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<?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=3 -->
<taxa id="taxa1">
<taxon id="human"/>
<taxon id="chimp"/>
<taxon id="gorilla"/>
</taxa>
<!-- The sequence alignment (each sequence refers to a taxon above). -->
<!-- ntax=3 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="gorilla"/>
AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGAGGTTTAAACCCCCTTATTTCTACTAGGACTATGAGAATTGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTGTCACACCCCATCCTAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTCACATCCTTCCCGTACTAAGAAATTTAGGTTAAACATAGACCAAGAGCCTTCAAAGCCCTTAGTAAGTTA-CAACACTTAATTTCTGTAAGGACTGCAAAACCCTACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTCTAGATCAATGGGACTCAAACCCACAAACATTTAGTTAACAGCTAAACACCCTAGTCAAC-TGGCTTCAATCTAAAGCCCCGGCAGG-TTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAT-TCACCTCGGAGCTTGGTAAAAAGAGGCCCAGCCTCTGTCTTTAGATTTACAGTCCAATGCCTTA-CTCAGCCATTTTACCACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGACCTTCATGACTTTTTCAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAGGTTAAATTACGGGTT-AAACCCCGTATATCTTA-CACTGTAAAGCTAACCTAGCGTTAACCTTTTAAGTTAAAGATTAAGAGTATCGGCACCTCTTTGCAGTGA
</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="0.2">
<node height="0.1">
<node height="0.000000">
<taxon idref="human"/>
</node>
<node height="0.000000">
<taxon idref="chimp"/>
</node>
</node>
<node height="0.000000">
<taxon idref="gorilla"/>
</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>
<!-- JC -->
<!--<hkyModel id="jc69">-->
<!--<frequencies>-->
<!--<frequencyModel dataType="nucleotide">-->
<!--<frequencies>-->
<!--<parameter dimension="4" value="0.25 0.25 0.25 0.25"/>-->
<!--</frequencies>-->
<!--</frequencyModel>-->
<!--</frequencies>-->
<!--<kappa>-->
<!--<parameter id="jc69.kappa" value="1.0" lower="0.0" upper="100.0"/>-->
<!--</kappa>-->
<!--</hkyModel>-->
<complexSubstitutionModel id="circulant" dataType="nucleotide">
<rootFrequencies>
<frequencyModel dataType="nucleotide">
<frequencies>
<parameter dimension="4" value="0.25 0.25 0.25 0.25"/>
</frequencies>
</frequencyModel>
</rootFrequencies>
<rates>
<parameter id="circulant.rates" value="1 0 0 1 0 1 0 0 1 0 0 0"/>
</rates>
</complexSubstitutionModel>
<siteModel id="siteModel1">
<substitutionModel>
<complexSubstitutionModel idref="circulant"/>
</substitutionModel>
</siteModel>
<treeLikelihood id="treeLikelihood1">
<patterns idref="patterns1"/>
<treeModel idref="treeModel1"/>
<siteModel idref="siteModel1"/>
</treeLikelihood>
<report>
Circulant:
ln L = <likelihood idref="treeLikelihood1"/>
</report>
</beast>
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