns1"/>
		<treeModel idref="treeModel1"/>
		<siteModel idref="siteModel7"/>
	</OTFPCTreeLikelihood>

	<report>
		GTR:
		ln L = <likelihood idref="OTFPCTreeLikelihood7"/>
		(PAUP = -1969.14584)

	</report>

    <!-- GTR+I -->

	<gtrModel id="gtrI">
		<frequencies>
			<frequencyModel dataType="nucleotide">
				<alignment idref="alignment1"/>
				<frequencies>
					<parameter id="gtrI.frequencies" dimension="4"/>
				</frequencies>
			</frequencyModel>
		</frequencies>
		<rateAC>
			<parameter id="gtrI.ac" value="1.0" lower="1.0E-8" upper="Infinity"/>
		</rateAC>
		<rateAG>
			<parameter id="gtrI.ag" value="1.0" lower="1.0E-8" upper="Infinity"/>
		</rateAG>
		<rateAT>
			<parameter id="gtrI.at" value="1.0" lower="1.0E-8" upper="Infinity"/>
		</rateAT>
		<rateCG>
			<parameter id="gtrI.cg" value="1.0" lower="1.0E-8" upper="Infinity"/>
		</rateCG>
		<rateGT>
			<parameter id="gtrI.gt" value="1.0" lower="1.0E-8" upper="Infinity"/>
		</rateGT>
	</gtrModel>

    <siteModel id="siteModel8">
		<substitutionModel>
			<gtrModel idref="gtrI"/>
		</substitutionModel>
        <mutationRate>
			<parameter id="siteModel8.mu" value="1.0" lower="0.0"/>
		</mutationRate>
		<proportionInvariant>
			<parameter id="siteModel8.pInv" value="0.5" lower="0.0" upper="1.0"/>
		</proportionInvariant>
    </siteModel>

	<OTFPCTreeLikelihood id="OTFPCTreeLikelihood8">
		<patterns idref="patterns1"/>
		<treeModel idref="treeModel1"/>
		<siteModel idref="siteModel8"/>
	</OTFPCTreeLikelihood>

	<report>
		GTR+I:
		ln L = <likelihood idref="OTFPCTreeLikelihood8"/>
		(PAUP = -1948.84175)

	</report>

    <!-- GTR+G -->

	<gtrModel id="gtrG">
		<frequencies>
			<frequencyModel dataType="nucleotide">
				<alignment idref="alignment1"/>
				<frequencies>
					<parameter id="gtrG.frequencies" dimension="4"/>
				</frequencies>
			</frequencyModel>
		</frequencies>
		<rateAC>
			<parameter id="gtrG.ac" value="1.0" lower="1.0E-8" upper="Infinity"/>
		</rateAC>
		<rateAG>
			<parameter id="gtrG.ag" value="1.0" lower="1.0E-8" upper="Infinity"/>
		</rateAG>
		<rateAT>
			<parameter id="gtrG.at" value="1.0" lower="1.0E-8" upper="Infinity"/>
		</rateAT>
		<rateCG>
			<parameter id="gtrG.cg" value="1.0" lower="1.0E-8" upper="Infinity"/>
		</rateCG>
		<rateGT>
			<parameter id="gtrG.gt" value="1.0" lower="1.0E-8" upper="Infinity"/>
		</rateGT>
	</gtrModel>

    <siteModel id="siteModel9">
		<substitutionModel>
			<gtrModel idref="gtrG"/>
		</substitutionModel>
        <mutationRate>
			<parameter id="siteModel9.mu" value="1.0" lower="0.0"/>
		</mutationRate>
        <gammaShape gammaCategories="4">
			<parameter id="siteModel9.alpha" value="0.5" lower="0.0" upper="100.0"/>
		</gammaShape>
    </siteModel>

	<OTFPCTreeLikelihood id="OTFPCTreeLikelihood9">
		<patterns idref="patterns1"/>
		<treeModel idref="treeModel1"/>
		<siteModel idref="siteModel9"/>
	</OTFPCTreeLikelihood>

	<report>
		GTR+G:
		ln L = <likelihood idref="OTFPCTreeLikelihood9"/>
		(PAUP = -1949.03601)

	</report>

    <!-- GTR+GI -->

	<gtrModel id="gtrGI">
		<frequencies>
			<frequencyModel dataType="nucleotide">
				<alignment idref="alignment1"/>
				<frequencies>
					<parameter id="gtrGI.frequencies" dimension="4"/>
				</frequencies>
			</frequencyModel>
		</frequencies>
		<rateAC>
			<parameter id="gtrGI.ac" value="1.0" lower="1.0E-8" upper="Infinity"/>
		</rateAC>
		<rateAG>
			<parameter id="gtrGI.ag" value="1.0" lower="1.0E-8" upper="Infinity"/>
		</rateAG>
		<rateAT>
			<parameter id="gtrGI.at" value="1.0" lower="1.0E-8" upper="Infinity"/>
		</rateAT>
		<rateCG>
			<parameter id="gtrGI.cg" value="1.0" lower="1.0E-8" upper="Infinity"/>
		</rateCG>
		<rateGT>
			<parameter id="gtrGI.gt" value="1.0" lower="1.0E-8" upper="Infinity"/>
		</rateGT>
	</gtrModel>

    <siteModel id="siteModel10">
		<substitutionModel>
			<gtrModel idref="gtrGI"/>
		</substitutionModel>
        <mutationRate>
			<parameter id="siteModel10.mu" value="1.0" lower="0.0"/>
		</mutationRate>
        <gammaShape gammaCategories="4">
			<parameter id="siteModel10.alpha" value="0.5" lower="0.0" upper="100.0"/>
		</gammaShape>
		<proportionInvariant>
			<parameter id="siteModel10.pInv" value="0.5" lower="0.0" upper="1.0"/>
		</proportionInvariant>
    </siteModel>

	<OTFPCTreeLikelihood id="OTFPCTreeLikelihood10">
		<patterns idref="patterns1"/>
		<treeModel idref="treeModel1"/>
		<siteModel idref="siteModel10"/>
	</OTFPCTreeLikelihood>

	<report>
		GTR+GI:
		ln L = <likelihood idref="OTFPCTreeLikelihood10"/>
		(PAUP = -1947.58294)

	</report>

</beast>


<!-- NEXUS File

#NEXUS
BEGIN TAXA;
	Dimensions ntax=6;
	Taxlabels
		human
		chimp
		bonobo
		gorilla
		orangutan
		siamang
		;
END;

BEGIN CHARACTERS;
	dimensions nchar=768;
	format datatype=dna missing=? gap=-;
	matrix

	human	AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCCTTATTTCTACTAGGACTATGAGAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAATACAGAC
		CAAGAGCCTTCAAAGCCCTCAGTAAGTTG-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCGGAGCTTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGGCCTCCATGACTTTTTCAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAATTATAGGCT-AAATCCTATATATCTTA-CACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACACCTCTTTACAGTGA

	chimp	AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTCAAATCCCCTTATTTCTACTAGGACTATAAGAATCGAACTCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTAAGCACAGAC
		CAAGAGCCTTCAAAGCCCTCAGCAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCTCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AACCCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCGACACCTCTTTACAGTGA

	bonobo	AGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATAATAGGAGTTTAAATCCCCTTATTTCTACTAGGACTATGAGAGTCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAAGAAATTTAGGTTAAACACAGAC
		CAAGAGCCTTCAAAGCTCTCAGTAAGTTA-CAATACTTAATTTCTGTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATTAATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAATCAGC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTTGAATTTGCAATTCAATATGAAAA-TCACCTCAGAGCTTGGTAAAAAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCCCCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCAACACCTCTTTACAGTGA

	gorilla	AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGAGGTTTAAACCCCCTTATTTCTACTAGGACTATGAGAATTGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTGTCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTCACATCCTTCCCGTACTAAGAAATTTAGGTTAAACATAGAC
		CAAGAGCCTTCAAAGCCCTTAGTAAGTTA-CAACACTTAATTTCTGTAAGGACTGCAAAACCCTACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCAATGGGACTCAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAT-TCACCTCGGAGCTTGGTAAAAAGAGGCCCAGCCTCTGTCTTTAGATTTACAGTCCAATGCCTTA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGACCTTCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAGGTTAAATTACGGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCGTTAACCTTTTAAGTTAAAGATTAAGAGTATCGGCACCTCTTTGCAGTGA

	orangutan	AGAAATATGTCTGACAAAAGAGTTACTTTGATAGAGTAAAAAATAGAGGTCTAAATCCCCTTATTTCTACTAGGACTATGGGAATTGAACCCACCCCTGAGAATCCAAAATTCTCCGTGCCACCCATCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAAGAAATTTAGGTTA-
		-CACAGACCAAGAGCCTTCAAAGCCCTCAGCAAGTCA-CAGCACTTAATTTCTGTAAGGACTGCAAAACCCCACTTTGCATCAACTGAGCGCAAATCAGCCACTTTAATTAAGCTAAGCCCTCCTAGACCGATGGGACTTAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAT-TGGCTTCAGTCCAAAGCCCCGGCAGGCCTTAAAGCTGCTCCTTCGAATTTGCAATTCAACATGACAA-TCACCTCAGGGCTTGGTAAAAAGAGGTCTGACCCCTGTTCTTAGATTTACAGCCTAATGCCTTAACTCGGCCATTTTACCGCAAAAAAGGAAGGAATCGAACCTCCTAAAGCTGGTTTCAAGCCAACCCCATAACCCCCATGACTTTTTCAAAAGGTACTAGAAAAACCATTTCGTAACTTTGTCAAAGTTAAATTACAGGTC-AGACCCTGTGTATCTTA-CATTGCAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACCAGCCTCTCTTTGCAATGA

	siamang	AGAAATACGTCTGACGAAAGAGTTACTTTGATAGAGTAAATAACAGGGGTTTAAATCCCCTTATTTCTACTAGAACCATAGGAGTCGAACCCATCCTTGAGAATCCAAAACTCTCCGTGCCACCCGTCGCACCCTGTTCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCATACTAAGAAATTTAGGTTAAACACAGAC
		CAAGAGCCTTCAAAGCCCTCAGTAAGTTAACAAAACTTAATTTCTGCAAGGGCTGCAAAACCCTACTTTGCATCAACCGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCGATGGGACTTAAACCCATAAAAATTTAGTTAACAGCTAAACACCCTAAACAACCTGGCTTCAATCTAAAGCCCCGGCAGA-GTTGAAGCTGCTTCTTTGAACTTGCAATTCAACGTGAAAAATCACTTCGGAGCTTGGCAAAAAGAGGTTTCACCTCTGTCCTTAGATTTACAGTCTAATGCTTTA-CTCAGCCACTTTACCACAAAAAAGGAAGGAATCGAACCCTCTAAAACCGGTTTCAAGCCAGCCCCATAACCTTTATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATCACAGGTCCAAACCCCGTATATCTTATCACTGTAGAGCTAGACCAGCATTAACCTTTTAAGTTAAAGACTAAGAGAACTACCGCCTCTTTACAGTGA
	;
END;

set
	criterion=likelihood
	storebrlens=yes;

BEGIN TREES;
	tree PAUP_1 = [&U] ((((human:0.024003,(chimp:0.010772,bonobo:0.010772):0.013231):0.012035,gorilla:0.036038):0.033087000000000005,orangutan:0.069125):0.030456999999999998,siamang:0.099582);
END;

BEGIN PAUP;

log
	file=exon_consensus_new.log replace;

[JC]
lscores  1/
	nst=1
	basefreq=equal
	rates=equal
	pinv=0
	reprate=median
	userbrlens=yes;

[K80]
lscores  1/
	nst=2
	basefreq=equal
	tratio=13.701296  [kappa = 27.402592]
	rates=equal
	pinv=0
	reprate=median
	userbrlens=yes;

[HKY]
lscores  1/
	nst=2
	basefreq=empirical
	tratio=13.841893  [kappa = 29.739445]
	rates=equal
	pinv=0
	reprate=mean
	userbrlens=yes;

[HKY+G]
lscores  1/
	nst=2
	basefreq=empirical
	tratio=18.0728692  [kappa = 38.829740]
	rates=gamma
	shape=0.137064
	pinv=0
	reprate=median
	userbrlens=yes;

[HKY+I]
lscores  1/
	nst=2
	basefreq=empirical
	tratio=17.9494965 [kappa = 38.564672]
	rates=equal
	pinv=0.701211
	reprate=median
	userbrlens=yes;

[HKY+I+G]
lscores  1/
	nst=2
	basefreq=empirical
	tratio=18.368329  [kappa = 39.464538]
	rates=gamma
	shape=0.587649
	pinv=0.486548
	reprate=median
	userbrlens=yes;

[GTR]
lscores  1/
	basefreq=empirical
	nst=6
	pinvar=0
	rates=equal
	userbrlens=yes;

[GTR + i]
lscores  1/
	basefreq=empirical
	nst=6
	pinvar=0.5
	rates=equal
	userbrlens=yes;

[GTR + g]
lscores  1/
	basefreq=empirical
	reprate=median
	nst=6
	rmatrix=(1.0 1.0 1.0 1.0 1.0 )
	pinvar=0
	rates=gamma
	ncat=4
	shape=0.5
	userbrlens=yes;

[GTR + i + g]
lscores  1/
	basefreq=empirical
	reprate=median
	nst=6
	rmatrix=(1.0 1.0 1.0 1.0 1.0 )
	pinvar=0.5
	rates=gamma
	ncat=4
	shape=0.5
	userbrlens=yes;

log
	stop;

END;

-->