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<?xml version="1.0" standalone="yes"?>
<!-- Generated by BEAUTi v1.4 -->
<!-- Alexei Drummond and Andrew Rambaut -->
<!-- Department of Zoology, University of Oxford -->
<!-- http://evolve.zoo.ox.ac.uk/beast/ -->
<beast>
<!-- The list of taxa analyse (can also include dates/ages). -->
<!-- ntax=17 -->
<taxa id="taxa">
<taxon id="D4Brazi82">
<date value="1982.0" direction="forwards" units="years"/>
</taxon>
<taxon id="D4ElSal83">
<date value="1983.0" direction="forwards" units="years"/>
</taxon>
<taxon id="D4ElSal94">
<date value="1994.0" direction="forwards" units="years"/>
</taxon>
<taxon id="D4Indon76">
<date value="1976.0" direction="forwards" units="years"/>
</taxon>
<taxon id="D4Indon77">
<date value="1977.0" direction="forwards" units="years"/>
</taxon>
<taxon id="D4Mexico84">
<date value="1984.0" direction="forwards" units="years"/>
</taxon>
<taxon id="D4NewCal81">
<date value="1981.0" direction="forwards" units="years"/>
</taxon>
<taxon id="D4Philip64">
<date value="1964.0" direction="forwards" units="years"/>
</taxon>
<taxon id="D4Philip56">
<date value="1956.0" direction="forwards" units="years"/>
</taxon>
<taxon id="D4Philip84">
<date value="1984.0" direction="forwards" units="years"/>
</taxon>
<taxon id="D4PRico86">
<date value="1986.0" direction="forwards" units="years"/>
</taxon>
<taxon id="D4SLanka78">
<date value="1978.0" direction="forwards" units="years"/>
</taxon>
<taxon id="D4Tahiti79">
<date value="1979.0" direction="forwards" units="years"/>
</taxon>
<taxon id="D4Tahiti85">
<date value="1985.0" direction="forwards" units="years"/>
</taxon>
<taxon id="D4Thai63">
<date value="1963.0" direction="forwards" units="years"/>
</taxon>
<taxon id="D4Thai78">
<date value="1978.0" direction="forwards" units="years"/>
</taxon>
<taxon id="D4Thai84">
<date value="1984.0" direction="forwards" units="years"/>
</taxon>
</taxa>
<!-- The sequence alignment (each sequence refers to a taxon above). -->
<!-- ntax=17 nchar=1485 -->
<alignment id="alignment" dataType="nucleotide">
<sequence>
<taxon idref="D4Brazi82"/>
ATGCGATGCGTAGGAGTAGGAAACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGACCTGGTGCTAGAACATGGAGGATGCGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGACCAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCAATATCAAACATAACTACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTATCTGAAAGAGGAACAGGACCAACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGTTTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGTTCGGGGAAGATAACAGGCAATTTGGTCCAAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGACACATCCAATCATGGAGTTACAGCCATGATAACTCCCAGGTCACCATCGGTGGAAGTCAAATTGCCGGACTATGGAGAACTAACACTCGATTGTGAACCCAGGTCTGGAATTGACTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACATGGCTCGTGCATAAGCAATGGTTTTTGGATCTGCCTCTTCCATGGACAGCAGGAGCAGACACATCAGAGGTTCACTGGAATTACAAAGAGAGAATGGTGACATTTAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTGGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCGCTGGAGCCACAGAAGTGGACTCCGGTGATGGAAATCACATGTTTGCAGGACATCTCAAGTGCAAAGTCCGTATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGTTCAGGAAAGTTTTCAATTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTGAAAGTCAAGTATGAAGGTGCTGGAGCTCCGTGTAAAGTCCCCATAGAGATAAGAGATGTAAACAAGGAAAAAGTGGTTGGGCGTATCATCTCATCCACCCCTTTGGCTGAGAATACCAACAGTGTAACCAACATAGAATTAGAACCCCCCTTTGGGGACAGCTACATAGTGATAGGTGTTGGAAACAGCGCATTAACACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAACGAATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCCGTTGGTGGATTGTTCACATCATTGGGAAAGGCTGTGCACCAGGTTTTTGGAAGTGTGTATACAACCATGTTTGGAGGAGTCTCATGGATGATTAGAATCCTAATTGGGTTCTTAGTGTTGTGGATTGGCACGAACTCAAGGAACACTTCAATGGCTATGACGTGCATAGCTGTTGGAGGAATCACTCTGTTTCTGGGCTTCACAGTTCAAGCA
</sequence>
<sequence>
<taxon idref="D4ElSal83"/>
ATGCGATGCGTAGGAGTAGGAAACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGACCTGGTGCTAGAACATGGAGGATGCGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGACTAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCAATATCAAACATAACTACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTATCTGAAAGAGGAACAGGACCAACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGTTTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGTTCGGGGAAGATAACAGGCAATTTGGTCCAAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGACACATCCAATCATGGAGTTACAGCCATGATAACTCCCAGGTCACCATCGGTGGAAGTCAAATTGCCGGACTATGGAGAACTAACACTCGATTGTGAACCCAGGTCTGGAATTGACTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACATGGCTCGTGCATAAGCAATGGTTTTTGGATCTGCCTCTTCCATGGACAGCAGGAGCAGACACATCAGAGGTTCACTGGAATTACAAAGAGAGAATGGTGACATTTAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTGGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCGCTGGAGCCACAGAAGTGGACTCCGGTGATGGAAATCATATGTTTGCAGGACATCTCAAGTGCAAAGTCCGTATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGTTCAGGAAAGTTTTCAATTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTGAAAGTCAAGTATGAAGGTGCTGGAGCTCCGTGTAAAGTCCCCATAGAGATAAGAGATGTAAACAAGGAAAAAGTGGTTGGGCGTATCATCTCATCCACCCCTTTGGCTGAGAATACCAACAGTGTAACCAACATAGAATTAGAACCCCCCTTTGGGGACAGCTACATAGTGATAGGTGTTGGAAACAGCGCATTAACACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAACGAATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCCGTTGGTGGACTGTTCACATCATTGGGAAAGGCTGTGCACCAGGTTTTTGGAAGTGTGTATACAACCATGTTTGGAGGAGTCTCATGGATGATTAGAATCCTAATTGGGTTCTTAGTGTTGTGGATTGGCACGAACTCAAGGAACACTTCAATGGCTATGACGTGCATAGCTGTTGGAGGAATCACTCTGTTTCTGGGCTTCACAGTTCAAGCA
</sequence>
<sequence>
<taxon idref="D4ElSal94"/>
ATGCGATGCGTAGGAGTAGGAAACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGACCTGGTGCTAGAACATGGAGGATGCGTCACAACCATAGCCCAGGGAAAACCAACCTTGGATTTTGAATTGACTAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCAATATCAAACATAACTACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTATCTGAAAGAGGAACAGGACCAACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGGAATGGCTGTGGCTTGCTTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGTTCGGGGAAGATAACAGGCAATTTGGTCCAAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGATACCCATGCAGTAGGAAATGACACATCCAATCATGGAGTTACAGCCACGATAACTCCCAGGTCACCATCGGTGGAAGTCAAATTGCCGGACTATGGAGAACTAACACTCGATTGTGAACCCAGATCTGGAATTGATTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACATGGCTCGTGCATAAGCAATGGTTTTTGGATCTGCCTCTTCCATGGACAGCAGGAGCAGACACATCAGAGGTTCACTGGAATTACAAAGAGAGAATGGTGACATTCAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTGGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCGCTGGAGCCACAGAAGTGGACTCCGGTGATGGAAATCACATGTTTGCAGGACATCTCAAGTGCAAAGTCCGCATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGTTCAGGAAAGTTTTCAATTGATAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTGAAAGTCAAGTATGAAGGTGCTGGAGCTCCGTGTAAAGTCCCCATAGAGATAAGAGATGTAAACAAGGAAAAAGTGGTTGGGCGTATCATCTCATCCACCCCTTTGGCTGAGAATACCAACAGTGTAACCAACATAGAATTAGAACCCCCCTTTGGGGACAGCTACATAGTGATAGGTGTCGGAAACAGCGCATTAACACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAACGAATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCCGTTGGTGGACTGTTCACATCATTGGGAAAGGCTGTGCACCAGGTTTTTGGAAGTGTGTACACAACCATGTTTGGAGGAGTCTCATGGATGATTAGAATCCTAATTGGGTTCTTAGTGTTATGGATTGGCACGAACTCAAGGAACACTTCAATGGCTATGACGTGCATAGCTGTTGGAGGAATCACTCTGTTTCTGGGCTTCACAGCTCAAGCA
</sequence>
<sequence>
<taxon idref="D4Indon76"/>
ATGCGATGCGTAGGAGTAGGAAACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGATCTGGTGCTAGAACATGGAGGATGCGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGACTAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCAATATCAAACATAACCACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTATCTAAAAGAGGAACAAGACCAACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGTTTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGTTCGGGGAAGATAACAGGCAATTTGGTCCAAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGACACATCCAATCATGGAGTTACAGCCACGATAACTCCCAGGTCACCATCGGTGGAAGTCAAATTGCCGGACTATGGAGAACTAACACTCGATTGTGAACCCAGGTCTGGAATTGACTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACATGGCTTGTGCATAAGCAATGGTTTTTGGATCTACCTCTACCATGGACAGCAGGAGCAGACACATCAGAGGTTCACTGGAATTACAAAGAGAGAATGGTGACATTTAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTGGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCGCTGGAGCCACAGAAGTGGACTCCGGTGATGGAAATCACATGTTTGCAGGACATCTCAAGTGCAAAGTCCGTATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGTCCAGGAAAGTTCTCAATTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTGAAAGTCAAGTATGAAGGTGCTGGAGCTCCGTGTAAAGTCCCCATAGAGATAAGAGATGTGAACAAGGAAAAAGTGGTTGGGCGTATCATCTCATCCACCCCTTTGGCTGAGAATACCAACAGTGCAACCAACATAGAGTTAGAACCCCCCTTTGGGGACAGCTACATAGTGATAGGTGTTGGAAACAGTGCATTAACACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAACGAATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCCGTTGGTGGACTGCTCACATCATTGGGAAAGGCTGTGCACCAGGTTTTTGGAAGTGTGTATACAACCATGTTTGGAGGAGTCTCATGGATGATTAGAATCCTAATTGGGTTCCTAGTGTTGTGGATTGGCACGAACTCAAGGAACACTTCAATGGCTATGACGTGCATAGCTGTTGGAGGAATCACTCTGTTTCTGGGCTTCACAGTTCAAGCA
</sequence>
<sequence>
<taxon idref="D4Indon77"/>
ATGCGATGCGTAGGAGTAGGAAACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGATCTGGTGCTAGAACATGGAGGATGCGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGACTAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCAATATCAAACATAACCACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTATCTAAAAGAGGAACAAGACCAACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGTTTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGTTCGGGGAAGATAACAGGCAATTTGGTCCAAATTGAGAACCTTGAATACACAGTAGTTGTAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGACACATCCAACCATGGAGTTACAGCCACGATAACTCCCAGGTCACCATCGGTGGAAGTCAAATTGCCGGACTATGGAGAACTAACACTCGATTGTGAACCCAGGTCTGGAATTGACTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACATGGCTTGTGCATAAGCAATGGTTTTTGGATCTACCTCTACCATGGACAGCAGGAGCAGACACATCAGAGGTTCACTGGAATTACAAAGAGAGAATGGTGACATTTAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTGGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCGCTGGAGCCACAGAAGTGGACTCCGGTGATGGAAATCACATGTTTGCAGGACATCTCAAGTGCAAAGTCCGTATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGTTCAGGAAAGTTCTCAATTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTGAAAGTCAAGTATGAAGGTGCTGGAGCTCCGTGCAAAGTCCCCATAGAGATAAGAGATGTAAACAAGGAAAAAGTGGTTGGGCGTATCATCTCATCCACCCCTTTGGCTGAGAATACCAACAGTGTAACCAACATAGAATTAGAACCCCCCTTTGGGGACAGCTACATAGTGATAGGTGTTGGAAACAGTGCATTAACACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAACGAATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCCGTTGGTGGACTGTTCACATCATTGGGAAAGGCTGTGCACCAGGTTTTTGGAAGTGTGTATACAACCATGTTTGGAGGAGTCTCATGGATGATTAGAATCCTAATTGGCTTCTTAGTGTTGTGGATTGGCACGAACTCAAGGAACACTTCAATGGCTATGACGTGCATAGCTGTTGGAGGAATCACTCTGTTTCTGGGCTTCACAGTTCAAGCA
</sequence>
<sequence>
<taxon idref="D4Mexico84"/>
ATGCGATGCGTAGGAGTAGGAAACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGACCTAGTGCTAGAACATGGAGGATGCGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGACTAAGACAACAGCCAAGGAAGTGGCTCTGCTAAGAACCTATTGCATTGAAGCCTCAATATCAAACATAACTACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTATCTGAAAGAGGAACAGGACCAACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGTTTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGTTCGGGGAAGATAACAGGCAATTTGGTCCAAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGACACATCCAATCATGGAGTTACAGCCATGATAACTCCCAGGTCACCATCGGTGGAAGTCAAATTGCCGGACTATGGAGAACTAACACTCGATTGTGAACCCAGGTCTGGAATTGACTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACATGGCTCGTGCATAAGCAATGGTTTTTGGATCTGCCTCTTCCATGGACAGCAGGAGCAGACACATCAGAGGTTCACTGGAATTACAAAGAGAGAATGGTGACATTTAAGGTTCCCCATGCCAAGAGACAGGATGTGACAGTGCTGGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCGCTGGAGCCACAGAAGTGGACTCCGGTGATGGAAATCACATGTTTGCAGGACATCTCAAGTGCAAAGTCCGTATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGTTCAGGAAAGTTTTCAATTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTGAAAGTCAAGTGTGAAGGTGCTGGAGCTCCCTGTAAAGTCCCCATAGAGATAAGAGATGTAAACAAGGAAAAAGTGGTTGGGCGTATCATCTCATCCACCCCTTTGGCTGAGAATACCAACAGTGTAACCAACATAGAATTAGAACCTCCCTTTGGGGACAGCTACATAGTGATAGGTGTTGGAAACAGCGCATTAACACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAACGAATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCCGTTGGTGGACTGTTCACATCATTGGGAAAGGCTGTGCACCAGGTTTTTGGAAGTGTGTATACAACCATGTTTGGAGGAGTCTCATGGATGATTAGAATCCTAATTGGGTTCTTAGTGTTGTGGATTGGCACGAACTCAAGGAACACTTCAATGGCTATGACGTGCATAGCTGTTGGAGGAATCACTCTGTTTCTGGGCTTCACAGTTCAAGCA
</sequence>
<sequence>
<taxon idref="D4NewCal81"/>
ATGCGATGCGTAGGAGTAGGAAACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGACCTGGTGCTAGAACATGGAGGATGCGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGACTAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCAATATCAAACATAACTACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTATCTGAAAGAGGAACAGGACCAACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGTTTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGTTCGGGGAAGATAACAGGCAATTTGGTCCAAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGACACATCCAATCATGGAGTTACAGCCATGATAACTCCCAGGTCACCATCGGTGGAAGTCAAATTGCCGGACTATGGAGAACTAACACTCGATTGTGAACCCAGGTCTGGAATTGACTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACATGGCTCGTGCATAAGCAATGGTTTTTGGATCTGCCTCTTCCATGGACAGCAGGAGCAGACACATCAGAGGTTCACTGGAATTACAAAGAGAGAATGGTGACATTTAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTGGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCGCTGGAGCCACAGAAGTGGACTCCGGTGATGGAAATCACATGTTTGCAGGACATCTCAAGTGCAAAGTCCGTATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGTTCAGGAAAGTTTTCAATTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTGAAAGTCAAGTATGAAGGTGCTGGAGCTCCGTGTAAAGTCCCCATAGAGATAAGAGATGTAAACAAGGAAAAAGTGGTTGGGCGTATCATCTCATCCACCCCTTTGGCTGAGAATACCAACAGTGTAACCAACATAGAATTAGAACCCCCCTTTGGGGACAGCTACATAGTGATAGGTGTTGGAAACAGCGCATTAACACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAACGAATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCCGTTGGTGGACTGTTCACATCATTGGGAAAGGCTGTGCACCAGGTTTTTGGAAGTGTGTATACAACCATGTTTGGAGGAGTCTCATGGATGATTAGAATCCTAATTGGGTTCTTAGTGTTGTGGATTGGCACGAACTCAAGGAACACTTCAATGGCTATGACGTGCATAGCTGTTGGAGGAATCACTCTGTTTCTGGGCTTCACAGTTCAAGCA
</sequence>
<sequence>
<taxon idref="D4Philip64"/>
ATGCGATGCGTGGGAGTGGGGAACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGATTTGGTGCTAGAACATGGAGGATGTGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGATCAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCGATATCAAACATAACCACGGCAACAAGATGTCCAACGCAAGGAGAACCTTATCTCAAAGAGGAACAAGATCAACAGTACATCTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGTTTGGGAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGCTCGGGGAAGATAACAGGCAATTTGGTCCAAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGATACATCCAACCATGGAGTGACAGCCACGATAACCCCCAGGTCACCATCGGTAGAAGTTAAATTACCGGATTATGGAGAATTAACACTCGATTGTGAACCCAGGTCCGGAATTGATTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACGTGGCTTGTGCACAAGCAATGGTTTTTGGATCTACCTCTACCATGGGCAGCAGGAGCAGATACATCAGAAGTTCATTGGAATTACAAAGAGAGAATGGTGACATTCAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTAGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCACCGGAGCTACAGAAGTGGATTCCGGTGATGGAAACCACATGTTTGCAGGACATCTGAAATGCAAAGTTCGCATGGAGAAATTGAGAATTAAGGGAATGTCATACACGATGTGCTCAGGAAAGTTCTCAATTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTAAAAGTCAAATATGAGGGTGCTGGAGCTCCATGTAAAGTTCCCATAGAGATAAGAGATGTGAACAAGGAAAAAGTGGTAGGGCGTATCATCTCATCTACCCCTTTGGCTGAGAACACCAACAGTGTAACCAACATAGAATTAGAACCCCCTTTTGGGGACAGCTACATAGTAATAGGTGTTGGAGACAGTGCATTAACACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAGCGAATGGCCATTCTAGGTGAAACAGCCTGGGATTTTGGTTCGGTTGGTGGACTGCTCACATCATTGGGAAAGGCTGTACACCAGGTTTTTGGTAGTGTGTATACAACTATGTTTGGAGGAGTCTCATGGATGGTTAGAATCCTAATTGGGTTCTTAGTGTTGTGGATTGGCACGAATTCGAGAAACACCTCAATGGCAATGACGTGCATAGCTGTTGGAGGAATCACTCTGTTTCTGGGTTTCACAGTTCACGCA
</sequence>
<sequence>
<taxon idref="D4Philip56"/>
ATGCGATGCGTGGGAGTGGGGAACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGATTTGGTGCTAGAACATGGAGGATGTGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGATCAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCGATATCAAACATAACCACGGCAACAAGATGTCCAACGCAAGGAGAACCTTATCTCAAAGAGGAACAAGATCAACAGTACATCTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGCTTGGGAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGCTCGGGGAAGATAACAGGCAATTTGGTCCAAATTGAGAACCTTGAATACACAGTAGTTGTAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGACATATCCAACCATGGAGTGACAGCCACGATAACCCCCAGGTCACCATCGGTAGAAGTTAAATTACCGGATTATGGAGAATTAACACTCGATTGTGAACCCAGGTCCGGAATTGATTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACGTGGCTTGTGCACAAGCAATGGTTTTTGGATCTACCTCTACCATGGGCAGCAGGAGCAGACACATCAGAAGTTCATTGGAATTACAAAGAGAGAATGGTGACATTCAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTAGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCACCGGAGCTACAGAAGTGGATTCCGGTGATGGAAACCACATGTATGCAGGACATCTGAAATGCAAAGTTCGCATGGAGAAATTGAGAATTAAGGGAATGTCATACACGATGTGCTCAGGAAAGTTCTCAATTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTAAAAGTCAAGTATGAGGGTGCTGGAGCTCCATGTAAAGTTCCCATAGAGATAAGAGATGTGAACAAGGAAAAAGTGGTAGGGCGCATCATCTCATCTACCCCTTTGGCTGAGTATACCAACAGTGTAACCAACATAGAATTAGAACCCCCCTTTGGGGACAGCTACATAGTAATAGGTGTTGGAGACAGTGCATTAACACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGCGCAAAGCGAATGGCCATTCTAGGTGAAACAGCCTGGGATTTTGGTTCTGTTGGTGGACTGCTCACATCATTGGGAAAGGCTGTACACCAGGTTTTTGGTAGTGTGTATACAACTATGTTTGGAGGAGTCTCATGGATGGTTAGAATCCTAATTGGGTTCTTAGTGTTGTGGATTGGCACGAATTCGAGAAACACCTCAATGGCAATGACGTGCATAGCTGTTGGAGGAATCACTCTGTTTCTGGGTTTCACAGTTCACGCA
</sequence>
<sequence>
<taxon idref="D4Philip84"/>
ATGCGATGCGTAGGAGTGGGGAACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGACTTAGTGCTAGAACATGGAGGATGTGTCACAACCATGGCCCAAGGAAAACCAACCTTGGATTTTGAACTGATCAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCGATATCAAACATAACCACGGCAACAAGATGCCCAACGCAAGGAGAACCTTATCTCAAAGAGGAACAAGATCAACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGTTTGGGAAAGGAGGAGTTGTGACATGTGCGAAGTTCTCATGCTCGGGAAAGATAACAGGCAATTTGGTCCAAATTGAGAACCTTGAATATACAGTGGTTGTAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGACACATCCAACCATGGAGTGACAGCCACGATAACCCCTAGGTCACCATCGGTAGAAGTTAAATTACCGGATTATGGAGAATTAACACTTGATTGTGAACCCAGGTCCGGAATTGACTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACGTGGCTTGTGCACAAGCAATGGTTTCTGGATCTGCCTCTACCATGGGCAGCAGGAGCAGATACATCAGAAGTTCATTGGAATTACAAAGAGAGAATGGTGACATTCAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTAGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCACCGGAGCTACAGAAGTGGATTCCGGTGATGGAAACCACATGTTTGCAGGACATCTGAAATGCAAAGTTCGCATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGCTCAGGGAAGTTCTCAATTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTTAAAGTCAAATATGAAGGTGCTGGAGCTCCGTGCAAAGTTCCCATAGAGATAAGAGATGTGAACAGGGAAAAAGTGGTAGGGCGTGTCATCTCATCTACCCCTTTGGCCGAGAATACCAACAGTGTAACCAACATAGAATTAGAACCCCCTTTTGGGGACAGCTACATAGTAATAGGTGTTGGAGACAGTGCATTAACACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAGCGAATGGCCATTCTAGGTGAAACAGCCTGGGATTTTGGTTCTGTTGGTGGACTGCTCACATCATTGGGAAAGGCTGTACACCAGGTTTTTGGTAGTGTGTATACAACTATGTTTGGAGGAGTCTCATGGATGGTTAGAATCCTAATTGGGTTCCTAGTGTTGTGGATTGGCACGAATTCGAGAAACACCTCAATGGCAATGACGTGCATAGCTGTTGGAGGAATCACTCTGTTCATGGGTTTCACAGTTCACGCA
</sequence>
<sequence>
<taxon idref="D4PRico86"/>
ATGCGATGCGTAGGAGTAGGAAACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGACCTGGTGCTAGAACATGGAGGATGCGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGACTAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCAATATCAAACATAACTACGGCAACAAGATGTCCAACGCAAGGGGAGCCCTATCTGAAAGAGGAACAGGACCAACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGTTTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGTTCGGGGAAGATAACAGGCAATCTGGTCCAAATTGAGAACCTTGAGTACACAGTGGTTGTAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGACACATCCAATCATGGAGTTACAGCCACGATAACTCCCAGGTCACCATCGGTGGAAGTCAAATTGCCGGACTATGGAGAACTAACACTCGATTGTGAACCCAGGTCTGGAATTGACTTTAATGAGATGATTCTAATGAAAATGAAAAAGAAAACATGGCTCGTGCATAAGCAATGGTTTTTGGATCTGCCTCTTCCATGGACAGCAGGAGCAGACACATCAGAGGTTCACTGGAATTACAAAGAGAGAATGGTGACATTTAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTGGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCGCTGGAGCCACAGAAGTGGACTCCGGTGATGGAAATCACATGTTTGCAGGACATCTCAAGTGCAAAGTCCGTATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGTTCAGGAAAGTTTTCAATCGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTGAAAGTCAAGTATGAAGGTGCTGGAGCTCCGTGTAAAGTCCCCATAGAGATAAGAGATGTAAACAAGGAAAAAGTGGTTGGGCGCGTCATCTCATCCACCCCTTTGGCTGAGAATACCAACAGTGTAACCAACATAGAATTAGAACCCCCCTTTGGGGACAGCTACATAGTGATAGGTGTTGGAAACAGCGCATTAACACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAACGAATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCCGTTGGTGGACTGTTCACATCATTGGGAAAGGCTGTGCACCAGGTTTTTGGAAGCGTGTATACAACCATGTTTGGAGGAGTCTCATGGATGATTAGAATCCTAATTGGGTTCTTAGTGTTGTGGATTGGCACGAACTCAAGGAACACTTCAATGGCTATGACGTGCATAGCTGTTGGAGGTATCACTCTGTTTCTGGGCTTCACAGTTCAAGCG
</sequence>
<sequence>
<taxon idref="D4SLanka78"/>
ATGCGATGCGTGGGAGTGGGGAACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGATCTGGTGCTAGAACATGGAGGATGTGTCACAACCATGGCCCAAGGAAAACCAACCTTGGATTTTGAACTGATCAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCCATATCAAACATAACCACGGCAACAAGATGTCCAACGCAAGGAGAGCCCTGTCTCAAAGAGGAACAGGATCAACAGTACATCTGCCGGAGAGACGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCCTGCTTGGGAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGCTCGGGGAAGATAACAGGCAACTTAGTCCGAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGACACATCCAACCACGGAGTGACAGCCACGATAACCCCCAGGTCACCATCGGTAGAAGTTAAATTACCGGACTATGGAGAATTGACACTCGATTGTGAACCCAGGTCCGGAATTGATTTTAATGAGATGATTCTGATGGAAATGAGAAAGAAAACGTGGCTTGTGCACAAGCAATGGTTTTTGGATCTACCTCTACCATGGACAGCAGGAGCAGACACGTCAGAAGTTCATTGGAATCACAAAGAGAGAATGGTGACGTTCAAGGTCCCTCATGCCAAGAGACAGGATGTGACAGTGCTAGGATCTCAGGAAGGAGCCATGCATTCAGCCCTCACCGGAGCCACAGAAGTGGATTCCGGTGATGGAAACCACATGTTTGCAGGACATTTGAAGTGCAAAGTTCGCATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGCTCAGGAAAGTTCTCAATTGATAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTAAAAGTCAAGTATGAGGGTGCCGGAGCTCCATGTAAAGTTCCCATAGAGATAAGAGATGTGAACAAGGAAAAAGTGGTTGGGCGCATCATCTCATCTACCCCTTTTGCTGAGAATACCAACAGTGTGACCAACATAGAATTGGAACCCCCCTTTGGGGATAGCTACATAGTAATAGGTGTAGGAAACAGTGCATTAACACTCCATTGGTTTAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGCGCAAAGCGCATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCTGTTGGTGGACTGCTCACATCATTGGGAAAGGCTGTACACCAGGTTTTTGGTAGTGTGTATACAACTATGTTTGGAGGAGTCTCATGGATGGTTAGAATCCTAATCGGGTTCTTAGTATTGTGGATTGGCACGAATTCAAGAAACACTTCAATGGCAATGTCGTGCATAGCTGTTGGAGGAATTACTTTGTTTCTGGGTTTCACAGTTCATGCA
</sequence>
<sequence>
<taxon idref="D4Tahiti79"/>
ATGCGATGCGTAGGAGTAGGAAACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGATCTGGTGCTAGAACATGGAGGATGCGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGACTAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCAATATCAAACATAACTACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTATCTGAAAGAGGAACAGGACCAACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGTTTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGTTCGGGGAAGATAACAGGCAATTTGGTCCAAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGACACATCCAATCATGGAGTTACAGCCACGATAACTCCCAGGTCACCATCGGTGGAAGTCAAATTGCCGGACTATGGAGAACTAACACTCGATTGTGAACCCAGGTCTGGAATTGACTTTAATGAGATGATCCTGATGAAAATGAGAAAGAAGACATGGCTCGTGCATAAGCAATGGTTTTTGGATCTGCCTCTTCCATGGACAGCAGGAGCAGACACATCAGAGGTTCACTGGAATTACAAAGAGAGAATGGTGACATTTAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTGGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCGCTGGAGCCACAGAAGTGGACTCCGGTGATGGAAATCACATGTTTGCAGGACATCTCAAGTGCAAAGTCCGTATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGTTCAGGAAAGTTTTCAATTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTGAAAGTCAAGTATGAAGGTGCTGGAGCTCCGTGTAAAGTCCCCATAGAGATAAGAGATGTAAACAAGGAAAAAGTGGTTGGGCGTATCATCTCATCCACCCCTTTGGCTGAGAATACCAACAGTGTAACCAACATAGAATTAGAACCCCCCTTTGGGGACAGCTACATAGTGATAGGTGTTGGAAACAGCGCATTAACACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAACGAATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCCGTTGGTGGACTGTTCACATCATTGGGAAAGGCTGTGCACCAGGTTTTTGGAAGTGTGTATACAACCATGTTTGGAGGAGTCTCATGGATGATTAGAATCCTAATTGGGTTCTTAGTGTTGTGGATTGGCACGAACTCAAGGAACACTTCAATGGCTATGACGTGCATAGCTGTTGGAGGAATCACTCTGTTTCTGGGCTTCACAGTTCAAGCA
</sequence>
<sequence>
<taxon idref="D4Tahiti85"/>
ATGCGATGCGTAGGAGTAGGAAACAGAGACTTTGTGGAAGGAGTTTCAGGTGGAGCATGGGTCGATTTGGTGCTAGAACATGGAGGATGCGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGACTAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCAATATCAAACATAACTACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTATCTGAAAGAGGAACAGGACCAACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGTTTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGTTCGGGGAAGATAACAGGCAATCTGGTCCAAATTGAGAACCTTGAATACACAGTGGTCATAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGACACATCCAATCATGGAGTTACAGCCACGATAACTCCCAGGTCACCATCGGTGGAAGTCAAATTGCCGGACTATGGAGAACTAACACTCGATTGTGAACCCAGGTCTGGAATTGACTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACATGGCTCGTGCATAAGCAATGGTTTTTGGATCTGCCTCTTCCATGGACAGCAGGAGCAGACACAACAGAGGTTCACTGGAATTACAAAGAGAGAATGGTGACATTTAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTACTGGGATCTCAGGAAGGAGCCATGCATTCTGCCCTAGCTGGAGCTACAGAAGTGGACTCCGGTGATGGGAATCACATGTTTGCAGGACATCTCAAGTGCAAAATCCGTATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGTTCAGGAAAGTTTTCAATTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTGAAAGTCAAGTATGAAGGTGCTGGAGCTCCGTGTAAAGTCCCCATAGAGATAAGAGATGTAAACAAGGAAAAAGTGGTTGGGCGTGTCATCTCATCCACCCCTTTGGCTGAGAATACCAACAGTGTAACCAACATAGAATTAGAACCCCCCTTTGGGGACAGCTACATAGTGATAGGTGTTGGAAACAGCGCATTAACACTCCATTGGTTCAGGAAAGGGAGTTCCATCGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAACGAATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCCGTTGGTGGACTGTTCACATCATTGGGAAAGGCTGTGCACCAGGTTTTTGGAAGTGTGTATACAACCATGTTTGGAGGAGTCTCATGGATGATTAGAATCCTAATTGGGTTCTTAGTGTTGTGGATTGGCACGAACTCAAGGAACACTTCAATGGCTATGACGTGCATAGCTGTTGGAGGAATCACTCTGTTTCTGGGCTTCACAGTTCAAGCA
</sequence>
<sequence>
<taxon idref="D4Thai63"/>
ATGCGATGCGTAGGAGTGGGGAACAGGGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGATCTGGTGCTAGAACATGGAGGATGTGTCACAACCATGGCTCAAGGAAAACCAACCTTGGATTTTGAACTGATCAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCGATATCAAACATAACCACGGCGACAAGATGTCCAACGCAAGGAGAGCCTTATCTCAAAGAGGAACAAGATCAACAGTACATCTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTACTTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGCTCGGGGAAGATAACAGGCAACTTGGTTCGAATTGAGAACCTTGAATACACAGTGGTTGTGACAGTCCACAACGGAGACACCCATGCAGTAGGAAATGACATATCCAACCATGGAGTGACAGCCACGATAACTCCCAGGTCACCATCGGTAGAAGTCAAATTACCGGATTATGGAGAATTAACGCTCGATTGTGAACCCAGGTCCGGAATTGATTTTAATGAGATGATTCTGATGGAAATGAGAAAGAAGACGTGGCTTGTGCACAAGCAATGGTTTTTGGATCTACCTCTACCATGGACAGCAGGAGCAGACACAGCAGAAGTTCATTGGAATTACAAAGAGAGAATGGTGACATTCAAGGTCCCTCATGCTAAGAGACAAGATGTGACAGTGCTAGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCACCGGAGCTACAGAAGTGGATTCCGGTGATGGAAACCACATGTTTGCAGGACATCTTAAGTGCAAGGTTCGTATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGCTCAGGAAAGTTCTCAATTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTAGTGAAAGTTAAGTATGAAGGCGCTGAAGCTCCATGTAAAATCCCCATAGAGATAAGAGATGTGAACAAGGAAAAAGTTGTTGGGCGCATCATCTCATCCACTCCTTTGGCTGAAAACACCAACAGCGTGACCAATATAGAATTAGAACCTCCCTTTGGGGACAGCTACATAGTAATAGGTGTTGGAGACAGTGCATTAACACTCCATTGGTTCAGGAAGGGGAGTTCCATTGGCAAGATGTTTGAGTCTACATATAGAGGAGCAAAGCGAATGGCCATTCTAGGTGAAACAGCTTGGGACTTTGGCTCTGTTGGCGGACTGTCTACATCATTGGGAAAGGCTGTACACCAGGTTTTTGGTAGTGTGTACACAACCATGTTTGGAGGAGTCTCATGGATGGTTAGAATCCTAATCGGGCTCTTGGTGTTGTGGATTGGCACAAATTCAAGAAACACCTCAATGGCAATGACGTGCATAGCTGTTGGAGGAATCACTCTATTTCTGGGTTTCACAGCTCACGCA
</sequence>
<sequence>
<taxon idref="D4Thai78"/>
ATGCGATGCGTAGGAGTGGGGAACAGAGACTTTGTAGAAGGAGTCTCAGGTGGAGCATGGGTCGATCTGGTGCTAGAACATGGAGGATGTGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGATCAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCCATATCAAACATAACCACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTACCTCAAAGAGGAACAAGATCAACAGTACATCTGCCGGAGAGACGTGGTAGATAGAGGGTGGGGCAACGGCTGTGGCTTGCTTGGGAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGCTCGGGGAAGATAACAGGCAACTTAGTCCAAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGACACCCATGCTGTAGGAAATGATACATCCAACCACGGAGTGACAGCCACGATAACCCCCAGGTCACCATCGGTAGAAGTTAAATTACCGGACTATGGAGAATTAACACTTGATTGTGAACCTAGGTCCGGAATTGACTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACGTGGCTCGTGCACAAGCAATGGTTTTTGGATCTACCTCTACCATGGACAGCAGGAGCAGACACGTCAGAAGTTCACTGGAATCACAAAGAGAGAATGGTGACATTCAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTAGGATCTCAGGAAGGAGCTATGCATTCAGCCCTCACCGGAGCCACAGAAGTGGATTCCGGTGATGGAAACCATATGTTTGCAGGACATCTTAAGTGTAAAGTTCGTATGGAGAAATTGAGGATCAAGGGAATGTCATACACGATGTGCTCAGGAAAGTTCTCAATTGATAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTAAAAGTCAAGTATGAAGGTGCTGGAGCTCCATGTAAAGTCCCCATAGAGATAAGAGATGTGAACAAGGAAAAAGTGGTTGGGCGTATCATCTCATCTACCCCTTTTGCTGAGAATACCAACAGTGTGACCAATATAGAATTGGAACCCCCTTTTGGGGATAGCTACATAGTAATAGGTGTAGGAGACAGTGCATTAACACTCCATTGGTTCAGGAAAGGGAGCTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGCGCAAAGCGCATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCTGTCGGTGGACTGCTCACATCATTGGGAAAGGCTGTACACCAGGTTTTTGGCAGTGTGTATACAACTATGTTTGGAGGAGTCTCATGGATGGTTAGAATCCTAATCGGGTTCTTAGTGTTGTGGATTGGCACGAATTCAAGAAACACTTCAATGGCAATGTCGTGCATAGCTGTTGGAGGAATCACTCTGTTTCTGGGCTTCACAGTTCATGCA
</sequence>
<sequence>
<taxon idref="D4Thai84"/>
ATGCGATGCGTAGGAGTAGGGAACAGAGACTTTGTAGAAGGAGTCTCAGGTGGAGCATGGGTCGATCTGGTGCTAGAACATGGAGGATGTGTCACAACCATGGCCCAGGGAAAACCAACCCTGGATTTTGAACTGATCAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCCATATCAAACATAACCACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTACCTCAAAGAGGAACAAGATCAACAGTACATCTGCCGGAGAGACGTGGTAGACAGAGGGTGGGGCAACGGCTGTGGCTTGTTTGGGAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGCTCGGGGAAGATAACGGGCAACTTAGTCCAAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGACACCCATGCTGTAGGAAATGATACATCCAACCACGGAGTGACAGCCACGATAACCCCCAGGTCACCATCGGTAGAAGTTAAATTACCGGACTATGGAGAATTAACACTTGATTGTGAACCTAGGTCCGGAATTGATTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACGTGGCTCGTGCACAAGCAATGGTTTTTGGATCTACCTCTACCATGGACAGCAGGAGCAGACACGTCAGAAGTTCACTGGAATCACAAAGAGAGAATGGTGACATTCAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTAGGATCTCAGGAAGGAGCCATGCATTCAGCCCTCGCCGGAGCCACAGAAGTGGATTCCGGTGATGGAAACCATATGTTTGCAGGACACTTAAAGTGTAAAGTTCGTATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGCTCAGGAAAGTTCTCAATTGATAAAGAGATGGCAGAAACACAGCATGGAACAACAGTGGTAAAGGTCAAGTATGAAGGCACTGGAGCTCCATGTAAAGTCCCCATAGAGATAAGAGATGTGAACAAGGAAAAAGTGGTTGGGCGTATCATCTCATCTACCCCTTTGGCTGAGAATACCAACAGTGTGACCAATATAGAATTGGAACCTCCTTTTGGGGATAGCTACATAGTGATAGGTGTGGGAGACAGTGCATTAACACTCCATTGGTTCAGGAAAGGGAGCTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAGCGCATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCTGTTGGCGGACTGCTCACATCATTGGGAAAGGCTGTACACCAGGTTTTTGGCAGTGTGTATACAACTATGTTTGGAGGAGTCTCATGGATGGTTAGAATCCTAATCGGGTTCTTAGTGTTGTGGATTGGCACGAATTCAAGAAACACTTCAATGGCTATGTCGTGCATAGCTGTTGGAGGAATTACTCTGTTTCTGGGCTTCACAGTTCATGCA
</sequence>
</alignment>
<!-- The unique patterns for all positions -->
<!-- npatterns=138 -->
<patterns id="patterns" from="1">
<alignment idref="alignment"/>
</patterns>
<!-- A prior assumption that the population size has remained constant -->
<!-- throughout the time spanned by the genealogy. -->
<constantSize id="constant" units="years">
<populationSize>
<parameter id="constant.popSize" value="380.0" lower="0.0" upper="38000.0"/>
</populationSize>
</constantSize>
<!-- Generate a random starting tree under the coalescent process -->
<coalescentTree id="startingTree">
<taxa idref="taxa"/>
<constantSize idref="constant"/>
</coalescentTree>
<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>
<coalescentLikelihood id="coalescent">
<model>
<constantSize idref="constant"/>
</model>
<populationTree>
<treeModel idref="treeModel"/>
</populationTree>
</coalescentLikelihood>
<!-- The strict clock (Uniform rates across branches) -->
<strictClockBranchRates id="branchRates">
<rate>
<parameter id="clock.rate" value="2.3E-5" lower="0.0" upper="100.0"/>
</rate>
</strictClockBranchRates>
<!-- The example plugin creates an element that returns a simple instance
of an HKY DNA substitution model in its parser.
HKY substitution model (Hasegawa, Kishino & Yano, 1985)
You'll need to modify this element in your example as you test your plugin.
-->
<@PLUGIN_XML_ELEMENT@ id="hky">
<frequencies>
<frequencyModel dataType="nucleotide">
<alignment idref="alignment"/>
<frequencies>
<parameter id="hky.frequencies" dimension="4"/>
</frequencies>
</frequencyModel>
</frequencies>
<kappa>
<parameter id="hky.kappa" value="1.0" lower="0.0" upper="100.0"/>
</kappa>
</@PLUGIN_XML_ELEMENT@>
<!-- site model -->
<siteModel id="siteModel">
<substitutionModel>
<hkyModel idref="hky"/>
</substitutionModel>
</siteModel>
<treeLikelihood id="treeLikelihood" useAmbiguities="true">
<patterns idref="patterns"/>
<treeModel idref="treeModel"/>
<siteModel idref="siteModel"/>
<strictClockBranchRates idref="branchRates"/>
</treeLikelihood>
<operators id="operators">
<scaleOperator scaleFactor="0.75" weight="1">
<parameter idref="hky.kappa"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="3">
<parameter idref="clock.rate"/>
</scaleOperator>
<upDownOperator scaleFactor="0.75" weight="3">
<up>
<parameter idref="clock.rate"/>
</up>
<down>
<parameter idref="treeModel.allInternalNodeHeights"/>
</down>
</upDownOperator>
<scaleOperator scaleFactor="0.75" weight="3">
<parameter idref="constant.popSize"/>
</scaleOperator>
<scaleOperator scaleFactor="0.75" weight="3">
<parameter idref="treeModel.rootHeight"/>
</scaleOperator>
<uniformOperator weight="30">
<parameter idref="treeModel.internalNodeHeights"/>
</uniformOperator>
<subtreeSlide size="1.0" 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>
</operators>
<mcmc id="mcmc" chainLength="1000" autoOptimize="true">
<posterior id="posterior">
<prior id="prior">
<coalescentLikelihood idref="coalescent"/>
</prior>
<likelihood id="likelihood">
<treeLikelihood idref="treeLikelihood"/>
</likelihood>
</posterior>
<operators idref="operators"/>
<log id="screenLog" logEvery="10000">
<column label="Posterior" dp="4" width="12">
<posterior idref="posterior"/>
</column>
<column label="Root Height" sf="6" width="12">
<parameter idref="treeModel.rootHeight"/>
</column>
<column label="L(tree)" dp="4" width="12">
<treeLikelihood idref="treeLikelihood"/>
</column>
<column label="L(coalecent)" dp="4" width="12">
<coalescentLikelihood idref="coalescent"/>
</column>
</log>
<log id="fileLog" logEvery="500" fileName="testStrictClock.log">
<posterior idref="posterior"/>
<parameter idref="clock.rate"/>
<parameter idref="constant.popSize"/>
<parameter idref="hky.kappa"/>
<parameter idref="treeModel.rootHeight"/>
<treeLikelihood idref="treeLikelihood"/>
<coalescentLikelihood idref="coalescent"/>
</log>
<logTree id="treeFileLog" logEvery="500" nexusFormat="true" fileName="testStrictClock.trees">
<treeModel idref="treeModel"/>
<posterior idref="posterior"/>
</logTree>
</mcmc>
<report>
<property name="timer">
<object idref="mcmc"/>
</property>
</report>
<!--
To check that the program is working, the results are compared to previously
run results. The following are for a run of 10,000,000 steps:
18.146116666666668 minutes
burnIn=1000000
maxState=10000000
statistic mean hpdLower hpdUpper ESS
posterior -3928.71 -3936.77 -3921.22 6007.89
clock.rate 8.04835E-4 6.14761E-4 9.9785E-4 4548.69
constant.popSize 37.3762 17.5853 60.2203 6696.56
hky.kappa 18.2782 11.9770 25.5550 8090.05
treeModel.rootHeight 69.0580 57.6331 81.9754 5044.06
treeLikelihood -3856.59 -3863.13 -3850.89 8249.32
coalescent -72.1285 -77.1410 -67.2787 4393.94
-->
<traceAnalysis fileName="testStrictClock.log">
<expectation name="posterior" value="-3928.71"/>
<expectation name="clock.rate" value="8.04835E-4"/>
<expectation name="constant.popSize" value="37.3762"/>
<expectation name="hky.kappa" value="18.2782"/>
<expectation name="treeModel.rootHeight" value="69.0580"/>
<expectation name="treeLikelihood" value="-3856.59"/>
<expectation name="coalescent" value="-72.1285"/>
</traceAnalysis>
<treeTraceAnalysis fileName="testStrictClock.trees"/>
<marginalLikelihoodAnalysis fileName="testStrictClock.log">
<likelihoodColumn name="treeLikelihood" harmonicOnly="false" bootstrap="true"/>
</marginalLikelihoodAnalysis>
</beast>
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