<?xml version="1.0" standalone="yes"?>
<!-- Testing the "ECM+2kappa" model by Kosiol et al. (2007) -->

<beast>
  <taxa id="taxa">
    <taxon id="HUMAN05790"/>
    <taxon id="MOUSE12058"/>
    <taxon id="CANFA04576"/>
    <taxon id="RATNO13702"/>
    <taxon id="BOVIN10866"/>
    <taxon id="PANTR05396"/>
    <taxon id="MONDO08684"/>
    <taxon id="MACMU11173"/>
    <taxon id="LOXAF15456"/>
    <taxon id="CAVPO08377"/>
    <taxon id="PONAB00848"/>
    <taxon id="HORSE08417"/>
    <taxon id="LAMPA05747"/>
    <taxon id="PROCA04268"/>
    <taxon id="DIPOR12987"/>
    <taxon id="TARSY03417"/>
  </taxa>
  <alignment id="alignment" dataType="nucleotide">
    <sequence>
      <taxon idref="HUMAN05790"/>
GGAGATTCTACAGTGGTTGGAACGAGTAGGCTTCGTGACTTATATGACAAATTTGAGGAGGAGTTGGGGAGCAGGCAAGAAAAGGCCAAAGCTGCTCGGCCTCCGTGGGAACCTCCAAAGACGAAGCTCGATGAAGATTTAATGAATGATGGACCACTCTGCAAATGCAGCGCAAAGGCAAGACGCACAGGAATTAGGCACAGCATTTATCCTGGAGAAGAGACTGACAGGCCAACTGTTATAGAATACGATGATCACGAGTATATCTTTGAAGGATTTTCTATGTTTGCACATGCCCCCCTGACCAATATTCCACTGTGTAAAGTAATTAGATTCAACATAGACTACACGATTCATTTCATTGAAGAGATGATGCCGGAGCCTTTGTTTGAAGACAGCCCTCCCTGCTGCCCAAGATTTCATTTCATGCCACGTTTTGTAAGATTTCTTCCAGATGGAGGAAAGGAAGTGCTGTCCATGCACCAGATTCTCCTGTACTTGTTAAGGTGCAGCAAAGCCCTGGTGCCTGAGGAGGAGATTGCCAATATGCTTCAGTGGGAGGAGCTGGAGTGGCAGAAATATGCAGAAGAATGCAAAGGCATGATTGTTACCAACCCTGGGACGAAACCAAGCCGTATCGATCAACTGGATCGTGAACAGTTCAACCCCGATGTGATTACTTACCAAAAACTGTGGAAGAGTTATGTGAAACTTCGCCACCTCCTAGCAAATAGTCCCGTCAAACAAACTGACAAACAGAAGCTGCAGAGGGAGATTAACCACAATGAACGGTTGGAATTCCTGGGTGATGCTGTTGTTGAATTTCTGACCGGCCACAATCAGAGAATGGAATTCCTAGGTGACTCCATAATGCAACTGGTAGCCACAGAGTACTTATTCATTCATTTCCCAGATCATCATGAAGGACACTTAACTATAGGCTGTGGGGGACCAAATTTTCCCCAGATGGCCCATCAGAAGCGGTTCATCGAACAAGAGTTAAAAGAAATGAGGTGGGAAAGAGAGCATCAAGAGAGAGAGCCAGATGAGACTGAAGACATCAAGAAA
    </sequence>
    <sequence>
      <taxon idref="MOUSE12058"/>
GGAGACTCGACTGTCGTAGGGACAAGCAGGCTCCGTGATTTGTATGACAAATTTGAGGAAGAATTGGGGAATAGGCAAGAGAAGGCCAAAGCTGCCCGGCCTCCGTGGGAGCCTCCGAAGACAAAGCTGGATGAAGATTTAATGAACGATGGACCGCTTTGCAAATGCAGTGCAAAAGCCAGACGCACAGGAATCCGCCACAGCATTTATCCCGGAGAAGAGACTGACAGGCCAACAGTCATAGAATATGATGACCACGAGTATATTTTTGAAGGATTTTCTATGTTTGCACATGCTCCTCTGACCAATATTCCACTGTGTAAAGTGATTCGATTCAACATAGACTACACGATTCATTTTATCGAAGAGATGATGCCTGAGCCTTTGTTTGAAGACAGCCCTCCCTGCTGTCCGAGATTTCATTTCATGCCACGTTTTGTAAGATTTCTTCCAGATGGAGGCAAAGAAGTGTTATCCATGCACCAGATCCTTCTCTACCTGCTGCGCTGCAGCAAGGCTCTGGTGCCCGAGGAGGAGATTGCCAACATGCTCCAGTGGGAGGAGCTCGAGTGGCAGAAATACGCAGAGGAGTGCAAAGGCATGATCGTTACCAACCCTGGGACGAAACCGAGCCGCATTGATCAGCTGGATCGTGAACAGTTCAACCCCGAAGTGATCACTTATCAGAAATTATGGAAAAGCTATGTGAAACTTCGCCACCTCCTAGCAAACAGTCCCGTCAAACAAACTGACAAGCAGAAGCTGCAGAGGGAGATTAATCACAACGAAAGGTTGGAGTTCCTGGGGGATGCTGTTGTTGAGTTTCTGACCGGCCACAATCAGAGGATGGAATTTCTGGGCGACTCCATAATGCAGCTGGTGGCCACAGAGTACTTGTTCATTCATTTCCCGGACCATCACGAAGGACACTTGACGATAGGCTGTGGGGGACCAAACTTTCCCCAGATGGCCCATCAGAAGCGGTTCATTGAGCAAGAGTTAAAGGAAATGAGGTGGGAAAGAGAGCATCAGGAGAGAGAGCCGGAGGAGGCTGAAGACATCAAGAAG
    </sequence>
    <sequence>
      <taxon idref="CANFA04576"/>
GGAGATTCTACTGTGGTTGGAACAAGTAGGCTTCGTGACTTATATGACAAATTTGAGGAAGAACTGGGGAGTAGGCAAGAAAAGGCCAAAGCTGCTAGACCTCCGTGGGAGCCTCCCAAGACAAAGCTAGATGAAGATTTGATGAATGATGGGCCACTCTGCAAATGCAGCGCCAAAGCAAGACGCACAGGAATCAGGCACAGCATTTATCCTGGAGAAGAGACTGACAGGCCAACTGTTATAGAATATGATGATCATGAGTATATCTTTGAAGGATTTTCTATGTTTGCACATGCCCCCCTGACCAATATTCCACTGTGTAAAGTAATTAGGTTCAACATAGACTACACAATCCATTTCATCGAGGAGATGATGCCTGAGCCTTTGTTTGAAGACAATCCTCCCTGCTGCCCAAGATTTCATTTCATGCCACGTTTTGTGAGATTTCTTCCAGGATGGAGAAAGGAAGTGTTGTCCATCCCCCAGTTTCTCCTTTACTTATTAGGAGGTAGCAAACCCCTGGTTCCGAAAGAGGAGTTCCCCAATTTGTTTCAGGGGGAAAAACTTGAGGGGCAGAAATATGCAGGGGAATCCAAAGGCATGTTTTTCCCCATTCCGGAAACGAAACCTAGCCGCATTGATCAACTGGATCGTGAACAGTTCAACCCTGATGTGATTACCTACCAGAAACTGTGGAAGAGTTATGTGAAACTTCGCCACCTCCTAGCAAATAGTCCCGTTAAACAAACTGACAAACAGAAGCTGCAAAGAGAGATTAATCACAATGAAAGGTTGGAGTTCCTAGGTGATGCTGTTGTTGAATTTCTGACAGGCCACAATCAGAGGATGGAATTCCTAGGTGACTCCATAATGCAGCTGGTTGCCACTGAGTACTTATTTATTCATTTCCCAGATCATCATGAAGGACACTTAACTATAGGCTGTGGGGGACCAAACTTTCCCCAGATGGCCCATCAGAAGCGGTTCATTGAACAAGAGTTAAAAGAAATGAGGTGGGAAAGAGAGCATCAAGAGAAAGAGCCAGATGAGACTGAAGACATAAAGAAA
    </sequence>
    <sequence>
      <taxon idref="RATNO13702"/>
GGAGACTCTACTGTCGTAGGAACAAGCAGGCTCCGGGATCTGTATGACAAATTTGAGGAAGAGTTGGGGAACAGGCAAGAGAAGGCCAAAGCTGCCCGGCCTCCATGGGAGCCCCCAAAGACAAAGCTGGATGAAGATTTAATGAACGACGGACCACTTTGCAAATGCAGTGCAAAAGCAAGACGCACAGGAATTCGGCACAGCATTTATCCCGGAGAAGAGACGGACAGGCCAACAGTCATAGAATACGATGATCATGAGTATATCTTTGAAGGATTTTCTATGTTTGCACATGCCCCTCTGACCAATATTCCACTGTGTAAAGTAATTCGATTCAACATAGACTACACGATTCATTTTATTGAAGAGATGATGCCTGAGCCTTTGTTTGAAGACAGCCCTCCCTGCTGTCCAAGATTTCATTTCATGCCACGTTTTGTAAGATTTCTTCCAGATGGCGGCAAAGAAGTGTTATCAATGCACCAGATTCTTCTCTACCTGCTTCGCTGTAGCAAGGCTTTGGTCCCTGAGGAGGAGATTGCCAATATGCTCCAATGGGAGGAGCTCGAGTGGCAGAAATATGCGGAAGAGTGCAAAGGCATGATAGTTACCAACCCTGGGACGAAACCAAGCCGCATCGATCAACTGGATCGTGAGCAGTTCAACCCTGAAGTGATCACTTACCAAAAATTATGGAAAAGTTACGTGAAACTTCGCCACCTCTTAGCAAATAGTCCCGTCAAACAGACTGACAAACAGAAGCTGCAGAGGGAGATTAATCACAATGAAAGGTTGGAGTTCCTGGGAGATGCTGTTGTTGAGTTTCTGACCGGCCACAATCAGAGGATGGAATTCCTGGGTGACTCCATAATGCAGCTGGTAGCCACGGAGTACTTGTTCATCCACTTCCCCGACCACCACGAAGGACACTTGACGATAGGCTGTGGGGGACCAAACTTTCCCCAGATGGCTCATCAGAAGCGGTTCATTGAACAAGAGTTAAAGGAAATGAGGTGGGAAAGAGAGCATCAGGAGAGAGAGCCGGATGAGGCTGAAGACATAAAGAAG
    </sequence>
    <sequence>
      <taxon idref="BOVIN10866"/>
GGAGATTCTACTGTAGTTGGAACAAGTAGGCTCCGTGACTTATATGACAAATTTGAGGAAGAGTTGGGGAGCAGGCAAGAGAAGGCCAAAGCTGCTAGACCCCCATGGGAGCCTCCCAAGACGAAGCTAGATGAAGATTTAATGAATGATGGCCCACTCTGCAAATGCAGCGCAAAAGCGAGACGCACGGGCATCAGGCACAGCATTTATCCCGGAGAAGAGACTGACAGGCCAACTGTTATTGAATATGATGATCACGAGTATATCTTTGAAGGATTTTCTATGTTTGCACACGCCCCCCTGACCAATATTCCACTGTGTAAAGTAATTAGATTCAACATAGACTACACGATTCATTTCATAGAAGAGATGATGCCTGAGCCTTTGTTTGAAGACAGTCCTCCCTGCTGTCCAAGATTTCATTTTATGCCACGTTTTGTAAGATTTCTTCCAGATGGAGGGAAAGAAGTACTGTCTATGCACCAGATCCTCCTCTACTTACTACGGTGTAGCAAAGCCCTTGTTCCCGAAGAGGAGATTGCCAATATGCTTCAGTGGGAGGAACTTGAGTGGCAGAAATACGCGGAAGAGTGCAAAGGCATGATTGTCACCAACCCTGGAGCGAAACCAAGCCGCATCGATCAACTGGATCGTGAACAGTTCAACCCTGATGTGATTACTTACCAGAAACTGTGGAAGAGTTATGTTAAGCTTCGCCACCTCCTAGCAAATAGTCCAGTCAAACAGACTGACAAGCAGAAGCTGCAGAGGGAGATTAATCACAACGAACGGTTGGAGTTCCTGGGTGATGCTGTCGTTGAATTTCTGACCGGCCACAATCAGAGGATGGAATTCCTTGGTGACTCCATAATGCAGCTGGTAGCAACGGAGTACTTATTCATTCATTTTCCAGATCATCACGAAGGACACTTAACTATTGGCTGTGGGGGACCAAACTTTCCCCAGATGGCCCATCAGAAACGGTTCATTGAACAAGAGTTAAAAGAAATGAGGTGGGAAAGAGAGCATCAAGAGAAGGAGCCAGATGAGACCGAAGACATAAAGAAA
    </sequence>
    <sequence>
      <taxon idref="PANTR05396"/>
GGAGATTCTACAGTGGTTGGAACGAGTAGGCTTCGTGACTTATATGACAAATTTGAGGAGGAGTTGGGGAGCAGGCAAGAAAAGGCCAAAGCTGCTCGGCCTCCGTGGGAACCTCCAAAGACGAAGCTCGATGAAGATTTAATGAATGATGGACCACTCTGCAAATGCAGCGCAAAGGCAAGACGCACAGGAATTAGGCACAGCATTTATCCTGGAGAAGAGACTGACAGGCCAACTGTTATAGAATACGATGATCACGAGTATATCTTTGAAGGATTTTCTATGTTTGCACATGCCCCCCTGACCAATATTCCACTGTGTAAAGTAATTAGATTCAACATAGACTACACGATTCATTTCATTGAAGAGATGATGCCGGAGCCTTTGTTTGAAGACAGTCCTCCCTGCTGCCCAAGATTTCATTTCATGCCACGTTTTGTAAGATTTCTTCCAGATGGAGGAAAGGAAGTGCTGTCCATGCACCAGATTCTCCTGTATTTGTTAAGGTGCAGCAAAGCCCTGGTGCCCGAGGAGGAGATTGCCAATATGCTTCAGTGGGAGGAGCTGGAGTGGCAGAAATATGCAGAAGAATGCAAAGGCATGATTGTTACCAACCCTGGGACGAAACCAAGCCGTATCGATCAACTGGATCGTGAACAGTTCAACCCCGATGTGATTACTTACCAAAAACTGTGGAAGAGTTATGTGAAACTTCGCCACCTCCTAGCAAATAGTCCCGTCAAACAAACTGACAAACAGAAGCTGCAGAGGGAGATTAACCACAATGAACGGTTGGAATTCCTGGGTGATGCTGTTGTTGAATTTCTAACCGGCCACAATCAGAGAATGGAATTCCTAGGTGACTCCATAATGCAACTGGTAGCCACAGAGTACTTATTCATTCATTTCCCAGATCATCATGAAGGACACTTAACTATAGGCTGTGGGGGACCAAATTTTCCCCAGATGGCCCATCAGAAGCGGTTCATCGAACAAGAGTTAAAAGAAATGAGGTGGGAAAGAGAGCATCAAGAGAGAGAGCCAGATGAGACTGAAGACATCAAGAAA
    </sequence>
    <sequence>
      <taxon idref="MONDO08684"/>
GGCGATTCTACAGTTGTTGGAACTAGTAGGCTCCGAGACTTGTATGAAAAGTTTGAAGAGGAATTAGGGAAGAGGCAAGCAAAAGCAAAAGCTGTGAGACCCCCCTGGGAGCCACCCAAGACCAAACTAGATGAGGATTTAATGAATGATGGTCCTCTCTGTAAATGCAGTGCAAAAGCAAGGCGCACAGGAATCCGGCACAGCATCTACCCAGGAGAAGAGACTGACAGACCAACTGTTATAGAATATGATGATCATGAATATATTTTTGAAGGATTTTCTATGTTTGCACATGCTCCCCTGACCAATATTCCCCTATGTAAAGTAATTAGATTTAACATAGACTACACAATTCACTTCATTGAAGAGATGATGCCTGAGCCTTCATTTGAAAATAATAGTTCATGCTGTCCAAGATTTCATTTCATGCCACGTTTTGTAAGATTTCTTCCAGATGGAGGAAAGGAGGTGCTATCAATGCATCAGATCCTTCTCTATTTGTTGAGATGTAATAAAGCTTTGGTTCCTGAAGAGGAGATTGCTAACATGCTTCAATGGGAAGAACTTGAATGGCAGAAATATGCAGAGGAATGCAAAGGAATGATTGTTAACAATCCTGGCATGAAACCTAGCCGCATTGATCAATTGGATCGGGAACAGTTCAACCCAGATGTGATTACCTATCAGAAACTATGGAAAAGCTATGTGAAGCTCCGCCACCTGTTGGCAAACAGCCCCGTCAAACAGGCTGACAAGCAAAAGCTGCAGAGAGAGATTAACCACAATGAACGTTTGGAATTCCTGGGTGATGCTGTTGTTGAATTCCTAACTGGCCATAATCAGAGAATGGAATTTCTGGGTGACTCCATAATGCAACTGGTAGCTACAGAATATTTATTCATTCATTTTCCTGATCATCATGAAGGTCACTTAACGATAGGCTGTGGTGGCCCAAACTTTCCCCAGATGGCCCATCAGAAGCGGTTCATTGAACAAGAGTTGAAAGAAATGAGGTGGGAAAGAGAGCATCAAGAGAAAGAACCAGATGAGGCTGATGAAGTAAGGAAT
    </sequence>
    <sequence>
      <taxon idref="MACMU11173"/>
GGAGATTCTACAGTAGTTGGAACAAGTAGGCTTCGTGACTTATATGACAAATTTGAGGAGGAGTTGGGGAGCAGGCAAGAAAAGGCCAAAGCTGCTCGGCCTCCGTGGGAACCTCCGAAGACGAAGCTCGATGAAGATTTAATGAATGATGGACCACTCTGCAAATGCAGCGCAAAGGCAAGACGCACAGGAATTAGGCACAGCATTTATCCTGGAGAAGAGACTGACAGGCCAACTGTCATAGAATACGATGATCACGAGTATATCTTTGAAGGATTTTCTATGTTTGCACATGCCCCCCTGACCAATATTCCACTGTGTAAAGTAATTAGATTCAACATAGACTACACGATTCATTTCATTGAAGAGATGATGCCAGAGCCTTTGTTTGAAGACAGTCCTCCCTGCTGCCCAAGATTTCATTTCATGCCACGTTTTGTAAGATTTCTTCCAGATGGAGGAAAGGAAGTGCTGTCCATGCACCAGATTCTCCTGTACTTGTTAAGGTGCAGCAAAGCCCTGGTGCCCGAGGAGGAGATTGCCAATATGCTTCAGTGGGAGGAGCTGGAGTGGCAGAAATATGCAGAAGAATGCAAAGGCATGATTGTTACCAACCCTGGGACGAAACCAAGCCGTATCGATCAACTGGATCGTGAACAGTTCAACCCTGATGTGATTACTTACCAAAAACTGTGGAAGAGTTATGTGAAACTTCGCCACCTCCTAGCAAATAGTCCCGTCAAACAAACTGATAAACAGAAGCTGCAGAGGGAGATTAACCACAATGAGCGGTTGGAATTCCTGGGTGATGCTGTTGTTGAATTTCTGACCGGCCACAATCAGAGAATGGAATTCCTAGGTGACTCCATAATGCAACTGGTAGCCACAGAGTACTTATTCATTCATTTCCCAGATCATCATGAAGGACACTTAACTATAGGCTGTGGGGGACCAAATTTTCCCCAGATGGCCCATCAGAAGCGGTTCATCGAACAAGAGTTAAAAGAAATGAGGTGGGAAAGAGAGCATCAAGAGAGAGAGCCAGATGAGACTGAAGACGTCAAGAAA
    </sequence>
    <sequence>
      <taxon idref="LOXAF15456"/>
GGGGATTCCACTGTAGTTGGAACAAGTAGGCTCCGGGACTTATATGACAAATTTGAAGAGGAGTTGGGGAGCAGGCAAGAAAAGGCCAAAGCAGCCAGACCGCCATGGGAGCCTCCCAAGACGAAGCTGGATGAAGATTTAATGAATGACGGACCACTCTGCAAATGCAGCGCGAAAGCCCGGCGCACAGGAATTAGGCACAGCATTTACCCCGGAGAAGAGACCGACAGGCCTACTGTTATAGAGTATGATGATCATGAGTATATCTTTGAAGGGTTTTCTATGTTTGCACATGCGCCCCTGACCAATATTCCACTGTGTAAAGTGATTAGATTCAACATAGACTACACCATTCATTTCATTGAAGAGATGATGCCTGAGCCTTTGTTTGAAGACAGTCCTCCCTGCTGCCCAAGATTTCATTTCATGCCACGTTTTGTAAGATTTCTTCCAGATGGAGGCAAGGAGGTGCTGTCCATGCACCAGATTCTTCTTTACCTACTGCGGTGCAGCAAAGCCCTGGTCCCGGAGGAGGAGATCGCCAACATGCTTCAGTGGGAAGAGCTGGAGTGGCAGAAGTACGCAGAGGAGTGCAAAGGCATGATCGTTACCAACCCCGGAACGAAACCAAGCCGCATTGATCAACTGGATCGTGAACAGTTCAACCCCGATGTGATTACTTACCAGAAGTTGTGGAAGAGTTACGTAAAGCTTCGACACCTCCTGGCAAATAGTCCCGTTAAACAAACTGACAAACAGAAGCTGCAGAGGGAGATTAACCACAATGAACGGTTGGAGTTCCTGGGTGATGCTGTTGTTGAATTTCTGACCGGGCACAATCAGAGGATGGAATTCCTAGGTGATTCCATAATGCAACTGGTCGCTACAGAGTACTTGTTCATTCATTTCCCAGACCATCATGAGGGGCACTTAACTATAGGCTGTGGGGGACCAAACTTTCCCCAGATGGCCCATCAGAAGCGGTTCATCGAACAAGAGTTAAAAGAAATGAGGTGGGAAAGAGAACATCAAGAGAGAGAACCAGATGAGACCGAAGACATAAAGAAA
    </sequence>
    <sequence>
      <taxon idref="CAVPO08377"/>
GGAGACTCTACTGTAGTTGGAACAAGTAGACTCCGTGACCTGTATGATAAATTCGAGGAAGAGCTGGGGAGTCGGCAGGAAAAAGCCAAGGCTGCCCGGCCACCGTGGGAGCCTCCGAAGACGAAACTGGATGAAGATTTAATGAATGATGGACCACTCTGCAAATGCAGCGCAAAAGCAAGACGCACAGGAATTCGGCACAGCATTTATCCCGGAGAGGAGACTGACAGGCCAACTGTGATAGAGTATGATGATCACGAGTACATCTTTGAAGGATTCTCTATGTTTGCACATGCCCCCCTGACCAATATTCCACTGTGTAAGGTAATTAGATTCAACATAGACTACACAATTCATTTCATTGAAGAGATGATGCCCGAGCCTTTGTTTGAAGACAGCCCTCCCTGCTGCCCAAGATTTCATTTCATGCCACGTTTTGTGAGATTTCTTCCAGATGGAGGTAAGGAAGTGCTGTCCATGCACCAGATTCTTCTGTACCTGTTACGGTGTAGCAAAGCCCTGGTGCCGGAAGAGGAGATTGCTAATATGCTTCAGTGGGAGGAGCTGGAGTGGCAGAAGTATGCAGAAGAATGCAAAGGCATGATCGTTACCAACCCCGGAACGAAACCAAGTCGCATTGATCAACTGGATCGTGAGCAGTTCAATCCCGACGTGATTACTTACCAGAAACTATGGAAGAGTTACGTGAAACTCCGCCACCTCCTTGCAAACAGTCCCGTTAAACAAACTGACAAACAGAAGCTGCAGAGGGAGATTAATCACAATGAACGGTTGGAGTTTCTAGGTGATGCTGTTGTGGAGTTCCTGACCGGCCACAATCAGAGGATGGAATTTCTAGGTGATTCCATAATGCAACTGGTGGCTACAGAGTACCTGTTCATTCATTTCCCAGATCATCATGAAGGACACTTAACTATAGGTTGTGGGGGACCAAACTTTCCCCAGATGGCCCATCAGAAGCGGTTCATTGAACAAGAGTTAAAAGAAATGAGGTGGGAAAGAGAGCATCAAGAGAGAGAGCCAGATGAGACTGAAGACATAAAGAAG
    </sequence>
    <sequence>
      <taxon idref="PONAB00848"/>
GGAGATTCTACAGTGGTTGGAACAAGTAGGCTTCGTGACTTATATGACAAATTTGAGGAGGAGTTGGGGAGCAGGCAAGAAAAGGCCAAAGCTGCTCGGCCTCCGTGGGAACCTCCGAAGACGAAGCTTGATGAAGATTTAATGAATGATGGACCACTCTGCAAATGCAGCGCAAAGGCAAGACGCACGGGAATTAGGCACAGCATTTATCCTGGAGAAGAGACTGACAGGCCAACTGTTATAGAATACGATGATCACGAGTATATCTTTGAAGGATTTTCTATGTTTGCACATGCCCCCCTGACCAATATTCCACTGTGTAAAGTAATTAGATTCAACATCGACTACACGATTCATTTCATTGAAGAGATGATGCCGGAGCCTTTGTTTGAAGACAGTCCTCCCTGCTGCCCAAGATTTCATTTCATGCCACGTTTTGTAAGATTTCTTCCAGATGGAGGAAAGGAAGTGCTGTCCATGCACCAGATTCTCCTGTACTTGTTAAGGTGCAGCAAAGCCCTGGTGCCCGAGGAGGAGATTGCCAATATGCTTCAGTGGGAGGAGCTGGAGTGGCAGAAATATGCAGAAGAATGCAAAGGCATGATTGTTACCAACCCTGGGACGAAACCAAGCCGTATCGATCAACTGGATCGTGAACAGTTCAACCCCGATGTGATTACTTACCAAAAACTGTGGAAGAGTTATGTGAAACTTCGCCACCTCCTAGCAAATAGTCCCGTCAAACAAACTGACAAACAGAAGCTGCAGAGGGAGATTAACCACAATGAACGGTTGGAATTCCTGGGTGATGCTGTTGTTGAATTTCTGACCGGCCACAATCAGAGAATGGAATTCCTAGGTGACTCCATAATGCAACTGGTAGCCACAGAGTACTTATTCATTCATTTCCCAGATCATCATGAAGGACATTTAACTATAGGCTGTGGGGGACCAAATTTTCCCCAGATGGCCCATCAGAAGCGGTTCATCGAACAAGAGTTAAAAGAAATGAGGTGGGAAAGAGAGCATCAAGAGAGAGAGCCAGATGAGACTGAAGACATCAAGAAA
    </sequence>
    <sequence>
      <taxon idref="HORSE08417"/>
GGAGATTCTACTGTAGTTGGAACAAGTAGACTCCGTGACTTATATGACAAATTTGAGGAAGAGTTGGGGAGCAGGCAAGAAAAAGCCAAAGCTGCTAGACCTCCGTGGGAACCTCCCAAGACAAAGCTAGATGAAGATTTAATGAATGACGGACCACTCTGCAAATGCAGCGCAAAAGCGAGACGCACAGGAATTAGGCACAGCATTTATCCCGGAGAAGAGACTGACAGGCCAACCGTTATAGAATATGATGATCATGAGTATATCTTTGAAGGTTTTTCTATGTTTGCACACGCCCCCCTGACCAATATTCCACTGTGTAAAGTGATTAGATTCAACATAGACTACACGATTCATTTCATTGAAGAGATGATGCCTGAGCCTTTGTTTGAAGACAGTCCTCCCTGCTGCCCAAGATTTCATTTCATGCCACGTTTTGTACGATTTCTTCCAGATGGAGGGAAGGAAGTGCTTTCCATGCACCAGATTCTCCTTTATTTATTACGGTGCAGCAAAGCTCTGGTTCCCGAAGAGGAGATTGCCAATATGCTTCAGTGGGAAGAACTTGAGTGGCAGAAATACGCAGAAGAATGCAAAGGCATGATCGTCACCAACCCTGGCACGAAACCAAGCCGCATCGATCAACTGGATCGTGAACAGTTCAACCCCGATGTGATTACTTACCAGAAACTGTGGAAAAGTTATGTGAAGCTTCGCCACCTCCTAGCAAATAGTCCCGTCAAGCAAACTGACAAACAGAAGCTGCAGAGGGAGATTAATCACAACGAACGGTTGGAGTTTCTGGGTGATGCTGTTGTTGAATTTTTGACCGGCCACAATCAGAGGATGGAATTCCTAGGTGACTCCATAATGCAACTGGTAGCTACAGAGTACTTATTCATTCATTTCCCGGATCATCATGAAGGACACTTAACTATTGGCTGTGGGGGACCAAACTTTCCCCAGATGGCCCATCAGAAGCGGTTCATTGAACAAGAGTTAAAAGAAATGAGGTGGGAAAGAGAGCATCAAGAGAAAGAGCCAGACGAGACTGAAGACATAAAGAAA
    </sequence>
    <sequence>
      <taxon idref="LAMPA05747"/>
GGAGATTCTACTGTAGTTGGAACAAGTAGGCTCCGTGACTTATATGACAAATTTGAGGAAGAGCTGGGGAGCAGGCAAGAGAAGGCCAAAGCTGCTAGACCCCCGTGGGAGCCTCCCAAGACGAAGCTAGATGAAGATTTAATGAATGATGGCCCACTCTGCAAATGCAGCGCAAAGGCGAGACGCACAGGAATCAGGCACAGCATTTATCCCGGAGAAGAGACTGACAGGCCAACTGTTATAGAATATGATGATCATGAGTATATATTCGAAGGATTTTCTATGTTTGCACATGCCCCCCTGACCAATATTCCGCTGTGTAAAGTAATTCGATTCAACATAGACTACACGATTCATTTCATTGAAGAGATGATGCCTGAGCCTTTGTTTGAAGACAGTCCTCCCTGCTGCCCAAGATTTCATTTCATGCCACGTTTTGTAAGGTTTCTTCCAGATGGAGGAAAGGAAGTGCTGTCCATGCACCAGATTCTCCTGTACTTGTTACGATGTAGCAAAGCCCTGGTTCCAGAAGAGGAGATTGCCAATATGCTTCAGTGGGAGGAACTTGAGTGGCAGAAATATGCAGAAGAATGCAAGGGCATGATCGTCACCAACCCTGGAACGAAACCAAGCCGCATCGATCAACTGGATCGTGAACAGTTCAACCCCGATGTGATTACTTACCAGAAACTGTGGAAGAGTTATGTGAAGCTTCGCCACCTCCTAGCAAATAGTCCCGTCAAACAAACTGACAAGCAGAAGCTGCAGAGGGAGATTAATCACAATGAGCGGTTGGAGTTCCTGGGTGATGCTGTTGTTGAATTTCTGACCGGCCACAATCAGAGGATGGAATTCCTAGGTGACTCCATAATGCAGCTGGTAGCCACAGAATACTTATTCATTCATTTCCCAGATCATCATGAAGGACACCTAACAATCGGCTGTGGGGGACCAAACTTTCCCCAGATGGCCCATCAGAAGCGGTTCATTGAACAAGAGTTAAAAGAAATGAGGTGGGAAAGAGAGCATCAGGAGAAAGAGCCAGATGAGACTGAAGACATAAAGAAA
    </sequence>
    <sequence>
      <taxon idref="PROCA04268"/>
GGGGATTTTACTGTAGTTGGAACAAGTAGGCTCCGGGATTTATATGACAAATTTGAAGAAGAGTTGGGGAGCAGGCAAGAAAAGGCCAAAGCAGCCAGGCCACCATGGGAGCCCCCCAAGACGAAGCTAGATGAAGATTTAATGAATGACGGACCACTCTGCAAATGTAGCGCTAAAGCCCGACGTACAGGAATCAGGCACAGCATTTATCCCGGAGAAGAGACTGACAGGCCGACTGTGATAGAGTATGATGATCACGAATACATCTTTGAAGGGTTTTCTATGTTTGCACATGCTCCCCTGACCAATATTCCACTGTGCAAAGTAATTAGATTCAACATAGACTACACGATTCATTTCATTGAAGAGATGATGCCTGAGCCTTTGTTTGAAGACAATCCTCCCTGCTGCCCAAGATTTCATTTCATGCCACGTTTTGTAAGATTTCTTCCAGATGGAGGCAAGGAAGTGCTGTCCATGCACCAGATTCTTCTCTATCTGCTTCGGTGCAGCAAAGCCCTGGTCCCTGAGGAGGAGATTGCCAACATGCTTCAATGGGAAGAGCTTGAATGGCAGAAGTATGCAGAAGAATGCAAAGGCATGATCGTTACCAACCCTGGAACGAAAAGCTCTCGCATCGATCAACTGGATCGTGAGCAGTTCAACCCTGATGTGATTACTTACCAGAAGCTATGGAAAAGTTACGTGAAGCTTCGACACCTCCTAGCAAACAGTCCCGTTAAACAAACTGACAAACAGAAGCTGCAGAGGGAGATTAACCATAATGAACGGCTGGAGTTCCTGGGCGATGCTGTTGTTGAATTTCTGACCGGCCACAACCAGAGGATGGAATTCCTAGGAGACTCCATAATGCAACTGGTTGCAACAGAATACTTGTTCATTCATTTCCCCGATCACCATGAGGGGCACTTAACTATAGGCTGTGGGGGACCAAACTTTCCCCAGATGGCCCACCAGAAGCGGTTCATTGAACAAGAGTTAAAAGAAATGAGGTGGGAAAGAGAACATCAAGAGAGAGAACCAGATGAGACTGAAGATGTAAAGAAA
    </sequence>
    <sequence>
      <taxon idref="DIPOR12987"/>
GGAGATTCTACTGTAGTTGGAACAAGTAGGCTCCGAGACTTGTACGACAAATTTGAAGAAGAATTGGGGAGCAGACAAGAAAAGGCCAAGGCTGCTAGGCCTCCGTGGGAGCCTCCGAAGACGAAGCTAGATGAAGATTTAATGAATGATGGACCTCTGTGCAAATGCAGCGCCAAAGCGAGACGCACAGGAATTCGGCACAGCATTTATCCCGGAGAAGAGACCGACAGGCCAACTGTTATAGAATATGATGATCATGAATATATCTTTGAAGGATTTTCTATGTTTGCGCATGCCCCCCTAACCAATATTCCTCTGTGTAAAGTAATTAGATTCAACATAGACTACACCATTCATTTCATTGAAGAGATGATGCCTGAGCCTTTGTTTGAAGACAGCCCTCCATGCTGCCCAAGATTTCATTTCATGCCACGGTTTGTAAGATTTCTTCCAGATGGAGGCAAGGAAGTGTTGTCCATGCACCAGATTCTGCTCTATCTGTTACGGTGTAGCAAAGCACTGGTCCCAGAAGAGGAGATTGCCAATATGCTTCAGTGGGAGGAGCTTGAGTGGCAGAAATATGCAGAAGAGTGCAAAGGCATGATTGTCACCAACCCTGGGACGAAACCAAGCCGCATTGATCAACTGGATCGTGAACAGTTCAACCCTGAAGTGATTACTTACCAGAAACTATGGAAGAGTTATGTGAAACTTCGCCACCTCCTAGCAAACAGTCCCGTCAAACAAACGGACAAACAGAAGCTGCAGAGGGAGATTAATCACAATGAACGGTTGGAGTTCCTGGGTGATGCCGTTGTTGAGTTCCTGACCGGCCACAACCAGAGAATGGAGTTCCTAGGTGACTCCATTATGCAGCTGGTCGCCACGGAGTACTTATTCATTCATTTCCCGGATCATCACGAAGGCCACTTAACTATCGGCTGTGGGGGACCAAACTTTCCCCAGATGGCCCATCAGAAGCGGTTCATTGAACAAGAGTTAAAAGAAATGAGGTGGGAAAGAGAGCACCAGGAGAGAGAACCAGATGAGACTGAAGACAGAAAGAAG
    </sequence>
    <sequence>
      <taxon idref="TARSY03417"/>
GGAGATTCTACAGTGGTTGGAACAAGTAGGCTCCGTGACTTATATGACAAGTTTGAGGAGGAGTTGGGGAACAGGCAAGAAAAGGCCAAAGCTGCCCGGCCTCCATGGGAACCTCCGAAGACCAAGCTAGATGAAGATTTAATGAATGATGGACCACTCTGCAAATGCAGCGCGAAAGCGAGACGCACAGGAATCAGGCACAGCATTTATCCTGGAGAAGAGACTGATAGACCAACTGTTATAGAATATGATGATCATGAGTATATCTTTGAAGGATTTTCTATGTTTGCACACGCCCCCCTGACCAATATTCCACTGTGTAAAGTAATTAGATTCAACATAGACTACACGATTCATTTCATTGAAGAGATGATGCCGGAGCCTTTGTTTGAAGACAGTCCTCCCTGCTGCCCAAGATTTCATTTCATGCCACGTTTTGTAAGATTTCTTCCAGATGGAGGAAAGGAAGTGCTGTCCATGCACCAGATTCTCCTCTACTTGCTCCGGTGCAGCAAAGCTCTGGTGCCTGAGGAAGAGATTGCCAACATGCTTCAGTGGGAGGAGCTGGAGTGGCAGAAGTATGCAGAGGAATGCAAAGGCATGATTGTTACCAACCCCGGAACGAAACCAAGCCGTATCGATCAACTGGATCGTGAACAGTTCAACCCCGATGTGATTACTTACCAGAAACTGTGGAAGAGTTATGTGAAACTTCGCCACCTTCTAGCAAATAGTCCCGTTAAACAAACTGACAAACAGAAGCTGCAGAGGGAGATTAATCACAACGAACGGTTGGAGTTCCTGGGTGATGCTGTTGTTGAATTTCTGACCGGCCATAATCAGAGGATGGAATTCCTAGGTGACTCTATAATGCAACTGGTAGCCACAGAGTACTTATTCATTCATTTCCCAGATCATCATGAAGGACACTTAACTATAGGCTGTGGGGGGCCAAACTTTCCCCAGATGGCACATCAGAAGCGATTCATTGGACAAGATTTAAAAGAAATGAGGTGGGAAAGAGAGCACCAGGAGAGAGAGCCAGATGAGACTGAAGACGTAAAGAAA
    </sequence>
  </alignment>
  <newick id="startingTree">
((((((CANFA04576:0.2060844,((LAMPA05747:0.05541678,BOVIN10866:0.10831308):0.011007161,HORSE08417:0.074578677):0.0062470925):0.013901078,(TARSY03417:0.08933732,(MACMU11173:0.016264116,(PONAB00848:0.012301025,(PANTR05396:0.0061631393,HUMAN05790:0.0055504432):0.0052449023):0.0044280569):0.050448274):0.025486393):0.017264758,((PROCA04268:0.12592991,LOXAF15456:0.091949918):0.054763325,CAVPO08377:0.14987746):0.0098503993):0.0048522644,MONDO08684:0.37550148):0.0098331816,DIPOR12987:0.13500462):0.022223646,(RATNO13702:0.09233825,MOUSE12058:0.11163869):0.090388785):0;
  </newick>

  <convert id="codonAlignment" dataType="codon" geneticCode="universal">
    <alignment idref="alignment"/>
  </convert>

  <patterns id="patterns" from="1">
    <alignment idref="codonAlignment"/>
  </patterns>

  <treeModel id="treeModel">
    <newick 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>

  <arbitraryBranchRates id="branchRates">
    <treeModel idref="treeModel"/>
    <rates>
      <parameter id="branch.rates"/>
    </rates>
  </arbitraryBranchRates>

  <rateStatistic id="meanRate" name="meanRate" mode="mean" internal="true" external="true">
    <treeModel idref="treeModel"/>
    <arbitraryBranchRates idref="branchRates"/>
  </rateStatistic>

  <empiricalCodonModel id="ecm" geneticCode="universal"  ecmDataDir="codon-data/ecmdata" ecmRateFile="rates_k_unrest.csv" ecmFreqFile="freqs_zs.csv">
    <omega>
      <parameter id="omega" value="0.3"/>
    </omega>
    <kappaTsTv>
      <parameter id="kappatstv" value="1.2 1.5"/>
    </kappaTsTv>
    <frequencyModel id="freqmodel" dataType="codon-universal">
      <alignment idref="codonAlignment"/>
      <frequencies>
        <parameter id="codonfrequencies" dimension="61"/>
      </frequencies>
    </frequencyModel>
  </empiricalCodonModel>

  <siteModel id="siteModel">
    <substitutionModel>
      <empiricalCodonModel idref="ecm"/>
    </substitutionModel>
  </siteModel>

  <treeLikelihood id="treeLikelihood" useAmbiguities="false">
    <patterns idref="patterns"/>
    <treeModel idref="treeModel"/>
    <siteModel idref="siteModel"/>
    <arbitraryBranchRates idref="branchRates"/>
  </treeLikelihood>

  <!-- Define operators                                                        -->
  <operators id="operators">
    <scaleOperator scaleFactor="0.9" weight="1" autoOptimize="true">
      <parameter idref="omega"/>
    </scaleOperator>
    <scaleOperator scaleFactor="0.83" weight="1" autoOptimize="true">
      <parameter idref="kappatstv"/>
    </scaleOperator>
    <scaleOperator scaleFactor="0.75" weight="15.0">
      <parameter idref="branch.rates"/>
    </scaleOperator>
  </operators>

  <!-- Define MCMC                                                             -->
  <mcmc id="mcmc" chainLength="500000" autoOptimize="true">
    <posterior id="posterior">
      <prior id="prior">
        <uniformPrior lower="0.0" upper="100.0">
          <parameter idref="branch.rates"/>
        </uniformPrior>
      </prior>  		
      <likelihood id="likelihood">
        <treeLikelihood idref="treeLikelihood"/>
      </likelihood>
    </posterior>
    <operators idref="operators"/>

    <!-- write log to screen                                                     -->
    <log id="screenLog" logEvery="5000">
      <column label="Posterior" dp="4" width="12">
        <posterior idref="posterior"/>
      </column>
      <column label="Likelihood" dp="4" width="12">
        <likelihood idref="likelihood"/>
      </column>
      <column label="meanRate" sf="6" width="12">
        <rateStatistic idref="meanRate"/>
      </column>
      <column label="omega" sf="6" width="12">
        <parameter idref="omega"/>
      </column>
      <column label="kappatstv" sf="6" width="12">
        <parameter idref="kappatstv"/>
      </column>
    </log>
  
    <!-- write log to file                                                       -->
    <log id="fileLog" logEvery="1000" fileName="ecm+2k.log">
      <posterior idref="posterior"/>
      <likelihood idref="likelihood"/><parameter idref="omega"/><parameter idref="kappatstv"/>
      <rateStatistic idref="meanRate"/>
      <parameter idref="branch.rates"/>
      <treeLikelihood idref="treeLikelihood"/>
    </log>
  </mcmc>

  <report>
    <property name="timer">
      <mcmc idref="mcmc"/>
    </property>
  </report>
</beast>
