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annotate default_beastfile_template.xml @ 2:7eaf6f9abd28 draft default tip

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planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b-dirty
author bcclaywell
date Mon, 12 Oct 2015 17:57:38 -0400
parents d67268158946
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
1 <beast beautistatus="noAutoSetClockRate" beautitemplate="Standard" namespace="beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood" version="2.0">
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
2
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
3
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
4 <data id="trimmed" name="alignment"><sequence id="seq_MiniPusi.EU847197|bat|2005" taxon="MiniPusi.EU847197|bat|2005" totalcount="4" value="------NNGATTTTTAGGCATATAAAGTCTTTT---AGGTTTAGTATGCTTGACCCTGTTTATAAAACAGACACCAATAAAGCTGTCTAT------------GATTGGTATGTTAGTCAGCTGTTTTATAGGTATGTTCTGTTACCATCTGGTGAGATAACCATA---CAGGATCGTGGTAATCCGTCTGGTCAAATTTCTACCACCATGGATAATAACCTGGTTAACACCTTTCTCCAGGCATTTGAGTTCGCGTATTTG------AATCCTGAGCTCTCAGTTGATGAGCTCGATTGTTTATAT---------------------------GCGCAGTGTGACTCTTTAATCTATGGTGATGATAGGCTGAGTTCTTGG---CCTATT---GTTCCAGAT---------------GATTACCCA---TCCTTGGTCTCTGCCATGTATGAGCATATCNNT------------" /><sequence id="seq_TaphMela.FJ571090|bat|2007" taxon="TaphMela.FJ571090|bat|2007" totalcount="4" value="---------NNGTTTCGTCATATTAAGAGAATT---CGGTATTCTTTTATAGATGAATCACAGAGAACACCAGTCATTGATGAGATCTAT------------GAGTGGTATGTGAATAACCTTGTTTCTAGGTATGTGCTTATGCCATCTGGGGAGATCACCGTC---CAGAATCGAGGTAACCCTTCTGGGCAGATCTCGACGACCACTGATAACAACATGATAAATGTATTTCTTCAGGCTTTTGAGTTTGCTTACCTC------AATCAGGGTTATACAGAGCCAGAGCTCGATGACCTGTGG---------------------------CGTAAATATGATTCCCTTATTTATGGGGATGATAGGCTGAATACAACG---CCAGTC---TTGCCACAG---------------GACTATGTC---CCACGTGTTATTGACNNA---------------------------" /><sequence id="seq_MiniSchr.JQ814856|bat|2010" taxon="MiniSchr.JQ814856|bat|2010" totalcount="4" value="------NNGGTTTTTAGGCATATTAAGAACTTT---AGGTTTATGATGTTGGACCCAGTTTATCATACTGAGACTAATAAAGATATTTAT------------GAGTGGTACATTGGACAACTTATGTACCGTTATGTTTTGTTACCATCTGGAGAGGTTACCATA---CAAGACCGTGGTAATCCATCTGGCCAAATTTCCACTACCATGGATAATAATCTTGTTAATACCTTTTTGCAGGCTTTTGAGTTTGCGTATATG------AATCCTGAGCTCTCTCTCGATGAGCTTGATTGTTTGTAT---------------------------GCGCAATGTGACTCAGTGATATACGGTGATGACCGTTTGTCTTCATGG---CCTGTT---GTTCCAGAA---------------GATTATGAA---AAGAATGTATCATCTATGTATGAGCACATANNT------------" /><sequence id="seq_TaphMela.FJ571122|bat|2007" taxon="TaphMela.FJ571122|bat|2007" totalcount="4" value="------NNGGTTTTTCGGCATATTAAATCTTTT---CGGTTTAGTATGCTTGATAAAGCCTATCGGACGGAGCTTAATCGTTCTGTTTAC------------GACTGGTATGTCTCACAGTTGTGTTACCGGTATGTTTTGCTTCCATCTGGTGAGGTTACCGTT---CAAGATCGTGGTAACCCTTCTGGCCAAATTTCTACTACTATGGACAATAATATGATTAATACTTTTCTTCAAGCTTTTGAGTTTTCTTTTGTT------AATGGTCATCTTAATGATGATCAATTGTGGTCCTTGTGG---------------------------TGTGAGAGTGATTCTATCATTTATGGTGATGATCGTTTGTCATCGTGG---TCTCTC---ATACCTGAT---------------GATTACGTT---CAGAAAGTTATTCAGATGTATAAGGAAATT---------------" /><sequence id="seq_HippLarv.KJ571394|bat|2008" taxon="HippLarv.KJ571394|bat|2008" totalcount="4" value="---------NNCTGGAAAGCCATCAAGGAGATA---CGCTTTGAATTTTTGTCCCCAGAATATCGAACTCCAAGGAATCGCTCAGTTTAT------------ACCTGGTATTGCAAAAACCTAGTCGAAAGGTTAGTTCTCCTCCCTAGTGGGGAGATAACGAAG---CAAACCCGGGGCAATCCTTCAGGTCAGGTGTCTACCACCATGGACAACAACATGGTTAATGTGTTCCTGCAGGCTTTTGAGTTCATGTACACC------AAC---AATCTCTATTATAGTGAGGCTCAGGACTACTGG---------------------------AAGGAATATGACTCTCTTATCTATGGAGATGATCGGCTCACAGCTACA---CCACTA---TACAGCAGT---------------CACTATCCT---GAGAAAGTGATTGGCATGNNT------------------------" /><sequence id="seq_ScotKuhl.KJ571385|bat|2008" taxon="ScotKuhl.KJ571385|bat|2008" totalcount="4" value="------NNAGTGTTTCGGCATATAAAAAGGCTT---AGGTTCGCACTTTTAGACCCTGTATATAAGACTGATTTGAACAAGTCTATTTAT------------GAATGGTATGTTGATCAATTGTTACATCGCTATGTTTTGTTACCTACTGGAGAAGTTACAATT---CAAAACAGGGGTAATCCCTCTGGTCAAATCTCCACTACTATGGATAACAATATGGTTAACACCTTTTTGCAAGCTTTTGAGTTTGCTTATGTC------CATAGATCTTATAGTGATGATATGCTGCATGCCATGTGG---------------------------TCTAAGTGTGATTCTATTGTGTACGGTGATGACCGTGTTTCATCTTGG---CCTTCT---GTTCCACCT---------------AACTATGTC---GATAATGTCATCGAAATGTATCGAACCATC---------------" /><sequence id="seq_HomoSapi.JX179278|human|1983" taxon="HomoSapi.JX179278|human|1983" totalcount="4" value="------NNAGTTTTCAGTGCAATTAAAGACTTT---AGGTTTTCATGTCTCAGGAAGGAATTTAGAACAGAGAAGAATAAAAGTGTCTAT------------GACTGGTACTGTAAAAATATTTTTAAAAGGTATGTCATGTTGCCATCTGGAGAAGTCACAGTT---CAAGAGCGTGGAAATCCTTCAGGCCAGATATCAACTACCATGGATAATAATCTATGCAATGTATTTTTCCAGGCATTTGAGTTTGCTCATTTG------AATCCGGACAAAACAATTGATGAACTGAGAGAAGGATGG---------------------------GAGAAAGTTGATTCACTTATCTATGGTGATGACAGGCTTTCTACAGTT---CCATAT---GTTTGCTCT---------------AACTATGTT---GAAAAAGTAATAGACATGTATGAAAACATTNNT------------" /><sequence id="seq_MusMusc.JF755422|rodent|2012" taxon="MusMusc.JF755422|rodent|2012" totalcount="4" value="------NNAGTTTTCAAATTAATAAAACAATTT---AGGTTCTCAATGTTGTCACCAGAATATAAAACTGAGTTAAATAGATCCATATAT------------AATTGGTATTGCCATCATCTTATTAATAGGTATGTTTTGTTACCATCTGGTGAAATTACTAAA---CAAATTAAAGGAAACCCATCAGGACAAGTGTCTACAACTATGGATAATAATATGGTAAACACCTTCCTTCAAGCGTTTGAATTTATATATGTA------AAT---GATTTGAGTTACACCGAAGCAAAAGAAAAATGG---------------------------CGTAATTATGATACCTTAATATATGGAGATGACCGGCTAACCAGCACT---CCTTGT---GTTCCAACT---------------GATTACAAA---GAGAAAGTAATAAAAATGTATAAAGATATCNNT------------" /><sequence id="seq_HomoSapi.GQ267696|human|2008" taxon="HomoSapi.GQ267696|human|2008" totalcount="4" value="------NNAGTCTTTAGGGCTATTAAGGACTTT---AGATTCTCGTGTCTTAGGGGAGATTTGCAAACAAAGGAAAATAGAGATGTCTAT------------AATTGGTATTGTGAGAATATATTTAGAAGATATGTGATGTTACCTTCAGGAGAAGTGACAATC---CAGGACAGGGGGAACCCCTCTGGACAAATATCCACAACTATGGATAATAACATTTGTAATGTCTTCTTCCAGGCATTTGAGTTTGCATATCTG------AATACTGAATTGGATTCTGATGAATTAAAGGAAAATTGG---------------------------GATAAGTATGATTCACTTATATATGGAGATGACAGATTAACTACAACC---CCTATT---TTATGTGAT---------------AACTATGTA---GACAGAGTCATTAAAATGTATGCTGATGTCNNT------------" /><sequence id="seq_MyotRick.EU847162|bat|2004" taxon="MyotRick.EU847162|bat|2004" totalcount="4" value="---------NNGTTCCGACACATTAAGTGGTTT---CGTTTTAGCATGTTAGAACGCTCCTATAGGACTGAAATTAACCGTGGCATATAT------------GATTGGTACATAAACCAAATGTGCCATAGATATGTGCTTTTACCATCAGGTGAAGTTACCCTT---CAAACTAGAGGGAATCCATCCGGTCAGATTTCTACTACTATGGACAACAACCTAGTCAACACCTTCCTACAGGCTTTTGAATTTGCCTACCTT------CATGGAGATCTTGATGATGATGGTCTCGATCGTGTGTGG---------------------------AAAGATTGTGACACCATAATTTATGGTGACGATCGTATTACATCCTGG---CCATCA---GTTCCACCC---------------AACTATGTT---GGTGACGTAGTTGAGNNA---------------------------" /><sequence id="seq_HomoSapi.FJ755403|human|2006" taxon="HomoSapi.FJ755403|human|2006" totalcount="4" value="------NNACTCTTCAAACACATCAAAGAAATT---AGGTGGAATTTCATCAATAAAGACCAACGT---GAAAAGTACAGACATGTCCAT------------GAATGGTATGTTGATAACCTCCTTAATCGCCATGTACTTCTACCATCTGGTGAAGTCACCTTG---CAGACACGAGGCAATCCATCCGGGCAGTTTTCAACAACAATGGATAACAACATGGTCAACTTTTGGTTACAGGCTTTTGAGTTTGCTTATTTT------AAT---GGCCCAGAC---AAAGACCTT---------TGG---------------------------AGGACTTATGACACTGTAGTTTATGGAGATGACAGGCTTTCTACAACA---CCTTCA---GTGCCTGAT---------------GATTATGAA---GAGAGAGTGATTACTATGTATAGAGATATCNNT------------" /><sequence id="seq_HomoSapi.HM120878|human|2009" taxon="HomoSapi.HM120878|human|2009" totalcount="4" value="------------------------------------------------------------------------------------------------------------TATGTCGATAACCTCCTTAATCGTCATGTACTTCTACCATCTGGTGAAGTTACCTTG---CAGACACGAGGCAATCCATCTGGTCAGTTTTCAACAACGATGGATAACAACATGGTCAACTTTTGGTTACAAGCTTTTGAGTTTGCTTATTTC------AAT---GGTCCAGAT---AAAGATCTC---------TGG---------------------------AAAACTTATGATACTGTAGTCTATGGAGATGACAGGCTTTCAACAACA---CCTTCG---GTGCCTGAT---------------GACTATGAG---GAGGGAGTTATTACCATGTATAGAGATATTNNT------------" /><sequence id="seq_HomoSapi.JQ403108|human|2010" taxon="HomoSapi.JQ403108|human|2010" totalcount="4" value="------NNACTTTTTAGACACATCAAAGAAATT---AGGTGGAATTTCATAAACAAAGACCAACGT---GAGAAGTATAGACATGTACAT------------GAATGGTACGTTGATAATCTCCTCAACCGCCATGTACTCCTACCATCTGGTGAAGTCACCTTA---CAGACACGAGGCAATCCATCCGGACAATTTTCAACAACAATGGATAATAACATGGTCAACTTCTGGTTACAAGCGTTTGAGTTTGCCTACTTC------AAT---GGCCCAAAC---AAAGAACTT---------TGG---------------------------AAAACCTACGACACTGTGGTTTATGGTGATGATAGACTCTCTACTACA---CCCTCA---GTGCCAGAA---------------AATTATGAA---GAAAGAGTGATTGATATGTACAGGGATATTNNT------------" /><sequence id="seq_SusScroDome.KJ533344|pig|2012" taxon="SusScroDome.KJ533344|pig|2012" totalcount="4" value="------NNACTTTTCAGGCACATCAAAGAACTC---CGCTGGAAGTTGATCAATAGAGAACAACGC---GAGAAGTACGCAGGAGTCCAC------------AAGTGGTATGTAGACAATCTGTTGAACAGATATGTCCTTTTGCCATCTGGAGAAGTAACCCTC---CAAACGAGGGGTAACCCCTCAGGACAGTTCTCTACCACTATGGACAACAATATGATTAATTTCTGGCTCCAGGCATTTGAATTTGCCTGGATT------AAT---GGCCCAAAC---AAAGAACTC---------TGG---------------------------AAAAGTTATGATACCATTGTGTACGGTGATGATCGTTTAAACACGACA---CCGTAT---GTGCCTCCT---------------AACTATGAG---GAAATGATCATTGATATGTACAGAGATATCNNT------------" /><sequence id="seq_HomoSapi.KC342249|human|2012" taxon="HomoSapi.KC342249|human|2012" totalcount="4" value="------NNACTTTTCAAACATATCAAAGAAATT---AGGTGGAACTTCATCAATAAAGACCAACGT---GAAAAGTACAGACATGTGCAT------------GAATGGTATGTTGATAACCTCCTTAATCGCCATGTACTACTACCATCTGGTGAAGTTACCTTG---CAGACACGAGGCAATCCATCTGGCCAGTTTTCAACAACAATGGACAACAACATGGTCAACTTTTGGTTACAAGCTTTTGAGTTTGCTTATTTC------AAT---GGTCCAAAC---AAAGACCTC---------TGG---------------------------AAGACTTATGATACTGTGGTTTATGGAGATGATAGGCTTTCAACAACA---CCTTCA---GTGCCTGAT---------------AATTATGAG---GAGAGAGTGATTACCATGTATAGAGACATTNNT------------" /><sequence id="seq_HomoSapi.JF491430|human|2004" taxon="HomoSapi.JF491430|human|2004" totalcount="4" value="------NNTCTGTTCAGACACATCAAAGAGATA---AGGTGGAATTTTATAAACAAAGACCAACGT---GAAAAGTATAGACATGTGCAT------------GAATGGTATGTTGACAATCTCCTCAATCGCCATGTGTTATTACCATCTGGAGAGGTAACTGTA---CAAACACGGGGTAACCCGTCTGGACAATTTTCAACAACTATGGACAACAATATGGTCAATTTTTGGCTACAGGCTTTTGAATTTGCCTACTTC------AAT---GGGCCAAAC---AAGGAACTC---------TGG---------------------------AAGACCTATGATACTGTGGTCTATGGAGACGATAGACTCTCCACCACA---CCTTCA---GTACCAGAC---------------AATTATGAA---GAAAGAGTAATTGCCATGTATAGAGACATTNNT------------" /><sequence id="seq_MyotRick.EU847166|bat|2004" taxon="MyotRick.EU847166|bat|2004" totalcount="4" value="------NNAGTGTTTCGACACATTWAGTGGTTT---CGGTATCACATGCTAGATCCAGTTTACCACACTGATGAAAATCGCGGTGTTTAT------------TCGTGGTATATTGATCAGATGTGCAGGAGGCATGTCCTTTTGCCTAGTGGTGAAGTCACGATT---CAGGATCGTGGCAACCCATCTGGTCAAATTTCAACAACCATGGATAATAATATGGTAAACACTTTTTTGCAGGCTTTTGAGTTTGCATATGTC------CATCCTCAATACACTGATCAAGAGCTTGAGGACGAGTGG---------------------------AAGAAATGTGATTCCATCGTTTATGGTGATGACCGCGTTTCCTCGTGG---CCCAGT---GTTCCACCT---------------AATTATGTT---GAAAAAGTTGTTGAGATGTATAAGGTTGTGNNT------------" /><sequence id="seq_HippArmi.FJ571094|bat|2007" taxon="HippArmi.FJ571094|bat|2007" totalcount="4" value="------NNAGTGTTTAGACATATCAAGAATTTT---AGATTTAAGATGCTTGATAGGTCTTGTCGCACACTCGTAAACAAGCAAGTTTAC------------GATTGGTATGTTGACCAAATGTGTTATCGTTATGTTCTGTTACCATCTGGTGAGGTTACGATA---CAAGATCGTGGCAATCCATCTGGTCAAATATCCACTACTATGGACAATAATATGATTAATACCTTTCTCCAGGCCTTTGAGTTTGCGTATGTC------CATCCATCTAAAACAGACTTGGAATTGAAGTCTGATTGG---------------------------TCCAAGTGTGATGCACTTGTTTATGGTGATGACCGCATTTCATCATGG---CCTTCA---GTTCCGATT---------------AACTATGTT---GAGACAGTTGTGGAGATGTATAAGGTTGTT---------------" /><sequence id="seq_HomoSapi.JX857869|human|2008" taxon="HomoSapi.JX857869|human|2008" totalcount="4" value="------NNGGTGTTAATTGCTATCAAAAAGTTT---AGATATTCTTGCCTTTCAGATCATTGCAAAAGTGCTAAATTGCTGGATGCCTAC------------AAGTGGTATTGCCACAACATCATGCATAGATATGTCATGTTACCATCTGGTGAAGTAACAATA---CAAAATCGGGGAAATCCCTCTGGCCAGATTTCCACAACTATGGACAACAACATGTGCAATGTGTTCTTCCAGGCATTTGAGTATGCATTCATA------CATCCAAACAAAACAGTTGAAGAGCTTTGTGACATGTGG---------------------------GATAAAGTCGATTCACTAATTTATGGTGATGACAGGCTTTCCACTTAT---CCTGAG---TTACCTGAT---------------AACTATAAG---GATATTGTCATTAGTATGTATGCAGACATANNT------------" /><sequence id="seq_RattNorv.HM450385|rodent|2008" taxon="RattNorv.HM450385|rodent|2008" totalcount="4" value="------------------------------------AGGTGGAGTTTTATGGAAAAGACCCACCAG---GAACGGTACGGTAAGATGTAC------------CGATGGTATTGCAAGAACTTGGTGGATCGTTATGTTGTGATGCCATCTGGAGAGATTACAAGG---CAAAAGAGAGGAAACCCATCTGGGCAGATATCAACAACAATGGATAATAACATGGTGAACTTTTGGCTCCAGGCCTTTGAGTGGGCCTGGTTC------AAT---GGCCCGGAT---TTTGAAAAG---------TTT---------------------------AATGAGTTTGAGACAGTTGTCTATGGTGATGATCGTTTGTCAACCTGG---TCTAGA---GTACCGGAT------------------------------------------------------------------------" /><sequence id="seq_HomoSapi.HM989955|human|2009" taxon="HomoSapi.HM989955|human|2009" totalcount="4" value="------------------------------------------NNCTTAATGGGTTCCATGTCCCGC------AAGTATGAAAATGTATAC------------AAGTGGTATTGTAGGAACCTAATCAACAGGTTTGTTGTGCTGCCTTCAGGTGAAGTTACAGCG---CAACAGCGTGGAAATCCATCAGGCCAGATGTCAACCACCATGGATAATAACATGATCAACTATTGGTTGCAGGCATTTGAATATAAATTTTTG------------AATTTACCA---GAAGAAGAG---------TGG---------------------------ATGCATTTTGATACTNNC---------------------------------------------------------------------------------------------------------------------------" /><sequence id="seq_HomoSapi.JQ673581|human|2011" taxon="HomoSapi.JQ673581|human|2011" totalcount="4" value="NNACCAACCCTGTTGATGCACATAAAGAAATTA---AGGTTTACCTTAATGGGTTCCGTGTCCCGC------AAGTATGAAAATGTATAC------------AAGTGGTACTGTAGGAATCTAATCAACAGGTTTGTTGTACTGCCTTCAGGTGAAGTTACAGCA---CAACAGCGTGGAAATCCATCGGGCCAGATATCTACCACCATGGACAATAACATGATCAACTATTGGTTGCAGGCATTTGAATATAAATTTTTG------------AACCTACCA---GAAGAAGAG---------TGG---------------------------ATGCATTTTGATACTTTGATCTATGGAGATGACAGAATATCCACATAT---CGAAGC---ATCCCTAAT---------------GAATACACC---AAGGTAATAGTTGACATGTATAAAAATGTTNNT------------" /><sequence id="seq_RhinPusi.KJ571428|bat|2009" taxon="RhinPusi.KJ571428|bat|2009" totalcount="4" value="------NNGGTTTTCCGGCATATTAAGGAATTT---CGGTTTCGAATGCTGGAGAAATCTTACCGTACCAATGTTAATAAGCAAGTTTAC------------CAGTGGTATGTTGATCAGATGTGTTATCGTTATGTTTTGTTACCTTCTGGTGAGGTTACTATA---CAAGATCGAGGTAATCCTTCTGGTCAGATTTCTACCACCATGGATAATAATATGGTAAACACCTTCTTGCAAGCTTTTGAGTTTGCCTATGTC------CATCCAAGTTACAGTGAACTTGAGCTTAGGCAGGAGTGG---------------------------TCTAAGTGTGATGCACTCGTCTATGGAGATGATAGGATATCATCTTGG---CCTAGT---GTGCCCCCC---------------AACTATGTT---GACACTGTTGTTGAAATGTACAAGGTAGTT---------------" /><sequence id="seq_HomoSapi.GQ502191|human|2008" taxon="HomoSapi.GQ502191|human|2008" totalcount="4" value="NNACCTACTCTTTTGATGCATATCAAAAAATTA---CGGTTCTCGCTTATGGGTGAGGTTGCCCAT------AAATATGAAAGAGTGTAT------------AAATGGTATTGTAGGAACCTAGTTAATAGGTTCGTTATACTCCCTTCTGGTGAGGTCACTCTG---CAGAACCGTGGTAATCCATCCGGTCAAATATCAACTACAATGGACAACAATATGATTAACTATTGGTTGCAAGCCTTTGAGTTCAAATATTTG------------GGCCTACCT---GAAGATGAA---------TGG---------------------------ATACATTTTGACACTATTGTGTATGGTGATGATGGGCTCTCTACCTAT---CGCACT---TTACCAGCT---------------GATTACATC---TCCAAAGTTGTAGCCATGTATAAAGATGTCNNT------------" /><sequence id="seq_EothCach.KJ571450|rodent|2012" taxon="EothCach.KJ571450|rodent|2012" totalcount="4" value="------NNTTTATTTCTCCATATCAAGAAACTT---AGGTTTCAATTATTAAATTCAGAGCAAAGG---ATTAGATATGCTCATGTATAT------------AAGTGGTATGTGTCCAATCTTATGAAAAGGTATACATTGCTTCCATCTGGGGAAATTACCATC---CAGAGACGTGGTAATCCAAGCGGCCAAATCTCCACTACTATGGATAATAATATGATTAATTATTGGTTACAGTGTTTTGAATTTGCTTTTTTC------TTT---GGCACTGAT---TACCAACTT---------TTC---------------------------CAACAATTTGATACCATAGTCTATGGAGATGACCGCTTGACACGATTT---CCTTTT---ACACCAGAG---------------GACTATGTG---CCACGTGTTGTAGCGATGTATAAAGATATA---------------" /><sequence id="seq_EothCach.KJ571440|rodent|2012" taxon="EothCach.KJ571440|rodent|2012" totalcount="4" value="------NNTTTGTTTCTCCATATTAAGAAACTT---AGATTTCAACTATTGAATTCAGAGCAGAGA---ACTAGATATGCCCATGTGTAC------------AAGTGGTATGTGTCCAACCTTATGAAAAGGTACACATTGCTTCCATCTGGAGAGGTAACTATT---CAGAGACGTGGTAATCCAAGCGGTCAGATCTCCACTACTATGGATAATAATATGATCAACTACTGGTTACAGTGCTTTGAATTTGCTTTCTTT------TTT---GGCACTGAC---TATCAACTT---------TTC---------------------------CAGCAGTTTGACACCATAGTGTATGGAGATGATCGTTTGACACGATTT---CCTTTT---ACACCAGAG---------------GACTATGTG---CCACGTGTTGTAGCAATGTATAAAGATATA---------------" /><sequence id="seq_EothCach.KJ571439|rodent|2012" taxon="EothCach.KJ571439|rodent|2012" totalcount="4" value="---------NTATTTCTTCATATTAAGAAATTG---AGATTTTCTTTGTTAAATTCAGAACAGAGA---ATTCGGTATGCCCACGTGTAC------------AAATGGTATGTGTCCAACCTTATGAAAAGGTACACATTGCTCCCGTCTGGAGAAGTTACCATC---CAGAGACGTGGTAATCCAAGTGGGCAGATCTCCACTACTATGGATAATAACATGATTAATTATTGGCTGCAGTGCTTTGAATTTGCTTTTTTC------TTT---GGCACTGAT---TACCAATTA---------TTC---------------------------CAACAGTTTGACACCATAGTGTATGGGGATGACCGCTTGACACGATTT---CCTTTT---ACACCAGAG---------------GACTATGTG---CCACGTGTCGTAGCAATGTATAAGGATATA---------------" /><sequence id="seq_EothCach.KJ571442|rodent|2012" taxon="EothCach.KJ571442|rodent|2012" totalcount="4" value="---------NTATTTCTTCATATCAAGAAACTT---AGATTCCAATTGCTAAATTCAGAGCAAAGG---ATTAGATATGCTCATGTGTAC------------AAATGGTATGTGTCCAACCTTATGAAGAGATATACATTGCTTCCATCTGGGGAAGTCACCATC---CAGAGACGTGGTAATCCAAGCGGTCAGATCTCAACTACTATGGATAATAATATGATTAATTACTGGTTGCAGTGCTTTGAATTTGCTTTCTTT------TTT---GGCACTGAC---TATCAGCTT---------TTC---------------------------CAGCAGTTTGATACTATAGTATATGGAGATGATCGTTTGACACGTTTT---CCTTTT---ACACCAGAG---------------GACTATGTG---CCACGTGTTGTTGCAATGTATAAAGATATA---------------" /><sequence id="seq_SusScroDome.JX519275|pig|2011" taxon="SusScroDome.JX519275|pig|2011" totalcount="4" value="------NNACTCTTGGGAAGGATCAAGAGACTT---CGCTTCAGCATGCTGTGTGAAGAACATCAA---CAGCGTTATGAGCATGTTTAC------------AAATGGTATGTGAAAAACCTCCTTAAGAGGTATGTGCTCATGCCAAGTGGAGAAGTCACCGTG---CAGAAGCGAGGGAACCCCTCCGGTCAGATTTCAACCACCATAGACAATAACATGGTTAACATCTGGCTGCAAGCATTTGAATTTTGCTACTTC------TTT---GGACCAGAT---AAAGAACTC---------TGG---------------------------CGCAGCTATGACACCATTGTCTATGGTGATGATAGACTCACCAGGTAC---CCAAGA---CTTCCTGAG---------------AACTACAAA---GAGAGGGTGATTGAAATGTACAGAAATATTNNT------------" /><sequence id="seq_SusScroDome.JX519281|pig|2011" taxon="SusScroDome.JX519281|pig|2011" totalcount="4" value="------NNCCTCCTCAAGCACATAAAAGACATT---CGTTGGGAGAAGATGAACAAAACACATAGA---GAGAGATACAAACACGTACAC------------GACTGGTACGTTGAAAACCTCCTGACAAGGTATGTGCTAATGCCATCTGGAGAGGTGACAATC---CAACGTCGGGGTAACCCATCAGGTCAGATTTCAACCACCATGGACAACAACATGGTGAACTTCTGGCTTCAAGCTTTTGAGTTCGCCTACATG------AACAAGGGGAAAGACATTGAAGCTCTT---------TGG---------------------------AAAGAGTATGACACCATCGTCTATGGTGATGACAGACTCTCTACAACA---CCATGT---CTACCTGAT---------------GAATATGTA---CCACGTGTCGTTCAGATGTACAAAGAAGTCNNT------------" /><sequence id="seq_Pig.HQ647383|pig|2009" taxon="Pig.HQ647383|pig|2009" totalcount="4" value="------NNCCTCTTCAAGCACATCAAAGGCCTA---CGTTGGGAGAAGATGAACAAAACACACAGG---GAAAGATACAGACACGTACAC------------GATTGGTACGTTGAAAATCTCCTGACTAAGTACGTGCTCATGCCATCTGGAGAGGTCACAATT---CAGCGCCGGGGGAACCCATCAGGTCAGATCTCAACCACCATGGACAACAATATGATAAACTTCCGGCTTCAGGCTTTCGAGTTTGCCTACCTC------AACAAAGGGAAGGACATTGAAGCCCTC---------TGG---------------------------AAAGAGTATGACACCATTGTCTATGGTGATGACAGGCTTACAACCACT---CCCTGC---CTGCCTGAT---------------GATTACGTG---CCACGTGTCGTTCAGATGTACAAAGAAGTGNNT------------" /><sequence id="seq_SusScroDome.KJ533345|pig|2012" taxon="SusScroDome.KJ533345|pig|2012" totalcount="4" value="------NNGCTATTTAAGCACATCAAAGATCTG---CGGTGGGAGAAGATGAACAAAACACACAGA---GAAAGGTATAAACATGTCCAC------------GACTGGTACGTGGAGAACCTCCTAACCCGCTACGTGCTCATGCCCTCTGGTGAAGTCACCGTC---CAACGCCGTGGTAATCCGTCAGGGCAGATATCTACAACACCAGACAACTGCATGGTGAACTATTGGCTTCAAGCTTTTGAGTTCGCTTATCTT------AACAAGGGGAAGGACATCAATAGCCTC---------TGG---------------------------AAAGACTATGACACCATCGTCTATGGGGACGATCGGCTGACGTCAACC---CCTTGC---ATCCCTGAC---------------AACTACGTC---GAGCGCGTGGTCGAGATGTATAAGACCGTCNNT------------" /><sequence id="seq_SusScroDome.KJ533357|pig|2012" taxon="SusScroDome.KJ533357|pig|2012" totalcount="4" value="---------------------------------------TGGGAGAAGATGAACAAGACACACAGA---GAAAGATACAAGCATGTCCAC------------GACTGGTACGTGGAGAATCTCCTCACCCGCTATGTGCTCATGCCCTCTGGGGAAGTCACCATC---CAACGCCGGGGTAATCCATCAGGACAAATCTCAACCACCCCGGACAACTGTATGGTGAACTACTGGCTTCAAGCCTTTGAGTTCGCCTACCTG------AACAAGGGGAAAGATATTGACACCCTT---------TGG---------------------------AAGGAGTATGACACCATTGTCTATGGTGATGATCGACTGACATCAACC---CCTTGC---ATACCTGAC---------------AACTATGTC---GAGCGTGTGGTCGAGATGTACAAGACAGTCNNT------------" /><sequence id="seq_SusScroDome.KJ533348|pig|2012" taxon="SusScroDome.KJ533348|pig|2012" totalcount="4" value="------NNTCTTCTCAAGCACATCAAAGACCTG---CGGTGGGAGAAGATGAACAAAACACATAGA---GAAAGATACCAGCATGTCCAC------------GATTGGTACGTGGAAAATCTCCTAACCCGGTACGTGCTCATGCCCTCTGGGGAAGTCACCATC---CAACGCCGAGGAAATCCGTCAGGGCAAATTTCAACAACTCCGGATAATTGCATGGTAAACTACTGGCTCCAGGCCTTTGAGTTCGCCCACTTC------AACAAGGGGAAAGACATTGATAGTCTG---------TGG---------------------------AAAGAGTATGACACCATCGTCTATGGTGATGATCGATTAACATCAACC---CCCTGT---ATTCCTGAC---------------AATTATGTG---CAGCGCGTCGTCCAGATGTACAAAACAGTCNNT------------" /><sequence id="seq_SusScroDome.KJ533355|pig|2012" taxon="SusScroDome.KJ533355|pig|2012" totalcount="4" value="------NNGCTCTTAAAGCACATTAAAGACCTG---CGGTGGGAGAAGATGAACAAGACACACAGA---GAGAGATACAAACATGTCCAC------------GAGTGGTACGTGGAAAATCTCCTCACCCGCTATGTGCTCATGCCCTCTGGGGAAGTCACCATC---CAACGCCGGGGTAATCCGTCAGGGCAAATTTCAACAACTCCAGATAACTGCATGGTGAACTACTGGCTCCAAGCCTTTGAGTTCGCTTACCTG------AACAAGGGGAAAGATATCAACAGTCTC---------TGG---------------------------AAGGAGTATGAAACCATCGTCTACGGTGACGATCGACTAACATCAACC---CCTTGC---ATCCCTGAC---------------AATTACGTC---GAGCGTGTGGTCGAGATGTACAAGACAGTCNNT------------" /><sequence id="seq_Swin.HM756267|pig|2006" taxon="Swin.HM756267|pig|2006" totalcount="4" value="------NNACTACTAAAGCACATTAAAGATCTG---CGGTGGGAGAAAATGAACAAAGTACACAGA---GAAAGATACAAACACATCCAC------------GATTGGTACGTGGAGAATCTCCTGACCCGCTATGTGCTCATGCCCTCTGGGGAGGTCACCATC---CAGCGCCGGGGCAATCCGTCAGGGCAGATCTCAACTACTCCAGACAACTGTATGGTGAACTACTGGCTACAAGCCTTTGAGTTCGCCTACCTT------AACAAGGGGAAAGACATCAATGAGCTG---------TGG---------------------------AAAGACTATGAAACCATCGTCTATGGAGACGACCGGCTGACGTCGACTNNCCCTTGT---ATCCCTGAC---------------AACTATGTT---GAACGTGTGGTCGAGATGTACAAAACAGTC---------------" /><sequence id="seq_EothCach.KJ571460|rodent|2012" taxon="EothCach.KJ571460|rodent|2012" totalcount="4" value="---NNTGAACTGTTTGTCCATGTTAAGAAATTG---AGATGGAATTTTATAAATCGTGACCAGAGG---TTGAAGTATGCTTCTATGTAT------------CAATGGTATGTGGAAAATCTTGTAAACCGGTTTGTTCTTATGCCTAGTGGTGAAGTAACATTT---CAAAACCGTGGAAATCCTTCTGGTCAAATTTCTACAACTATGGACAATAATATGTTGAATTATTGGCTACAAGCCTTTGAATTTGGATATTTG------TAT---GGTCTTGAT---TATGATGAG---------TGG---------------------------ATTAAATGTGATACAGTTATATATGGTGATGATCGTCTTAGCCGTATT---CCTTAT---GAACTGCCT---------------GACCATATT---GAGAGACTTGTCTCTATGTATAAAGAGATC---------------" /><sequence id="seq_Swin.HM756262|pig|2006" taxon="Swin.HM756262|pig|2006" totalcount="4" value="------NNAGTATTCATGCACATCAAGAAAGTC---CGTTACTCTTTCTTTGCGAAGGAGTTTAGGACGAAGCGTGTCCAAGAAGCTTAC------------CAATGGTACTGCGAACAGCTCTTACATAGGCATATTGTGCTCCCCTCGGGCGAGGTGACATTG---CAAACTCGTGGAAATCCTTCTGGACAGATTTCCACTACCATGGATAATAATATGGTGAATGTTTTCCTTCAGGCATTTGAGTACGCCTATCTG------CATCCAGGTTGTACAGATGATGAACTTGAGGCAAATTGG---------------------------TCTCGTATGGATACCTTAGTCTATGGTGATGATAGACTATCCGCATAT---GTTGGC---TTGCCCGCC---------------AATTATGTG---GAGAGGGTTGTTACAATGTACTCAGATGTC---------------" /><sequence id="seq_LaboMous.JQ408739|rodent|2011" taxon="LaboMous.JQ408739|rodent|2011" totalcount="4" value="------NNACTCTTCCGCAGGATAAAGAAGCTT---CGCTGGTCCATGATTTGTCCCGAACACCAG---CAGCGCTACGGGCACATGTAC------------CAGTGGTATGTTAACAATCTCTTGCACCGCTACACCGTGCTGCCCTCAGGTGAGGTGACCATC---CAAACTCGTGGCAACCCCTCAGGGCAAATCTCAACAACAATGGACAACAACATGGTTAACTACTGGCTTCAGGCATTTGAGTTCTGCTACTTC------TTT---GGCCCTGAT---AAAGATCTC---------TGG---------------------------CGGCAGTATGATACTGTCTGCTATGGTGATGACCGGCTCACGCGCTAC---CCTGTG---CTACCGCCC---------------CACTACATC---GATCGGGTGGTCGCCATGTATAAGGACATC---------------" /><sequence id="seq_HomoSapi.JQ673585|human|2011" taxon="HomoSapi.JQ673585|human|2011" totalcount="4" value="------NNAGTGTTTATGGCAATTAAACAGTTT---AGGTATTCATGTTTAGCTGAGGAGTTTAAGACAGAGGAGAACTTGAGTATCTAT------------AGATGGTATTGTGAGAGTATACTAGATAGGTACGTCATGTTACCTTCTGGTGAAGTCACCAAA---CAGGTTAGGGGGAACCCTTCAGGCCAGGTGTCAACAACTATGGATAATAACTTGTGTAATGTCTTCTTCCAAGCGTTTGAATACGCGTACATG------CATCCTGATAAGGATATAAGTCAACTTATGCATGATTGG---------------------------GAGAAGGTTGATTCACTTATCTATGGTGATGATAGGTTGTCTACTTAT---CCTGAG---CTGCCTGAA---------------GATTATGTA---GACAGAGTGGTTGACATGTACGCCACAGTGNNT------------" /><sequence id="seq_MiniSchr.HQ613158|bat|2008" taxon="MiniSchr.HQ613158|bat|2008" totalcount="4" value="------NNGGTCTTTCGTCATATCAAAAGACTT---CGTTTTGCCCTTTTGGACCCTGTCTATAAGACTCAACTTAATCGCTCTATATAT------------GGTTGGTATGTTGACCAACTTTTACATCGTTATGTCCTTTTGCCCACTGGTGAGGTCACCATC---CAGACTCGAGGTAACCCCTCTGGGCAGATATCCACCACAATGGACAATAATATGGTCAACACTTTTTTACAGGCGTTCGAGTTCGCCTATGTC------CATAGGTCCTATAGTGAGGAACGTCTTTTTCAGCAATGG---------------------------GCCCTTTGCGATTCCATTGTTTATGGTGATGATCGCATTTCATCTTGG---CCTTCT---GTCCTCCCA---------------ACTATGTTA---CAATGTGTT------------------------------------" /><sequence id="seq_NiviEha.KJ571477|rodent|2012" taxon="NiviEha.KJ571477|rodent|2012" totalcount="4" value="------NNTCTATTTCTTCACATTAAGAAGCTT---AGGTGGAGCTTTGTGAATGAGAAACAGCGG---GTGCGTTATGCCAGAATGTAT------------CGGTGGTATGTTAAGAATCTTGTCCACCGTTATGTGCTTATGCCCTCAGGTGAGATAACAATC---CAGACTAGGGGGAATCCCTCCGGTCAGATTTCAACTACAATGGACAATAACATGGTTAATTACTGGCTGCAGGCCTTTGAGTGGGCATGGTTC------AAC---GGTACTGAT---CATGAAGGG---------TGG---------------------------GATCAGTTTGACACTGTTATATATGGTGATGATCGGTTGAGTGTCTGG---CCACGT---GTTCCGAGT---------------GATTATCCA---AATTTAGTCTCGGACATGTATAGGCGTGTT---------------" /><sequence id="seq_EothCach.KJ571456|rodent|2012" taxon="EothCach.KJ571456|rodent|2012" totalcount="4" value="------NNCTTGTTTCTTCACATCAAGAAGCTT---AGATTCCAATTGTTGAATTCAGAGCAGAGG---GTTAGATATGCTCATGTGTAT------------AAATGGTATGTATCCAACCTCATGAAAAGATATACATTGCTTCCATCTGGAGAGGTTACTATT---CAGAGACGTGGTAATCCAAGCGGACAGATCTCTACTACTATGGACAATAATATGATTAATTATTGGTTACAGTGTTTTGAATTTGCTTTTTTC------TTT---GGCACTGAT---TACCAACTT---------TTC---------------------------CAACAATTTGACACCATAGTTTATGGAGATGATCGCTTGACACGATTT---CCTTTT---ACACCAGAG---------------GACTATGTG---CCACGTGTTGTAGCAATGTATAAGGATGTA---------------" /><sequence id="seq_VoleMill.KJ571473|rodent|2012" taxon="VoleMill.KJ571473|rodent|2012" totalcount="4" value="---NNGTCCCTCTTTATGCGAATTAAACAAATA---AGATGGCGATTGATGGATTCACAACATCGT---GAACGCTATAAACACATTCAT------------AAATGGTATTGTGCTAACCTAGCTAAAAGGTATGTTTGCATGCCTTCGGGAGAGATAACCATT---CAAACCAGAGGTAACCCTTCAGGCCAAATTTCAACAACAATGGATAACAACCTAGTGAACTACTGGTTGCAGGCCTTTGAATATCACTATTTA------------GGATGTGAT---GTCTCTCGC---------TGG---------------------------TCTGAGTATGATACACTCATCTATGGTGATGACAGGTTGAGTAGGCAT---CCCTGT---CTTCCAGAT---------------GATTATCAG---TCCAGGGTCATTACCATGTATAGGGAAGTC---------------" /><sequence id="seq_EothCach.KJ571449|rodent|2012" taxon="EothCach.KJ571449|rodent|2012" totalcount="4" value="------NNCCTCCTTATGCGCATAAAAGCCATC---AGGTGGCAACTTATGGATAGAGAACATCGT---GAGCGATACCGTCACATACAT------------CGATGGTATTGCTCCAATCTTGCTAAACGCTATGTCTGTCTTCCTTCAGGTGAGATCACTGTT---CAAACCCGTGGTAATCCCTCTGGTCAAATCTCAACAACTATGGATAATAATTTAGTGAATTACTGGCTACAGGCATTTGAATACCATTGGCTT------------GGTTGCCCA---GAAGAAGAG---------TGG---------------------------CCCAACTATGATACTCTTGTTTATGGTGATGATAGGCTAACCCGCCAC---CCCTGT---TTACCAGCA---------------AATTATATT---GAGAGGGTTATCAATATGTATAAGGATGTC---------------" /><sequence id="seq_SusScroDome.JX519276|pig|2011" taxon="SusScroDome.JX519276|pig|2011" totalcount="4" value="---------NNACTTCGTATCATTCGACAGGTC---AGGTGGGAGTTTCTTGATGATGTCTATAAGACTGCAGAGAATCGGAAGCTCTAC------------GAATGGTACGTACACAACTTGTTAAACCGTTATGTGCTCTTGCCCTCAGGTGAAGTCACATTT---CAGGATCGTGGCAATCCCTCTGGGCAGGTTTCCACCTCAGTTGACAACGGCATGGTTAACTACTATCTCCAAGCTTATGAGCACTATGTTCTC------AATGGTCCAGACGGC---------------------TGG---------------------------GAAGATACTGATACTTTAATCTATGGTGACGACAGGTTATCTGTCACC---AACTTC---CCGCCCGAC------------------------CCTGATGAGCTCATTAAGTTTTACCATGACTACTTTGGCATG------" /><sequence id="seq_MiniSchr.HQ613167|bat|2008" taxon="MiniSchr.HQ613167|bat|2008" totalcount="4" value="------NNGGTCCTTAGGCACATCAAGAATTTC---AGGTTTGAGATGCTTGATATTGTTTATAGGACTCCGATAAATAGATCCATCTAC------------AACGGGTATGTTGATCAACTATGTACCAGGTATGTTTTATTGCCCAGTGGGGAGGTTACCATA---CAAAAAAGGGGAAACCCTTCTGGCCAAATTTCCACAACCATGGATAATAACATGGTTAATACATTCTTGCAGGCATTTGAGTTCGCATATGTA------CATCCAGCACTTAATCATGATCAATTAGTTGATTTATGG---------------------------TGTAAGTGTGATGCCATTGTCTATGGTGATGATAGGATATCATCATGG---CCTTCT---GTCCTCCAA---------------ACTATGTTG---ATAACTGGT------------------------------------" /><sequence id="seq_SusScroDome.KJ533364|pig|2012" taxon="SusScroDome.KJ533364|pig|2012" totalcount="4" value="---------NNGCTTCGTATCATCCGGCAAGTG---AGGTGGGAGTTTCTTGACGATGTCTATAAGACCACGGAGAATCGGAAACTCTAT------------GAGTGGTATGTGCATAACTTGCTCAACCGCTATGTGCTCTTGCCCTCAGGCGAAGTCACCTTC---CAAGATCGTGGCAATCCCTCTGGGCAGGTTTCTACCTCAGTTGACAATGGCATGGTGAACTACTATCTTCAGGCTTATGAACACTATGTTCTC------AATGGTCCAGACGGT---------------------TGG---------------------------GAGGACACTGACACCTTAATTTATGGTGACGACAGGTTGTCCGTCACC---AACTTC---CCTCCCGAC------------------------CCTGATGAACTCATAAAGTTCTACCATGACTACTTTGGCNNA------" /></data><map name="Beta">beast.math.distributions.Beta</map>
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5 <map name="Exponential">beast.math.distributions.Exponential</map>
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6 <map name="InverseGamma">beast.math.distributions.InverseGamma</map>
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7 <map name="LogNormal">beast.math.distributions.LogNormalDistributionModel</map>
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8 <map name="Gamma">beast.math.distributions.Gamma</map>
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9 <map name="Uniform">beast.math.distributions.Uniform</map>
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10 <map name="prior">beast.math.distributions.Prior</map>
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11 <map name="LaplaceDistribution">beast.math.distributions.LaplaceDistribution</map>
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12 <map name="OneOnX">beast.math.distributions.OneOnX</map>
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13 <map name="Normal">beast.math.distributions.Normal</map>
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14
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15
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16 <run chainLength="100000000" id="mcmc" spec="MCMC">
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17 <state id="state" storeEvery="5000">
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18 <tree id="Tree.t:trimmed" name="stateNode">
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19 <taxonset id="TaxonSet.trimmed" spec="TaxonSet">
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20 <data idref="trimmed" name="alignment" />
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21 </taxonset>
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22 </tree>
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23 <parameter id="kappa.s:trimmed" lower="0.0" name="stateNode">2.0</parameter>
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24 <parameter id="gammaShape.s:trimmed" name="stateNode">1.0</parameter>
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25 <parameter dimension="5" id="bPopSizes.t:trimmed" lower="0.0" name="stateNode" upper="380000.0">380.0</parameter>
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26 <stateNode dimension="5" id="bGroupSizes.t:trimmed" spec="parameter.IntegerParameter">1</stateNode>
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27 <stateNode dimension="6" id="rateIndicator.s:deme" spec="parameter.BooleanParameter">true</stateNode>
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28 <parameter dimension="6" id="relativeGeoRates.s:deme" name="stateNode">1.0</parameter>
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29 <parameter id="traitClockRate.c:deme" name="stateNode">1.0</parameter>
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30 <parameter id="clockRate.c:trimmed" name="stateNode">1.0</parameter>
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31 </state>
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32
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33 <init estimate="false" id="RandomTree.t:trimmed" initial="@Tree.t:trimmed" spec="beast.evolution.tree.RandomTree" taxa="@trimmed">
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34 <populationModel id="ConstantPopulation0.t:trimmed" spec="ConstantPopulation">
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35 <parameter id="randomPopSize.t:trimmed" name="popSize">1.0</parameter>
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36 </populationModel>
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37 </init>
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38
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39 <distribution id="posterior" spec="util.CompoundDistribution">
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40 <distribution id="prior" spec="util.CompoundDistribution">
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41 <distribution groupSizes="@bGroupSizes.t:trimmed" id="BayesianSkyline.t:trimmed" popSizes="@bPopSizes.t:trimmed" spec="BayesianSkyline">
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42 <treeIntervals id="BSPTreeIntervals.t:trimmed" spec="TreeIntervals" tree="@Tree.t:trimmed" />
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43 </distribution>
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44 <distribution id="MarkovChainedPopSizes.t:trimmed" jeffreys="true" parameter="@bPopSizes.t:trimmed" spec="beast.math.distributions.MarkovChainDistribution" />
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45 <prior id="ClockPrior.c:trimmed" name="distribution" x="@clockRate.c:trimmed">
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46 <Uniform id="Uniform.0" name="distr" upper="Infinity" />
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47 </prior>
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48 <prior id="GammaShapePrior.s:trimmed" name="distribution" x="@gammaShape.s:trimmed">
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49 <Exponential id="Exponential.0" name="distr">
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50 <parameter id="RealParameter.0" lower="0.0" name="mean" upper="0.0">1.0</parameter>
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51 </Exponential>
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52 </prior>
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53 <prior id="KappaPrior.s:trimmed" name="distribution" x="@kappa.s:trimmed">
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54 <LogNormal id="LogNormalDistributionModel.0" name="distr">
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55 <parameter estimate="false" id="RealParameter.01" name="M">1.0</parameter>
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56 <parameter estimate="false" id="RealParameter.02" name="S">1.25</parameter>
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57 </LogNormal>
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58 </prior>
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59 <prior id="nonZeroRatePrior.s:deme" name="distribution">
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60 <x arg="@rateIndicator.s:deme" id="nonZeroRates.s:deme" spec="util.Sum" />
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61 <distr id="Poisson.0" offset="3.0" spec="beast.math.distributions.Poisson">
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diff changeset
62 <parameter id="RealParameter.03" lower="0.0" name="lambda" upper="0.0">0.693</parameter>
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63 </distr>
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64 </prior>
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65 <prior id="relativeGeoRatesPrior.s:deme" name="distribution" x="@relativeGeoRates.s:deme">
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66 <Gamma id="Gamma.0" name="distr">
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67 <parameter id="RealParameter.04" lower="0.0" name="alpha" upper="0.0">1.0</parameter>
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68 <parameter id="RealParameter.05" lower="0.0" name="beta" upper="0.0">1.0</parameter>
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69 </Gamma>
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70 </prior>
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71 <prior id="geoclockPrior.c:deme" name="distribution" x="@traitClockRate.c:deme">
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72 <Gamma id="Gamma.01" name="distr">
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73 <parameter id="RealParameter.06" lower="0.0" name="alpha" upper="0.0">0.001</parameter>
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74 <parameter id="RealParameter.07" lower="0.0" name="beta" upper="0.0">1000.0</parameter>
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75 </Gamma>
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76 </prior>
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77 </distribution>
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78 <distribution id="likelihood" spec="util.CompoundDistribution">
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79 <distribution data="@trimmed" id="treeLikelihood.trimmed" spec="TreeLikelihood" tree="@Tree.t:trimmed">
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80 <siteModel gammaCategoryCount="3" id="SiteModel.s:trimmed" shape="@gammaShape.s:trimmed" spec="SiteModel">
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81 <parameter estimate="false" id="mutationRate.s:trimmed" name="mutationRate">1.0</parameter>
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82 <parameter estimate="false" id="proportionInvariant.s:trimmed" lower="0.0" name="proportionInvariant" upper="1.0">0.0</parameter>
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83 <substModel id="hky.s:trimmed" kappa="@kappa.s:trimmed" spec="HKY">
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84 <frequencies data="@trimmed" id="empiricalFreqs.s:trimmed" spec="Frequencies" />
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85 </substModel>
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86 </siteModel>
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87 <branchRateModel clock.rate="@clockRate.c:trimmed" id="StrictClock.c:trimmed" spec="beast.evolution.branchratemodel.StrictClockModel" />
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88 </distribution>
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89 <distribution id="traitedtreeLikelihood.deme" spec="AncestralStateTreeLikelihood" tag="location" tree="@Tree.t:trimmed">
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90 <data id="deme" spec="AlignmentFromTrait">
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91 <traitSet id="traitSet.deme" spec="beast.evolution.tree.TraitSet" taxa="@TaxonSet.trimmed" traitname="discrete">MiniSchr.HQ613158|bat|2008=bat,
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92 MiniSchr.HQ613167|bat|2008=bat,
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93 MiniSchr.JQ814856|bat|2010=bat,
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94 MyotRick.EU847166|bat|2004=bat,
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95 HippArmi.FJ571094|bat|2007=bat,
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96 TaphMela.FJ571090|bat|2007=bat,
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97 MiniPusi.EU847197|bat|2005=bat,
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diff changeset
98 TaphMela.FJ571122|bat|2007=bat,
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diff changeset
99 MyotRick.EU847162|bat|2004=bat,
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100 ScotKuhl.KJ571385|bat|2008=bat,
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101 HippLarv.KJ571394|bat|2008=bat,
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102 RhinPusi.KJ571428|bat|2009=bat,
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103 Swin.HM756267|pig|2006=pig,
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104 Swin.HM756262|pig|2006=pig,
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105 SusScroDome.KJ533344|pig|2012=pig,
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106 SusScroDome.KJ533345|pig|2012=pig,
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107 SusScroDome.KJ533348|pig|2012=pig,
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108 SusScroDome.KJ533355|pig|2012=pig,
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109 SusScroDome.KJ533357|pig|2012=pig,
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110 SusScroDome.KJ533364|pig|2012=pig,
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111 SusScroDome.JX519275|pig|2011=pig,
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112 SusScroDome.JX519276|pig|2011=pig,
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113 SusScroDome.JX519281|pig|2011=pig,
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114 Pig.HQ647383|pig|2009=pig,
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115 LaboMous.JQ408739|rodent|2011=rodent,
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116 RattNorv.HM450385|rodent|2008=rodent,
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117 MusMusc.JF755422|rodent|2012=rodent,
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118 NiviEha.KJ571477|rodent|2012=rodent,
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119 EothCach.KJ571439|rodent|2012=rodent,
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120 EothCach.KJ571440|rodent|2012=rodent,
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121 EothCach.KJ571442|rodent|2012=rodent,
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122 EothCach.KJ571449|rodent|2012=rodent,
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123 EothCach.KJ571450|rodent|2012=rodent,
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124 EothCach.KJ571456|rodent|2012=rodent,
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125 EothCach.KJ571460|rodent|2012=rodent,
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126 VoleMill.KJ571473|rodent|2012=rodent,
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127 HomoSapi.FJ755403|human|2006=human,
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128 HomoSapi.KC342249|human|2012=human,
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129 HomoSapi.JQ403108|human|2010=human,
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130 HomoSapi.HM120878|human|2009=human,
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131 HomoSapi.JF491430|human|2004=human,
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132 HomoSapi.GQ267696|human|2008=human,
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133 HomoSapi.JX179278|human|1983=human,
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134 HomoSapi.JQ673585|human|2011=human,
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135 HomoSapi.JX857869|human|2008=human,
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136 HomoSapi.GQ502191|human|2008=human,
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137 HomoSapi.JQ673581|human|2011=human,
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138 HomoSapi.HM989955|human|2009=human</traitSet>
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139 <userDataType codeMap="bat=0,human=1,pig=2,rodent=3,? = 0 1 2 3 " codelength="-1" id="traitDataType.deme" spec="beast.evolution.datatype.UserDataType" states="4" />
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140 </data>
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141 <siteModel gammaCategoryCount="1" id="geoSiteModel.s:deme" spec="SiteModel">
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142 <parameter estimate="false" id="mutationRate.s:deme" name="mutationRate">1.0</parameter>
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143 <parameter estimate="false" id="gammaShape.s:deme" name="shape">1.0</parameter>
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144 <parameter estimate="false" id="proportionInvariant.s:deme" lower="0.0" name="proportionInvariant" upper="1.0">0.0</parameter>
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145 <substModel id="svs.s:deme" rateIndicator="@rateIndicator.s:deme" rates="@relativeGeoRates.s:deme" spec="SVSGeneralSubstitutionModel">
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146 <frequencies id="traitfreqs.s:deme" spec="Frequencies">
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147 <parameter dimension="4" id="traitfrequencies.s:deme" name="frequencies">0.25</parameter>
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148 </frequencies>
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149 </substModel>
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150 </siteModel>
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151 <branchRateModel clock.rate="@traitClockRate.c:deme" id="StrictClockModel.c:deme" spec="beast.evolution.branchratemodel.StrictClockModel" />
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152 </distribution>
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153 </distribution>
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154 </distribution>
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155
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156 <operator id="treeScaler.t:trimmed" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:trimmed" weight="3.0" />
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157
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158 <operator id="treeRootScaler.t:trimmed" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:trimmed" weight="3.0" />
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159
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160 <operator id="UniformOperator.t:trimmed" spec="Uniform" tree="@Tree.t:trimmed" weight="30.0" />
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161
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162 <operator id="SubtreeSlide.t:trimmed" spec="SubtreeSlide" tree="@Tree.t:trimmed" weight="15.0" />
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163
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164 <operator id="narrow.t:trimmed" spec="Exchange" tree="@Tree.t:trimmed" weight="15.0" />
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165
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166 <operator id="wide.t:trimmed" isNarrow="false" spec="Exchange" tree="@Tree.t:trimmed" weight="3.0" />
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167
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168 <operator id="WilsonBalding.t:trimmed" spec="WilsonBalding" tree="@Tree.t:trimmed" weight="3.0" />
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169
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170 <operator id="KappaScaler.s:trimmed" parameter="@kappa.s:trimmed" scaleFactor="0.5" spec="ScaleOperator" weight="0.1" />
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171
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172 <operator id="gammaShapeScaler.s:trimmed" parameter="@gammaShape.s:trimmed" scaleFactor="0.5" spec="ScaleOperator" weight="0.1" />
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173
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174 <operator id="popSizesScaler.t:trimmed" parameter="@bPopSizes.t:trimmed" scaleFactor="0.75" spec="ScaleOperator" weight="15.0" />
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175
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176 <operator id="groupSizesDelta.t:trimmed" integer="true" spec="DeltaExchangeOperator" weight="6.0">
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177 <intparameter idref="bGroupSizes.t:trimmed" />
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178 </operator>
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179
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180 <operator id="georateScaler.s:deme" parameter="@relativeGeoRates.s:deme" scaleAllIndependently="true" scaleFactor="0.99" spec="ScaleOperator" weight="30.0" />
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181
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182 <operator id="indicatorFlip.s:deme" parameter="@rateIndicator.s:deme" spec="BitFlipOperator" weight="30.0" />
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183
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184 <operator id="geoMuScaler.c:deme" parameter="@traitClockRate.c:deme" scaleFactor="0.9" spec="ScaleOperator" weight="3.0" />
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185
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186 <operator id="BSSVSoperator.c:deme" indicator="@rateIndicator.s:deme" mu="@traitClockRate.c:deme" spec="BitFlipBSSVSOperator" weight="30.0" />
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187
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188 <operator id="StrictClockRateScaler.c:trimmed" parameter="@clockRate.c:trimmed" scaleFactor="0.75" spec="ScaleOperator" weight="3.0" />
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189
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190 <operator id="strictClockUpDownOperator.c:trimmed" scaleFactor="0.75" spec="UpDownOperator" weight="3.0">
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191 <parameter idref="clockRate.c:trimmed" name="up" />
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192 <tree idref="Tree.t:trimmed" name="down" />
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193 </operator>
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194
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195 <logger fileName="posterior.log" id="tracelog" logEvery="10000" model="@posterior" sanitiseHeaders="true" sort="smart">
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196 <log idref="posterior" />
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197 <log idref="likelihood" />
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198 <log idref="prior" />
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199 <log idref="treeLikelihood.trimmed" />
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200 <log id="TreeHeight.t:trimmed" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:trimmed" />
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201 <parameter idref="kappa.s:trimmed" name="log" />
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202 <parameter idref="gammaShape.s:trimmed" name="log" />
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203 <log idref="BayesianSkyline.t:trimmed" />
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204 <parameter idref="bPopSizes.t:trimmed" name="log" />
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205 <log idref="bGroupSizes.t:trimmed" />
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206 <log idref="rateIndicator.s:deme" />
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207 <parameter idref="relativeGeoRates.s:deme" name="log" />
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208 <parameter idref="traitClockRate.c:deme" name="log" />
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209 <parameter idref="clockRate.c:trimmed" name="log" />
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210 </logger>
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211
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212 <logger id="screenlog" logEvery="100000">
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213 <log idref="posterior" />
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214 <log arg="@posterior" id="ESS.0" spec="util.ESS" />
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215 <log idref="likelihood" />
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216 <log idref="prior" />
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217 </logger>
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218
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219 <logger fileName="posterior.trees" id="treelog.t:trimmed" logEvery="1000" mode="tree">
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220 <log id="TreeWithMetaDataLogger.t:trimmed" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:trimmed" />
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221 </logger>
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222
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223 <logger fileName="posterior.trait.trees" id="treeWithTraitLogger.deme" logEvery="10000" mode="tree">
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224 <log id="TreeWithTraitLogger.0" spec="beast.evolution.tree.TreeWithTraitLogger" tree="@Tree.t:trimmed">
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225 <metadata idref="posterior" />
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226 <metadata idref="traitedtreeLikelihood.deme" />
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227 </log>
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228 </logger>
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229
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230 </run>
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231
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232 </beast>