Mercurial > repos > iuc > hyphy_strike_ambigs

annotate test-data/gard-out1.nex @ 10:f5bbd4b34541 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 821e0f3e4546bc55e093ab63bd9f9b57f2bf772d
author iuc
date Thu, 18 Aug 2022 14:02:58 +0000
parents 4bf743518e41
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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1 #NEXUS
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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2
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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3 BEGIN TAXA;
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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4 DIMENSIONS NTAX = 12;
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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5 TAXLABELS
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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6 'BRO1_1' 'BRO2' 'BRO3_1' 'BRO4' 'BRO5' 'BRO6' 'BRO7_1' 'BRO9' 'BRO10' 'BRO11_1' 'BRO12' 'BRO8' ;
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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7 END;
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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8
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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9 BEGIN CHARACTERS;
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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10 DIMENSIONS NCHAR = 428;
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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11 FORMAT
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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12 DATATYPE = DNA
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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13 GAP=-
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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14 MISSING=?
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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15 ;
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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16
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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17 MATRIX
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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18 'BRO1_1' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACCACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACATCAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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19 'BRO2' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACCACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACATCAACTGCAACCCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGTGCATAAAGCCATTTACCGTACATAGCACATTATA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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20 'BRO3_1' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACCACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACATCAGCTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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21 'BRO4' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACCACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCATACATCAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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22 'BRO5' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACAGTACCATAAA-TACTTGACCACCTGTAGTACATAAAAACCC-AATCC--ACACCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACATCAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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23 'BRO6' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACCACCTGTAATACATAAAAACCC-AATTC--ACACCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACATCAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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24 'BRO7_1' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACCACCTGTAGTACATAAAAACCC-AATCC--ACACCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACATCAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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25 'BRO9' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACCACCTGTAGTACATAAAAACCC-AACCC--ACATCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACATCAATTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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26 'BRO10' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACCACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAATCAACCTTCAA-CTATCACACATCAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGCACATAAAGCCATTTATCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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27 'BRO11_1' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACTACCTGTAGTACATAAAAACCC-AACCC--ACATCAAAA----CCCTGCCCC-CATGCTTACAAGCAAGTACAGCAATCAACCTTCAA-CTGTCACACATCAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGCACATAAAGTCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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28 'BRO12' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACAGTACCATAAA-TACTTGACTACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCTCCC-CATGCTTACAAGCAAGTACAGCAATCAACCTTCAA-CTATCACACATCAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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29 'BRO8' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACCACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACATCAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGAATACCAACAAACCTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC;
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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30 END;
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32 BEGIN ASSUMPTIONS;
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33 CHARSET span_1 = 1-428;
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34 END;
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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35 BEGIN TREES;
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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36 TREE tree_1 = (((BRO1_1:1e-10,BRO2:0.007446048662499141)Node2:1.699082282683926e-05,(((BRO5:0.002291051777868712,(BRO6:0.004965711012353363,BRO7_1:1e-10)Node9:0.0001955595843124865)Node7:0.002191267352110732,(BRO9:0.004469023573866088,((BRO10:0.002870586428367251,BRO11_1:0.01462820627459318)Node15:0.001454707803761366,BRO12:0.006027959855484483)Node14:0.005661145911839864)Node12:0.0003039715029625697)Node6:0.0002803682303139691,BRO8:0.002464847898104024)Node5:1.386828770154629e-05)Node1:3.347353150116037e-06,BRO3_1:0.002467834453766899,BRO4:0.002462875913900023);
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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37 END;