<?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>

    <!-- 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>

    <siteModel id="siteModel1">
        <substitutionModel>
            <hkyModel idref="jc69"/>
        </substitutionModel>
        <mutationRate>
            <parameter id="siteModel1.mu" value="1.0" lower="0.0"/>
        </mutationRate>
    </siteModel>

    <treeLikelihood id="treeLikelihood1">
        <patterns idref="patterns1"/>
        <treeModel idref="treeModel1"/>
        <siteModel idref="siteModel1"/>
    </treeLikelihood>

    <report>
        JC69:
        ln L =
        <treeLikelihood idref="treeLikelihood1"/>
        (PAUP = -1992.20564)

    </report>

    <!-- K80 -->

    <hkyModel id="k80">
        <frequencies>
            <frequencyModel id="frequencies1" dataType="nucleotide">
                <frequencies>
                    <parameter dimension="4" value="0.25 0.25 0.25 0.25"/>
                </frequencies>
            </frequencyModel>
        </frequencies>
        <kappa>
            <parameter id="k80.kappa" value="27.402591" lower="0.0" upper="100.0"/>
        </kappa>
    </hkyModel>

    <siteModel id="siteModel2">
        <substitutionModel>
            <hkyModel idref="k80"/>
        </substitutionModel>
        <mutationRate>
            <parameter id="siteModel2.mu" value="1.0" lower="0.0"/>
        </mutationRate>
    </siteModel>

    <treeLikelihood id="treeLikelihood2">
        <patterns idref="patterns1"/>
        <treeModel idref="treeModel1"/>
        <siteModel idref="siteModel2"/>
    </treeLikelihood>

    <report>
        K80:
        ln L =
        <treeLikelihood idref="treeLikelihood2"/>
        (PAUP = -1856.30305)

    </report>

    <!-- HKY -->

    <hkyModel id="hky85">
        <frequencies>
            <frequencyModel dataType="nucleotide">
                <alignment idref="alignment1"/>
                <frequencies>
                    <parameter id="hky85.frequencies" dimension="4"/>
                </frequencies>
            </frequencyModel>
        </frequencies>
        <kappa>
            <parameter id="hky85.kappa" value="29.739445" lower="0.0" upper="100.0"/>
        </kappa>
    </hkyModel>

    <siteModel id="siteModel3">
        <substitutionModel>
            <hkyModel idref="hky85"/>
        </substitutionModel>
        <mutationRate>
            <parameter id="siteModel3.mu" value="1.0" lower="0.0"/>
        </mutationRate>
    </siteModel>

    <treeLikelihood id="treeLikelihood3">
        <patterns idref="patterns1"/>
        <treeModel idref="treeModel1"/>
        <siteModel idref="siteModel3"/>
    </treeLikelihood>

    <report>
        HKY85:
        ln L =
        <treeLikelihood idref="treeLikelihood3"/>
        (PAUP = -1825.21317)

    </report>

    <!-- HKY+G -->

    <hkyModel id="hky85G">
        <frequencies>
            <frequencyModel dataType="nucleotide">
                <alignment idref="alignment1"/>
                <frequencies>
                    <parameter id="hky85G.frequencies" dimension="4"/>
                </frequencies>
            </frequencyModel>
        </frequencies>
        <kappa>
            <parameter id="hky85G.kappa" value="38.829740" lower="0.0" upper="100.0"/>
        </kappa>
    </hkyModel>

    <siteModel id="siteModel4">
        <substitutionModel>
            <hkyModel idref="hky85G"/>
        </substitutionModel>
        <mutationRate>
            <parameter id="siteModel4.mu" value="1.0" lower="0.0"/>
        </mutationRate>
        <gammaShape gammaCategories="4">
            <parameter id="siteModel4.shape" value="0.137064" lower="0.0" upper="1000.0"/>
        </gammaShape>
    </siteModel>

    <treeLikelihood id="treeLikelihood4">
        <patterns idref="patterns1"/>
        <treeModel idref="treeModel1"/>
        <siteModel idref="siteModel4"/>
    </treeLikelihood>

    <report>
        HKY85+G:
        ln L =
        <treeLikelihood idref="treeLikelihood4"/>
        (PAUP = -1789.75936, PAML = -1789.75936)

    </report>

    <!-- HKY+I -->

    <hkyModel id="hky85I">
        <frequencies>
            <frequencyModel dataType="nucleotide">
                <alignment idref="alignment1"/>
                <frequencies>
                    <parameter id="hky85I.frequencies" dimension="4"/>
                </frequencies>
            </frequencyModel>
        </frequencies>
        <kappa>
            <parameter id="hky85I.kappa" value="38.564672" lower="0.0" upper="100.0"/>
        </kappa>
    </hkyModel>

    <siteModel id="siteModel5">
        <substitutionModel>
            <hkyModel idref="hky85I"/>
        </substitutionModel>
        <mutationRate>
            <parameter id="siteModel5.mu" value="1.0" lower="0.0"/>
        </mutationRate>
        <proportionInvariant>
            <parameter id="siteModel5.pinv" value="0.701211" lower="0.0" upper="1.0"/>
        </proportionInvariant>
    </siteModel>

    <treeLikelihood id="treeLikelihood5">
        <patterns idref="patterns1"/>
        <treeModel idref="treeModel1"/>
        <siteModel idref="siteModel5"/>
    </treeLikelihood>

    <report>
        HKY85+I:
        ln L =
        <treeLikelihood idref="treeLikelihood5"/>
        (PAUP = -1789.91240)

    </report>

    <!-- HKY+GI -->

    <hkyModel id="hky85GI">
        <frequencies>
            <frequencyModel dataType="nucleotide">
                <alignment idref="alignment1"/>
                <frequencies>
                    <parameter id="hky85GI.frequencies" dimension="4"/>
                </frequencies>
            </frequencyModel>
        </frequencies>
        <kappa>
            <parameter id="hky85GI.kappa" value="39.464538" lower="0.0" upper="100.0"/>
        </kappa>
    </hkyModel>

    <siteModel id="siteModel6">
        <substitutionModel>
            <hkyModel idref="hky85GI"/>
        </substitutionModel>
        <mutationRate>
            <parameter id="siteModel6.mu" value="1.0" lower="0.0"/>
        </mutationRate>
        <gammaShape gammaCategories="4">
            <parameter id="siteModel6.shape" value="0.587649" lower="0.0" upper="1000.0"/>
        </gammaShape>
        <proportionInvariant>
            <parameter id="siteModel6.pinv" value="0.486548" lower="0.0" upper="1.0"/>
        </proportionInvariant>
    </siteModel>

    <treeLikelihood id="treeLikelihood6" useAmbiguous="true">
        <patterns idref="patterns1"/>
        <treeModel idref="treeModel1"/>
        <siteModel idref="siteModel6"/>
    </treeLikelihood>

    <report>
        HKY85+GI:
        ln L =
        <treeLikelihood idref="treeLikelihood6"/>
        (PAUP = -1789.63923)

    </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>

    <treeLikelihood id="treeLikelihood7">
        <patterns idref="patterns1"/>
        <treeModel idref="treeModel1"/>
        <siteModel idref="siteModel7"/>
    </treeLikelihood>

    <report>
        GTR:
        ln L =
        <treeLikelihood idref="treeLikelihood7"/>
        (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>

    <treeLikelihood id="treeLikelihood8">
        <patterns idref="patterns1"/>
        <treeModel idref="treeModel1"/>
        <siteModel idref="siteModel8"/>
    </treeLikelihood>

    <report>
        GTR+I:
        ln L =
        <treeLikelihood idref="treeLikelihood8"/>
        (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>

    <treeLikelihood id="treeLikelihood9">
        <patterns idref="patterns1"/>
        <treeModel idref="treeModel1"/>
        <siteModel idref="siteModel9"/>
    </treeLikelihood>

    <report>
        GTR+G:
        ln L =
        <treeLikelihood idref="treeLikelihood9"/>
        (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>

    <treeLikelihood id="treeLikelihood10">
        <patterns idref="patterns1"/>
        <treeModel idref="treeModel1"/>
        <siteModel idref="siteModel10"/>
    </treeLikelihood>

    <report>
        GTR+GI:
        ln L =
        <treeLikelihood idref="treeLikelihood10"/>
        (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;

        -->