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16
README
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16
README
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TIGER v 1.02:
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Installation:
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* To install the TIGER software, simply copy the files "tiger" and
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"tiger_fns_102.py" to /usr/local/bin. This will allow access to
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the executable from any location in the filesystem.
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* Please ensure that you are using Python version 2.5 or 2.6.
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* Type "tiger -h" for a full help menu.
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* Additional information is available in the supplied manual.
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TIGER_Manual.pdf
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BIN
TIGER_Manual.pdf
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sample_data/Chimp_Gorilla.ps
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sample_data/Chimp_Gorilla.ps
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sample_data/Human_Chimp.ps
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sample_data/Human_Chimp.ps
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sample_data/PAn_Gorilla.pdf
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sample_data/PAn_Gorilla.pdf
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sample_data/primate.fas
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sample_data/primate.fas
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>Lemur_catta
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AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATTCTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGGGATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCTAGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTCATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTCCCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAACCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATTTACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAACACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATGTATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGATAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTATAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTGCATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAACAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT
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>Homo_sapiens
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AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT
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>Pan
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AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATTCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCTCGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAAGCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TATAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCACCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCGCGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAGCTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT
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>Gorilla
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AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGGACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCTCGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTCCTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTCCCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAAACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCTATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CGTAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTACCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCGCATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAGCTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT
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>Pongo
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AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGGCCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCTTGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTCTTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTCTCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAAACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTTATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAACATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGATAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAACAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCGCTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCGCATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAACCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT
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>Hylobates
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AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATTCTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGGGCTCCAAGCCTTACTCCCACTGATAGCCTTCTGATGACTCGCAGCAAGCCTCGCTAACCTCGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTCCTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTCCCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAAACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCTAACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAACATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CACAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAGCCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTGCCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAACCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT
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>Macaca_fuscata
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AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGGACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTCCTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTCTCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAAGCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAACACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT
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>M._mulatta
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AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGGACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTCCTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTCCCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCTATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAACATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CGCGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT
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>M._fascicularis
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AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTTCTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGTACCATACTACTATCCCGAGGACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTCCTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTCTCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAACATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTGCCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAATATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAACAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT
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>M._sylvanus
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AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTTCTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGCATCATACTACTATCCCGAGGACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCTTGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTCCTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTCTCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAAACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCTATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAACATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TGCAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCGCTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAATATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAACAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT
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>Saimiri_sciureus
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AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTCTATGCTATTCTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAATAACATTTACTCGAGGGCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCTCGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTCTTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTCACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAAACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCTTACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAACATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CGCAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGATAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAATA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAGCTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCATCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAATCAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT
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>Tarsius_syrichta
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AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT
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sample_data/primate.tiger
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sample_data/primate.tiger
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#NEXUS
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[This file contains data that has been analysed for site specific rates]
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[using TIGER, developed by Carla Cummins in the laboratory of]
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[Dr James McInerney, National University of Ireland, Maynooth]
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[Histograms of number of sites in each category:]
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[Bin1 |============================================================ |373 ]
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[Bin2 | |0 ]
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[Bin3 |= |3 ]
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[Bin4 | |0 ]
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[Bin5 | |0 ]
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[Bin6 |=========== |68 ]
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[Bin7 |============ |73 ]
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[Bin8 |====== |37 ]
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[Bin9 |========================= |152 ]
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[Bin10 |=============================== |192 ]
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BEGIN TAXA;
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Dimensions NTax = 12 ;
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TaxLabels Lemur_catta Homo_sapiens Pan Gorilla Pongo Hylobates Macaca_fuscata M._mulatta M._fascicularis M._sylvanus Saimiri_sciureus Tarsius_syrichta ;
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END;
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BEGIN CHARACTERS;
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Dimensions nchar = 898 ;
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Format datatype = DNA gap = - interleave;
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Matrix
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Lemur_catta AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATT
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Homo_sapiens AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATT
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Pan AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATT
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Gorilla AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATT
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Pongo AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTT
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Hylobates AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATT
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Macaca_fuscata AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTT
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M._mulatta AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTT
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M._fascicularis AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTT
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M._sylvanus AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTT
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Saimiri_sciureus AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTCTATGCTATT
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Tarsius_syrichta AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATT
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[Bin Numbers 111711879111111771181911111861111111111191111111111191117911]
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[ 0 0 00 0 0 0 0 0 0 0 0 0 0 00 ]
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Lemur_catta CTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGG
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Homo_sapiens CTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGG
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Pan CTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGG
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Gorilla CTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGG
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Pongo CTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGG
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Hylobates CTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGG
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Macaca_fuscata CTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGG
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M._mulatta CTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGG
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M._fascicularis CTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGTACCATACTACTATCCCGAGG
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M._sylvanus CTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGCATCATACTACTATCCCGAGG
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Saimiri_sciureus CTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAATAACATTTACTCGAGG
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Tarsius_syrichta TTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGG
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[Bin Numbers 711671911911971611911911611979111817911119911111891111118911]
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[ 0 0 00 00 0 ]
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Lemur_catta GATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCT
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Homo_sapiens ACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCT
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Pan ACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCT
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Gorilla ACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCT
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Pongo CCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCT
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Hylobates GCTCCAAGCCTTACTCCCACTGATAGCCTTCTGATGACTCGCAGCAAGCCTCGCTAACCT
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Macaca_fuscata ACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCT
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M._mulatta ACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCT
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||||||
|
M._fascicularis ACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCT
|
||||||
|
M._sylvanus ACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCT
|
||||||
|
Saimiri_sciureus GCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCT
|
||||||
|
Tarsius_syrichta CCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCT
|
||||||
|
[Bin Numbers 161111167181611911161179119919111111171188911919971111911611]
|
||||||
|
[ 0 0 0 0 0 0 0 0 0 00 ]
|
||||||
|
|
||||||
|
|
||||||
|
Lemur_catta AGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTC
|
||||||
|
Homo_sapiens CGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTC
|
||||||
|
Pan CGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTC
|
||||||
|
Gorilla CGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTC
|
||||||
|
Pongo TGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTC
|
||||||
|
Hylobates CGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTC
|
||||||
|
Macaca_fuscata TGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTC
|
||||||
|
M._mulatta TGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTC
|
||||||
|
M._fascicularis TGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTC
|
||||||
|
M._sylvanus TGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTC
|
||||||
|
Saimiri_sciureus CGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTC
|
||||||
|
Tarsius_syrichta GGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTC
|
||||||
|
[Bin Numbers 111671711611191911911991811111111691999899986117811196911111]
|
||||||
|
[ 0 0 0 0 0 0 00 0 0 0 ]
|
||||||
|
|
||||||
|
|
||||||
|
Lemur_catta ATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTC
|
||||||
|
Homo_sapiens CTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTC
|
||||||
|
Pan CTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTC
|
||||||
|
Gorilla CTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTC
|
||||||
|
Pongo TTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTC
|
||||||
|
Hylobates CTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTC
|
||||||
|
Macaca_fuscata CTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTC
|
||||||
|
M._mulatta CTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTC
|
||||||
|
M._fascicularis CTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTC
|
||||||
|
M._sylvanus CTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTC
|
||||||
|
Saimiri_sciureus TTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTC
|
||||||
|
Tarsius_syrichta ATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTC
|
||||||
|
[Bin Numbers 111161191918111171996111179811116111167961931111161911911911]
|
||||||
|
[ 0 0 0 0 0 0 00 0 00 0 0 0 0 ]
|
||||||
|
|
||||||
|
|
||||||
|
Lemur_catta CCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAA
|
||||||
|
Homo_sapiens CCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAA
|
||||||
|
Pan CCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAA
|
||||||
|
Gorilla CCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAA
|
||||||
|
Pongo TCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAA
|
||||||
|
Hylobates CCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAA
|
||||||
|
Macaca_fuscata TCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAA
|
||||||
|
M._mulatta CCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAA
|
||||||
|
M._fascicularis TCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAA
|
||||||
|
M._sylvanus TCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAA
|
||||||
|
Saimiri_sciureus ACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAA
|
||||||
|
Tarsius_syrichta CCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCAT
|
||||||
|
[Bin Numbers 111111911179191999966711971311119679111791199969161911161717]
|
||||||
|
[ 0 00 0 0 0 00 0 0 0 0 0 ]
|
||||||
|
|
||||||
|
|
||||||
|
Lemur_catta CCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATT
|
||||||
|
Homo_sapiens ACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCT
|
||||||
|
Pan GCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCT
|
||||||
|
Gorilla ACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCT
|
||||||
|
Pongo ACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTT
|
||||||
|
Hylobates ACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCT
|
||||||
|
Macaca_fuscata GCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCT
|
||||||
|
M._mulatta ACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCT
|
||||||
|
M._fascicularis ACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCT
|
||||||
|
M._sylvanus ACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCT
|
||||||
|
Saimiri_sciureus ACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCT
|
||||||
|
Tarsius_syrichta GCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACT
|
||||||
|
[Bin Numbers 111119161911711611111119191911716161811991811111111191611181]
|
||||||
|
[ 0 00 0 0 0 0 0 000 00 0 0 ]
|
||||||
|
|
||||||
|
|
||||||
|
Lemur_catta TACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAAC
|
||||||
|
Homo_sapiens ATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAAC
|
||||||
|
Pan ATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAAC
|
||||||
|
Gorilla ATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAAC
|
||||||
|
Pongo ATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAAC
|
||||||
|
Hylobates AACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAAC
|
||||||
|
Macaca_fuscata ATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAAC
|
||||||
|
M._mulatta ATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAAC
|
||||||
|
M._fascicularis ATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAAC
|
||||||
|
M._sylvanus ATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAAC
|
||||||
|
Saimiri_sciureus TACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAAC
|
||||||
|
Tarsius_syrichta ATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAAC
|
||||||
|
[Bin Numbers 991197119611876111111998111199997119911116961111111191111111]
|
||||||
|
[ 0 0 00 0 0 0 00 00 ]
|
||||||
|
|
||||||
|
|
||||||
|
Lemur_catta ACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATG
|
||||||
|
Homo_sapiens ATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CA
|
||||||
|
Pan ATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TA
|
||||||
|
Gorilla ATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CG
|
||||||
|
Pongo ATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CA
|
||||||
|
Hylobates ATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CA
|
||||||
|
Macaca_fuscata ACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CG
|
||||||
|
M._mulatta ATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CG
|
||||||
|
M._fascicularis ATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CG
|
||||||
|
M._sylvanus ATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TG
|
||||||
|
Saimiri_sciureus ATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CG
|
||||||
|
Tarsius_syrichta ATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TG
|
||||||
|
[Bin Numbers 187111611111711676171711698911691167981116111111711111791618]
|
||||||
|
[ 0 00 00 0 0 0 ]
|
||||||
|
|
||||||
|
|
||||||
|
Lemur_catta TATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGA
|
||||||
|
Homo_sapiens CAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGA
|
||||||
|
Pan TAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGA
|
||||||
|
Gorilla TAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGA
|
||||||
|
Pongo CAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGA
|
||||||
|
Hylobates CAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGA
|
||||||
|
Macaca_fuscata CAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGA
|
||||||
|
M._mulatta CGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGA
|
||||||
|
M._fascicularis CAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGA
|
||||||
|
M._sylvanus CAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGA
|
||||||
|
Saimiri_sciureus CAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGA
|
||||||
|
Tarsius_syrichta CAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGA
|
||||||
|
[Bin Numbers 966176161111117181111111991111819171191171611177611111111111]
|
||||||
|
[ 0 00000 000 00 0 ]
|
||||||
|
|
||||||
|
|
||||||
|
Lemur_catta TAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAA
|
||||||
|
Homo_sapiens TAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAA
|
||||||
|
Pan TAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAA
|
||||||
|
Gorilla TAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAA
|
||||||
|
Pongo TAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAA
|
||||||
|
Hylobates TAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAA
|
||||||
|
Macaca_fuscata TAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAA
|
||||||
|
M._mulatta TAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAA
|
||||||
|
M._fascicularis TAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAA
|
||||||
|
M._sylvanus TAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAA
|
||||||
|
Saimiri_sciureus TAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAA
|
||||||
|
Tarsius_syrichta TAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAA
|
||||||
|
[Bin Numbers 119111991111717179111111797171111181111111111111111111111111]
|
||||||
|
[ 0 0 ]
|
||||||
|
|
||||||
|
|
||||||
|
Lemur_catta TAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTA
|
||||||
|
Homo_sapiens TAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTA
|
||||||
|
Pan TAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCA
|
||||||
|
Gorilla TAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTA
|
||||||
|
Pongo CAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCG
|
||||||
|
Hylobates TAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAG
|
||||||
|
Macaca_fuscata TAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTG
|
||||||
|
M._mulatta TAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTG
|
||||||
|
M._fascicularis TAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTG
|
||||||
|
M._sylvanus TAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCG
|
||||||
|
Saimiri_sciureus TA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAG
|
||||||
|
Tarsius_syrichta TAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTA
|
||||||
|
[Bin Numbers 611119191919999119786911811789116111911119169911111117191711]
|
||||||
|
[ 000 0 0 0 00 00 0 0 000 0000 0 0 00]
|
||||||
|
|
||||||
|
|
||||||
|
Lemur_catta TAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTG
|
||||||
|
Homo_sapiens CCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCG
|
||||||
|
Pan CCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCG
|
||||||
|
Gorilla CCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCG
|
||||||
|
Pongo CTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCG
|
||||||
|
Hylobates CCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTG
|
||||||
|
Macaca_fuscata CCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAA
|
||||||
|
M._mulatta CCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAA
|
||||||
|
M._fascicularis CCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAA
|
||||||
|
M._sylvanus CTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAA
|
||||||
|
Saimiri_sciureus CTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCA
|
||||||
|
Tarsius_syrichta TTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCG
|
||||||
|
[Bin Numbers 911679713191199911117111191111161116111611181161111111799191]
|
||||||
|
[ 0 0 0 00 0 0 00000 0 00 0 0000 0]
|
||||||
|
|
||||||
|
|
||||||
|
Lemur_catta CATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAA
|
||||||
|
Homo_sapiens CATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAG
|
||||||
|
Pan CGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAG
|
||||||
|
Gorilla CATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAG
|
||||||
|
Pongo CATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAA
|
||||||
|
Hylobates CCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAA
|
||||||
|
Macaca_fuscata TATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAA
|
||||||
|
M._mulatta TATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAA
|
||||||
|
M._fascicularis TATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAA
|
||||||
|
M._sylvanus TATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAA
|
||||||
|
Saimiri_sciureus TCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAAT
|
||||||
|
Tarsius_syrichta CCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAA
|
||||||
|
[Bin Numbers 111198199111611991119991711111197911191699111191919991111111]
|
||||||
|
[ 00 0 0 0 0 0 00 0 0 00 000 0 0]
|
||||||
|
|
||||||
|
|
||||||
|
Lemur_catta CAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT
|
||||||
|
Homo_sapiens TTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT
|
||||||
|
Pan CTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT
|
||||||
|
Gorilla CTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT
|
||||||
|
Pongo CCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT
|
||||||
|
Hylobates CCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT
|
||||||
|
Macaca_fuscata CAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT
|
||||||
|
M._mulatta CAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT
|
||||||
|
M._fascicularis CAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT
|
||||||
|
M._sylvanus CAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT
|
||||||
|
Saimiri_sciureus CAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT
|
||||||
|
Tarsius_syrichta TAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT
|
||||||
|
[Bin Numbers 7817161967119611866111178767119711911117116971877181611111]
|
||||||
|
[ 0 0 0 0 00 00 0 ]
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
;
|
||||||
|
END;
|
||||||
|
|
||||||
|
BEGIN PAUP;
|
||||||
|
Charset Bin1 = 1 2 3 5 6 11 12 14 15 23 24 26 27 30 32 33 35 36 38 39 42 44 45 47 48 50 51 54 59 60 62 63 66 68 69 71 72 75 77 78 80 81 83 84 86 87 92 93 95 98 99 101 104 105 106 111 114 116 119 120 123 125 126 127 132 135 137 138 141 145 146 152 153 154 155 156 157 159 164 165 167 171 174 176 177 179 180 182 183 186 188 189 192 195 197 198 200 201 204 207 209 210 212 213 216 231 236 237 239 240 242 243 246 249 254 255 258 264 269 270 275 276 282 285 287 288 291 293 294 296 297 299 300 302 303 306 308 309 323 324 327 329 330 338 339 342 353 354 357 359 362 363 369 371 372 374 375 377 378 379 380 381 383 387 389 390 396 398 399 402 407 408 411 414 416 417 420 423 428 431 432 438 440 441 446 447 458 459 460 461 465 466 467 468 469 470 471 472 476 477 478 479 480 481 484 485 486 488 489 490 491 492 494 495 501 503 504 519 520 521 524 525 526 527 528 530 531 532 533 534 544 547 549 550 551 552 553 556 563 564 570 572 574 579 580 582 585 586 590 591 592 593 594 595 596 597 598 599 600 601 602 605 606 609 610 611 612 614 616 619 620 621 622 623 624 628 630 631 632 633 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 662 667 676 691 694 696 701 703 711 712 715 723 732 733 739 742 743 744 753 754 757 762 763 765 766 768 769 770 778 783 787 790 792 795 798 799 808 810 817 819 823 830 834 835 836 837 838 839 843 847 852 855 856 861 862 863 870 873 874 876 877 886 892 894 895 896 897 898;
|
||||||
|
Charset Bin3 = 284 328 729;
|
||||||
|
Charset Bin6 = 29 64 76 85 122 128 133 140 178 184 190 214 225 234 245 261 273 278 281 290 320 321 334 347 350 356 368 376 393 395 415 430 435 462 464 487 496 498 505 511 515 522 538 542 543 546 548 583 589 661 681 693 704 724 752 756 760 767 793 820 846 849 854 858 859 867 883 893;
|
||||||
|
Charset Bin7 = 4 8 16 17 57 61 65 74 89 96 129 143 158 170 185 187 228 257 266 279 311 322 326 335 340 358 360 373 391 426 434 453 483 493 497 500 502 516 529 535 545 555 575 581 587 588 613 615 617 625 627 629 679 688 714 718 725 727 741 775 805 813 841 844 850 864 866 868 872 880 885 888 889;
|
||||||
|
Charset Bin8 = 7 20 28 94 109 117 131 161 162 205 220 224 229 252 268 397 403 419 433 444 482 507 518 540 557 571 635 680 685 689 764 786 842 857 865 887 891;
|
||||||
|
Charset Bin9 = 9 22 41 53 58 67 70 73 79 82 88 90 97 102 103 110 118 136 144 147 148 150 163 166 168 169 175 194 196 199 202 203 215 217 218 219 221 222 223 233 235 248 250 259 260 267 280 283 292 295 298 307 312 314 316 317 318 319 325 333 336 341 344 345 346 348 352 366 370 384 386 388 400 401 413 421 422 425 429 442 443 449 450 451 452 456 457 463 473 506 508 512 517 536 541 565 566 573 578 603 607 608 618 626 666 668 670 672 673 674 675 678 682 690 697 702 705 706 716 721 726 731 734 735 736 746 776 777 779 785 788 789 796 797 801 802 803 812 814 818 821 822 827 829 831 832 833 848 853 871 875 884;
|
||||||
|
Charset Bin10 = 10 13 18 19 21 25 31 34 37 40 43 46 49 52 55 56 91 100 107 108 112 113 115 121 124 130 134 139 142 149 151 160 172 173 181 191 193 206 208 211 226 227 230 232 238 241 244 247 251 253 256 262 263 265 271 272 274 277 286 289 301 304 305 310 313 315 331 332 337 343 349 351 355 361 364 365 367 382 385 392 394 404 405 406 409 410 412 418 424 427 436 437 439 445 448 454 455 474 475 499 509 510 513 514 523 537 539 554 558 559 560 561 562 567 568 569 576 577 584 604 634 663 664 665 669 671 677 683 684 686 687 692 695 698 699 700 707 708 709 710 713 717 719 720 722 728 730 737 738 740 745 747 748 749 750 751 755 758 759 761 771 772 773 774 780 781 782 784 791 794 800 804 806 807 809 811 815 816 824 825 826 828 840 845 851 860 869 878 879 881 882 890;
|
||||||
|
END;
|
||||||
|
[START TIME: 12 : 55 : 59 ]
|
||||||
|
[FINISH TIME: 12 : 56 : 2 ]
|
||||||
49
sample_data/primate.tiger.tre
Normal file
49
sample_data/primate.tiger.tre
Normal file
|
|
@ -0,0 +1,49 @@
|
||||||
|
#NEXUS
|
||||||
|
|
||||||
|
Begin trees; [Treefile saved Sun Jun 19 13:25:16 2011]
|
||||||
|
[!
|
||||||
|
>Data file = /Users/james/Lab/Dave Fitzpatrick/NewMito/tiger_unix_1.02/sample_data/primate.tiger
|
||||||
|
>Heuristic search settings:
|
||||||
|
> Optimality criterion = parsimony
|
||||||
|
> Character-status summary:
|
||||||
|
> Of 898 total characters:
|
||||||
|
> All characters are of type 'unord'
|
||||||
|
> All characters have equal weight
|
||||||
|
> 377 characters are constant
|
||||||
|
> 154 variable characters are parsimony-uninformative
|
||||||
|
> Number of parsimony-informative characters = 367
|
||||||
|
> Gaps are treated as "missing"
|
||||||
|
> Starting tree(s) obtained via stepwise addition
|
||||||
|
> Addition sequence: simple (reference taxon = Lemur catta)
|
||||||
|
> Number of trees held at each step during stepwise addition = 1
|
||||||
|
> Branch-swapping algorithm: tree-bisection-reconnection (TBR)
|
||||||
|
> Steepest descent option not in effect
|
||||||
|
> Initial 'MaxTrees' setting = 100
|
||||||
|
> Branches collapsed (creating polytomies) if maximum branch length is zero
|
||||||
|
> 'MulTrees' option in effect
|
||||||
|
> Topological constraints not enforced
|
||||||
|
> Trees are unrooted
|
||||||
|
>
|
||||||
|
>Heuristic search completed
|
||||||
|
> Total number of rearrangements tried = 1092
|
||||||
|
> Score of best tree(s) found = 1153
|
||||||
|
> Number of trees retained = 2
|
||||||
|
> Time used = <1 sec (CPU time = 0.01 sec)
|
||||||
|
]
|
||||||
|
Translate
|
||||||
|
1 Lemur_catta,
|
||||||
|
2 Homo_sapiens,
|
||||||
|
3 Pan,
|
||||||
|
4 Gorilla,
|
||||||
|
5 Pongo,
|
||||||
|
6 Hylobates,
|
||||||
|
7 Macaca_fuscata,
|
||||||
|
8 M._mulatta,
|
||||||
|
9 M._fascicularis,
|
||||||
|
10 M._sylvanus,
|
||||||
|
11 Saimiri_sciureus,
|
||||||
|
12 Tarsius_syrichta
|
||||||
|
;
|
||||||
|
tree PAUP_1 = [&U] (1,(((((((2,3),4),5),6),(((7,8),9),10)),11),12));
|
||||||
|
tree PAUP_2 = [&U] (1,((((((2,(3,4)),5),6),(((7,8),9),10)),11),12));
|
||||||
|
End;
|
||||||
305
sample_data/primate20.tiger
Normal file
305
sample_data/primate20.tiger
Normal file
|
|
@ -0,0 +1,305 @@
|
||||||
|
#NEXUS
|
||||||
|
|
||||||
|
[This file contains data that has been analysed for site specific rates]
|
||||||
|
[using TIGER, developed by Carla Cummins in the laboratory of]
|
||||||
|
[Dr James McInerney, National University of Ireland, Maynooth]
|
||||||
|
|
||||||
|
|
||||||
|
[Histograms of number of sites in each category:]
|
||||||
|
[Bin1 |============================================================ |373 ]
|
||||||
|
[Bin2 | |0 ]
|
||||||
|
[Bin3 | |0 ]
|
||||||
|
[Bin4 | |0 ]
|
||||||
|
[Bin5 | |0 ]
|
||||||
|
[Bin6 |= |3 ]
|
||||||
|
[Bin7 | |0 ]
|
||||||
|
[Bin8 | |0 ]
|
||||||
|
[Bin9 | |0 ]
|
||||||
|
[Bin10 | |0 ]
|
||||||
|
[Bin11 |======== |44 ]
|
||||||
|
[Bin12 |==== |24 ]
|
||||||
|
[Bin13 |== |10 ]
|
||||||
|
[Bin14 |=========== |63 ]
|
||||||
|
[Bin15 |== |8 ]
|
||||||
|
[Bin16 |===== |29 ]
|
||||||
|
[Bin17 |======= |40 ]
|
||||||
|
[Bin18 |=================== |112 ]
|
||||||
|
[Bin19 |==================== |122 ]
|
||||||
|
[Bin20 |============ |70 ]
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
BEGIN TAXA;
|
||||||
|
Dimensions NTax = 12 ;
|
||||||
|
TaxLabels Lemur_catta Homo_sapiens Pan Gorilla Pongo Hylobates Macaca_fuscata M._mulatta M._fascicularis M._sylvanus Saimiri_sciureus Tarsius_syrichta ;
|
||||||
|
END;
|
||||||
|
|
||||||
|
BEGIN CHARACTERS;
|
||||||
|
Dimensions nchar = 898 ;
|
||||||
|
Format datatype = DNA gap = - interleave;
|
||||||
|
Matrix
|
||||||
|
|
||||||
|
Lemur_catta AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATT
|
||||||
|
Homo_sapiens AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATT
|
||||||
|
Pan AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATT
|
||||||
|
Gorilla AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATT
|
||||||
|
Pongo AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTT
|
||||||
|
Hylobates AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATT
|
||||||
|
Macaca_fuscata AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTT
|
||||||
|
M._mulatta AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTT
|
||||||
|
M._fascicularis AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTT
|
||||||
|
M._sylvanus AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTT
|
||||||
|
Saimiri_sciureus AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTCTATGCTATT
|
||||||
|
Tarsius_syrichta AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATT
|
||||||
|
[Bin Numbers 111111111211211111211111211111211211211211111111111111211111]
|
||||||
|
[ 4 6480 0 4390598 0 62 0 0 0 08 9 9 9 98 0947 ]
|
||||||
|
|
||||||
|
|
||||||
|
Lemur_catta CTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGG
|
||||||
|
Homo_sapiens CTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGG
|
||||||
|
Pan CTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGG
|
||||||
|
Gorilla CTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGG
|
||||||
|
Pongo CTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGG
|
||||||
|
Hylobates CTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGG
|
||||||
|
Macaca_fuscata CTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGG
|
||||||
|
M._mulatta CTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGG
|
||||||
|
M._fascicularis CTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGTACCATACTACTATCCCGAGG
|
||||||
|
M._sylvanus CTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGCATCATACTACTATCCCGAGG
|
||||||
|
Saimiri_sciureus CTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAATAACATTTACTCGAGG
|
||||||
|
Tarsius_syrichta TTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGG
|
||||||
|
[Bin Numbers 111111111111111111111111111111211111111211111111111211111111]
|
||||||
|
[ 4 14 7 7 84 1 8 7 2 7470 6 37 0 87 9968 09 9 58 ]
|
||||||
|
|
||||||
|
|
||||||
|
Lemur_catta GATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCT
|
||||||
|
Homo_sapiens ACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCT
|
||||||
|
Pan ACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCT
|
||||||
|
Gorilla ACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCT
|
||||||
|
Pongo CCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCT
|
||||||
|
Hylobates GCTCCAAGCCTTACTCCCACTGATAGCCTTCTGATGACTCGCAGCAAGCCTCGCTAACCT
|
||||||
|
Macaca_fuscata ACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCT
|
||||||
|
M._mulatta ACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCT
|
||||||
|
M._fascicularis ACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCT
|
||||||
|
M._sylvanus ACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCT
|
||||||
|
Saimiri_sciureus GCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCT
|
||||||
|
Tarsius_syrichta CCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCT
|
||||||
|
[Bin Numbers 111111111211111111111111111111111111111211111111111111111111]
|
||||||
|
[ 91 9 1406 19 8 92 948 88989 4 0668 8 884 99 7 2 ]
|
||||||
|
|
||||||
|
|
||||||
|
Lemur_catta AGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTC
|
||||||
|
Homo_sapiens CGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTC
|
||||||
|
Pan CGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTC
|
||||||
|
Gorilla CGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTC
|
||||||
|
Pongo TGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTC
|
||||||
|
Hylobates CGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTC
|
||||||
|
Macaca_fuscata TGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTC
|
||||||
|
M._mulatta TGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTC
|
||||||
|
M._fascicularis TGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTC
|
||||||
|
M._sylvanus TGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTC
|
||||||
|
Saimiri_sciureus CGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTC
|
||||||
|
Tarsius_syrichta GGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTC
|
||||||
|
[Bin Numbers 111111111111111111111111111111211111111111111121111211111111]
|
||||||
|
[ 9 23 4 19 98 8 8 88 69 9 0 28 88868876190469 0818 9 ]
|
||||||
|
|
||||||
|
|
||||||
|
Lemur_catta ATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTC
|
||||||
|
Homo_sapiens CTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTC
|
||||||
|
Pan CTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTC
|
||||||
|
Gorilla CTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTC
|
||||||
|
Pongo TTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTC
|
||||||
|
Hylobates CTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTC
|
||||||
|
Macaca_fuscata CTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTC
|
||||||
|
M._mulatta CTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTC
|
||||||
|
M._fascicularis CTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTC
|
||||||
|
M._sylvanus CTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTC
|
||||||
|
Saimiri_sciureus TTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTC
|
||||||
|
Tarsius_syrichta ATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTC
|
||||||
|
[Bin Numbers 111111111111111111111211111111211211111111161211211111111111]
|
||||||
|
[ 9 91 98 7959 94 78109 9486 0920 91482 8 0 01 8 8 8 ]
|
||||||
|
|
||||||
|
|
||||||
|
Lemur_catta CCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAA
|
||||||
|
Homo_sapiens CCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAA
|
||||||
|
Pan CCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAA
|
||||||
|
Gorilla CCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAA
|
||||||
|
Pongo TCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAA
|
||||||
|
Hylobates CCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAA
|
||||||
|
Macaca_fuscata TCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAA
|
||||||
|
M._mulatta CCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAA
|
||||||
|
M._fascicularis TCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAA
|
||||||
|
M._sylvanus TCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAA
|
||||||
|
Saimiri_sciureus ACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAA
|
||||||
|
Tarsius_syrichta CCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCAT
|
||||||
|
[Bin Numbers 211211111211111111111111111611121111111111111111112111211111]
|
||||||
|
[ 0 09 7 0489897878224 84 9082479 37 9888189107 01 4 4]
|
||||||
|
|
||||||
|
|
||||||
|
Lemur_catta CCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATT
|
||||||
|
Homo_sapiens ACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCT
|
||||||
|
Pan GCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCT
|
||||||
|
Gorilla ACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCT
|
||||||
|
Pongo ACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTT
|
||||||
|
Hylobates ACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCT
|
||||||
|
Macaca_fuscata GCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCT
|
||||||
|
M._mulatta ACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCT
|
||||||
|
M._fascicularis ACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCT
|
||||||
|
M._sylvanus ACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCT
|
||||||
|
Saimiri_sciureus ACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCT
|
||||||
|
Tarsius_syrichta GCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACT
|
||||||
|
[Bin Numbers 211211211111111111111111111111111111111111111111111211111211]
|
||||||
|
[ 0 09801 8 4 1 9 898 8 39192 5 88 6999 99 08 2 06 ]
|
||||||
|
|
||||||
|
|
||||||
|
Lemur_catta TACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAAC
|
||||||
|
Homo_sapiens ATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAAC
|
||||||
|
Pan ATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAAC
|
||||||
|
Gorilla ATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAAC
|
||||||
|
Pongo ATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAAC
|
||||||
|
Hylobates AACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAAC
|
||||||
|
Macaca_fuscata ATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAAC
|
||||||
|
M._mulatta ATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAAC
|
||||||
|
M._fascicularis ATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAAC
|
||||||
|
M._sylvanus ATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAAC
|
||||||
|
Saimiri_sciureus TACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAAC
|
||||||
|
Tarsius_syrichta ATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAAC
|
||||||
|
[Bin Numbers 111111111111111111111111111111111211111111111111111112111111]
|
||||||
|
[ 88 9849 82 54199 9 8869 9877840988 281 809 ]
|
||||||
|
|
||||||
|
|
||||||
|
Lemur_catta ACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATG
|
||||||
|
Homo_sapiens ATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CA
|
||||||
|
Pan ATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TA
|
||||||
|
Gorilla ATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CG
|
||||||
|
Pongo ATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CA
|
||||||
|
Hylobates ATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CA
|
||||||
|
Macaca_fuscata ACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CG
|
||||||
|
M._mulatta ATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CG
|
||||||
|
M._fascicularis ATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CG
|
||||||
|
M._sylvanus ATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TG
|
||||||
|
Saimiri_sciureus ATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CG
|
||||||
|
Tarsius_syrichta ATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TG
|
||||||
|
[Bin Numbers 111111111111111111111111111122111111111111111111111111111121]
|
||||||
|
[ 64 2 4 14194 4 18680018991485 19 4 479106]
|
||||||
|
|
||||||
|
|
||||||
|
Lemur_catta TATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGA
|
||||||
|
Homo_sapiens CAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGA
|
||||||
|
Pan TAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGA
|
||||||
|
Gorilla TAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGA
|
||||||
|
Pongo CAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGA
|
||||||
|
Hylobates CAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGA
|
||||||
|
Macaca_fuscata CAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGA
|
||||||
|
M._mulatta CGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGA
|
||||||
|
M._fascicularis CAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGA
|
||||||
|
M._sylvanus CAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGA
|
||||||
|
Saimiri_sciureus CAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGA
|
||||||
|
Tarsius_syrichta CAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGA
|
||||||
|
[Bin Numbers 111111111111121111222211111121111111111111111111111111111111]
|
||||||
|
[ 721 42 2 04 690000 88990 6 7 4997 4 19 441 ]
|
||||||
|
|
||||||
|
|
||||||
|
Lemur_catta TAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAA
|
||||||
|
Homo_sapiens TAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAA
|
||||||
|
Pan TAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAA
|
||||||
|
Gorilla TAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAA
|
||||||
|
Pongo TAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAA
|
||||||
|
Hylobates TAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAA
|
||||||
|
Macaca_fuscata TAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAA
|
||||||
|
M._mulatta TAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAA
|
||||||
|
M._fascicularis TAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAA
|
||||||
|
M._sylvanus TAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAA
|
||||||
|
Saimiri_sciureus TAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAA
|
||||||
|
Tarsius_syrichta TAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAA
|
||||||
|
[Bin Numbers 111111111111111111111111111111111211111111111111111111111111]
|
||||||
|
[ 79 78 4 4 37 384 4 06 ]
|
||||||
|
|
||||||
|
|
||||||
|
Lemur_catta TAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTA
|
||||||
|
Homo_sapiens TAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTA
|
||||||
|
Pan TAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCA
|
||||||
|
Gorilla TAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTA
|
||||||
|
Pongo CAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCG
|
||||||
|
Hylobates TAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAG
|
||||||
|
Macaca_fuscata TAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTG
|
||||||
|
M._mulatta TAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTG
|
||||||
|
M._fascicularis TAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTG
|
||||||
|
M._sylvanus TAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCG
|
||||||
|
Saimiri_sciureus TA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAG
|
||||||
|
Tarsius_syrichta TAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTA
|
||||||
|
[Bin Numbers 111111112121111111111121111111111121111111111121121111111121]
|
||||||
|
[ 1 9998 70808878 98461809599467 91 0 8999 7 2870990 94 89409]
|
||||||
|
|
||||||
|
|
||||||
|
Lemur_catta TAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTG
|
||||||
|
Homo_sapiens CCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCG
|
||||||
|
Pan CCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCG
|
||||||
|
Gorilla CCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCG
|
||||||
|
Pongo CTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCG
|
||||||
|
Hylobates CCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTG
|
||||||
|
Macaca_fuscata CCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAA
|
||||||
|
M._mulatta CCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAA
|
||||||
|
M._fascicularis CCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAA
|
||||||
|
M._sylvanus CTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAA
|
||||||
|
Saimiri_sciureus CTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCA
|
||||||
|
Tarsius_syrichta TTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCG
|
||||||
|
[Bin Numbers 121111126111111122111111111222211111122111111111111112111111]
|
||||||
|
[ 80 14840 98 78800 94 98900001 91 0019 5 2 9990487 89]
|
||||||
|
|
||||||
|
|
||||||
|
Lemur_catta CATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAA
|
||||||
|
Homo_sapiens CATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAG
|
||||||
|
Pan CGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAG
|
||||||
|
Gorilla CATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAG
|
||||||
|
Pongo CATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAA
|
||||||
|
Hylobates CCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAA
|
||||||
|
Macaca_fuscata TATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAA
|
||||||
|
M._mulatta TATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAA
|
||||||
|
M._fascicularis TATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAA
|
||||||
|
M._sylvanus TATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAA
|
||||||
|
Saimiri_sciureus TCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAAT
|
||||||
|
Tarsius_syrichta CCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAA
|
||||||
|
[Bin Numbers 111111111111121111111112121111111112111111111111111111111111]
|
||||||
|
[ 99 986 88 9 10 88 98880409 9 984790 8 287 999898 888 9]
|
||||||
|
|
||||||
|
|
||||||
|
Lemur_catta CAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT
|
||||||
|
Homo_sapiens TTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT
|
||||||
|
Pan CTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT
|
||||||
|
Gorilla CTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT
|
||||||
|
Pongo CCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT
|
||||||
|
Hylobates CCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT
|
||||||
|
Macaca_fuscata CAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT
|
||||||
|
M._mulatta CAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT
|
||||||
|
M._fascicularis CAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT
|
||||||
|
M._sylvanus CAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT
|
||||||
|
Saimiri_sciureus CAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT
|
||||||
|
Tarsius_syrichta TAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT
|
||||||
|
[Bin Numbers 1111111111211111111211111111211111111111111111111111111111]
|
||||||
|
[ 46 391 8140 72 6110 463140 74 7 99399274 64496 1 ]
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
;
|
||||||
|
END;
|
||||||
|
|
||||||
|
BEGIN PAUP;
|
||||||
|
Charset Bin1 = 1 2 3 5 6 11 12 14 15 23 24 26 27 30 32 33 35 36 38 39 42 44 45 47 48 50 51 54 59 60 62 63 66 68 69 71 72 75 77 78 80 81 83 84 86 87 92 93 95 98 99 101 104 105 106 111 114 116 119 120 123 125 126 127 132 135 137 138 141 145 146 152 153 154 155 156 157 159 164 165 167 171 174 176 177 179 180 182 183 186 188 189 192 195 197 198 200 201 204 207 209 210 212 213 216 231 236 237 239 240 242 243 246 249 254 255 258 264 269 270 275 276 282 285 287 288 291 293 294 296 297 299 300 302 303 306 308 309 323 324 327 329 330 338 339 342 353 354 357 359 362 363 369 371 372 374 375 377 378 379 380 381 383 387 389 390 396 398 399 402 407 408 411 414 416 417 420 423 428 431 432 438 440 441 446 447 458 459 460 461 465 466 467 468 469 470 471 472 476 477 478 479 480 481 484 485 486 488 489 490 491 492 494 495 501 503 504 519 520 521 524 525 526 527 528 530 531 532 533 534 544 547 549 550 551 552 553 556 563 564 570 572 574 579 580 582 585 586 590 591 592 593 594 595 596 597 598 599 600 601 602 605 606 609 610 611 612 614 616 619 620 621 622 623 624 628 630 631 632 633 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 662 667 676 691 694 696 701 703 711 712 715 723 732 733 739 742 743 744 753 754 757 762 763 765 766 768 769 770 778 783 787 790 792 795 798 799 808 810 817 819 823 830 834 835 836 837 838 839 843 847 852 855 856 861 862 863 870 873 874 876 877 886 892 894 895 896 897 898;
|
||||||
|
Charset Bin6 = 284 328 729;
|
||||||
|
Charset Bin11 = 64 76 122 128 133 190 225 234 245 261 278 290 347 350 356 368 376 393 435 464 496 498 505 511 515 522 538 543 583 589 661 681 693 724 752 756 760 793 846 849 858 859 867 893;
|
||||||
|
Charset Bin12 = 29 85 140 178 184 214 273 281 320 321 334 395 415 430 462 487 542 546 548 704 767 820 854 883;
|
||||||
|
Charset Bin13 = 17 96 185 340 391 617 625 844 866 880;
|
||||||
|
Charset Bin14 = 4 8 16 57 61 65 74 89 129 143 158 170 187 228 257 266 279 311 322 326 335 358 360 373 426 434 453 483 493 497 500 502 516 529 535 545 555 575 581 587 588 613 615 627 629 679 688 714 718 725 727 741 775 805 813 841 850 864 868 872 885 888 889;
|
||||||
|
Charset Bin15 = 20 117 252 397 433 518 685 764;
|
||||||
|
Charset Bin16 = 7 28 94 109 131 161 162 205 220 224 229 268 403 419 444 482 507 540 557 571 635 680 689 786 842 857 865 887 891;
|
||||||
|
Charset Bin17 = 58 67 70 82 88 90 97 103 175 223 250 259 307 316 318 336 341 352 450 451 536 541 573 578 603 607 618 668 674 690 702 706 734 777 814 822 853 871 875 884;
|
||||||
|
Charset Bin18 = 9 22 41 53 73 79 102 110 118 136 144 147 148 150 163 166 168 169 194 196 199 202 203 215 217 218 219 221 222 233 235 248 260 267 280 283 292 295 298 312 314 317 319 325 333 344 345 346 348 366 370 384 386 388 400 401 413 421 422 425 429 442 443 449 452 456 457 463 473 506 508 512 517 565 566 608 626 666 670 672 673 675 678 682 697 705 716 721 726 731 735 736 746 776 779 785 788 789 796 797 801 802 803 812 818 821 827 829 831 832 833 848;
|
||||||
|
Charset Bin19 = 18 21 43 46 49 52 56 107 108 113 115 121 124 134 139 142 149 151 172 173 181 191 193 206 208 226 230 238 241 244 247 251 253 256 263 265 272 277 305 313 315 331 337 343 349 365 382 385 392 394 404 405 406 409 410 424 427 436 437 439 445 448 455 475 499 513 514 523 537 558 567 568 576 577 584 604 663 664 665 677 684 686 687 692 698 699 700 708 709 713 717 720 730 740 745 747 755 761 771 772 773 780 781 782 784 791 800 807 809 811 815 824 825 826 828 840 845 878 879 881 882 890;
|
||||||
|
Charset Bin20 = 10 13 19 25 31 34 37 40 55 91 100 112 130 160 211 227 232 262 271 274 286 289 301 304 310 332 351 355 361 364 367 412 418 454 474 509 510 539 554 559 560 561 562 569 634 669 671 683 695 707 710 719 722 728 737 738 748 749 750 751 758 759 774 794 804 806 816 851 860 869;
|
||||||
|
END;
|
||||||
|
[START TIME: 19 : 38 : 55 ]
|
||||||
|
[FINISH TIME: 19 : 38 : 58 ]
|
||||||
46
sample_data/primate_Bin10only.tre
Normal file
46
sample_data/primate_Bin10only.tre
Normal file
|
|
@ -0,0 +1,46 @@
|
||||||
|
#NEXUS
|
||||||
|
|
||||||
|
Begin trees; [Treefile saved Sun Jun 19 13:08:56 2011]
|
||||||
|
[!
|
||||||
|
>Data file = /Users/james/Lab/Dave Fitzpatrick/NewMito/tiger_unix_1.02/sample_data/primate.tiger
|
||||||
|
>Bootstrap method with heuristic search:
|
||||||
|
> Number of bootstrap replicates = 100
|
||||||
|
> Starting seed = 510469877
|
||||||
|
> Optimality criterion = parsimony
|
||||||
|
> Character-status summary:
|
||||||
|
> Of 898 total characters:
|
||||||
|
> All characters are of type 'unord'
|
||||||
|
> All characters have equal weight
|
||||||
|
> 377 characters are constant
|
||||||
|
> 154 variable characters are parsimony-uninformative
|
||||||
|
> Number of parsimony-informative characters = 367
|
||||||
|
> Gaps are treated as "missing"
|
||||||
|
> Starting tree(s) obtained via stepwise addition
|
||||||
|
> Addition sequence: simple (reference taxon = Lemur catta)
|
||||||
|
> Number of trees held at each step during stepwise addition = 1
|
||||||
|
> Branch-swapping algorithm: tree-bisection-reconnection (TBR)
|
||||||
|
> Steepest descent option not in effect
|
||||||
|
> Initial 'MaxTrees' setting = 100
|
||||||
|
> Branches collapsed (creating polytomies) if maximum branch length is zero
|
||||||
|
> 'MulTrees' option in effect
|
||||||
|
> Topological constraints not enforced
|
||||||
|
> Trees are unrooted
|
||||||
|
>
|
||||||
|
> 100 bootstrap replicates completed
|
||||||
|
> Time used = <1 sec (CPU time = 0.38 sec)
|
||||||
|
]
|
||||||
|
Translate
|
||||||
|
1 Lemur_catta,
|
||||||
|
2 Homo_sapiens,
|
||||||
|
3 Pan,
|
||||||
|
4 Gorilla,
|
||||||
|
5 Pongo,
|
||||||
|
6 Hylobates,
|
||||||
|
7 Macaca_fuscata,
|
||||||
|
8 M._mulatta,
|
||||||
|
9 M._fascicularis,
|
||||||
|
10 M._sylvanus,
|
||||||
|
11 Saimiri_sciureus,
|
||||||
|
12 Tarsius_syrichta
|
||||||
|
;
|
||||||
|
End;
|
||||||
115
sample_data/thermus.fas
Normal file
115
sample_data/thermus.fas
Normal file
|
|
@ -0,0 +1,115 @@
|
||||||
|
>Aquifex 1273 bp
|
||||||
|
CTCAGCGCGAACGCTGGCGGCGTGCCTAACACATGCAAGTCGTGCGCAGAGCGGCAAACG
|
||||||
|
GGTGAGTAACACGTGGGTAACCTACCCCCAGGAGGGGGATAACCCCGGGAAACCGGGGCT
|
||||||
|
AATACCCCATAAAGCCGATGGGCCCGCGGCCCATCAGGTAGTTGGTGGGGTAACGGCCCA
|
||||||
|
CCAAGCCTATGACGGGTAGCCGGCCTGAGAGGGTGGCCGGCCACAGCGGGACTGAGACAC
|
||||||
|
GGCCCGCACCCCTACGGGGGGCAGCAGTGGGGAATCGTGGGCAATGGGCGAAAGCCTGAC
|
||||||
|
CCCGCGACGCCGCGTGGGGGAAGAAGCCCTGCGGGGTGTAAACCCCTGTCGGGGGGGACG
|
||||||
|
TGACGGTACCCCCAGAGGGGACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGT
|
||||||
|
CCCGAGCGTTGCGCGAAGTCACTGGGCGTAAAGCGTCCGCAGCCGGTCGGGTAAGCGGGA
|
||||||
|
TGTCAAAGCCCACGGCTCAACCGTGGAATGGCATCCCGAACTGCCCGACTTGAGGCACGC
|
||||||
|
CCGGGCAGGCGGAATTCCCGGGGTAGCGGTGAAATGCGTAGATCTCGGGAGGAACACCGA
|
||||||
|
AGGGGAAGCCAGCCTGCTGGGGCTGTCCTGACGGTCAGGGACGAAAGCCGGGGGAGCGAA
|
||||||
|
CCGGATTAGATACCCGGGTAGTCCCGGCCGTAAACCATGGGCGCTAGGGCTGCAGGCTCG
|
||||||
|
CAGCTAACGCGTTAAGCGCCCCGCCTGGGGAGTACGGGCGCAAGCCTGAAACTCAAAGGA
|
||||||
|
ATTGGCGGGGGCCCGCACAACCGGTGGAGCGTCTGGTTCAATTCGATGCTAACCGAAGAA
|
||||||
|
CCTTACCCGGGCTTGACATGGCACAGGTGGTGCATGGCCGTCGTCAGCTCGTGTCGTGAG
|
||||||
|
ATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTGCCCCTAGTTGCTGAGCACTCTAGG
|
||||||
|
GGGACCGCCGGCGCCGGAGGAAGGGGGGGATGACGTCAGGTCAGTATGCCCTTTATGCCC
|
||||||
|
GGGGCCACACAGGCGCTACAGTGGCCGGGACAATGGGAAGCGACCCCGCAAGGGGGAGCT
|
||||||
|
AATCCCAGAAACCCGGTCATGGTGCGGATTGGGGGCTGAAACTCGCCCCCATGAAGCCGG
|
||||||
|
AATCGGTAGTAACGGGGTATCAGCGATGTCCCCGTGAATACGTTCTCGGGCCTTGCACAC
|
||||||
|
ACCGCCCGTCACGCCACGGAAGTCGGTCCGGCCGGAAGGACTGGGGCGAAGTCGTAACAA
|
||||||
|
GGTAGCCGTAGGG
|
||||||
|
>Deinococcus 1273 bp
|
||||||
|
CTCAGGGTGAACGCTGGCGGCGTGCTTAAGACATGCAAGTCGAACGCGGAGTGGCGCACG
|
||||||
|
GGTGAGTAACACGTAACTGACCTACCCAGAAGTCATGAATAACTGGCCGAAAGGTCAGCT
|
||||||
|
AATACGTGATGTGGTGGATGGGGTTGCGTTCCATCAGCTGGTTGGTGGGGTAAAGGCCTA
|
||||||
|
CCAAGGCGACGACGGATAGCCGGCCTGAGAGGGTGGCCGGCCACAGGGGCACTGAGACAC
|
||||||
|
GGGTCCCACTCCTACGGGAGGCAGCAGTTAGGAATCTTCCACAATGGGCGCAAGCCTGAT
|
||||||
|
GGAGCGACGCCGCGTGAGGGATGAAGGTTTTCGGATCGTAAACCTCTGAATCTGGG-ACG
|
||||||
|
TGACGGTACCAGAGTAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGG
|
||||||
|
TGCAAGCGTTACCCGGAATCACTGGGCGTAAAGGGCGTGTAGGCGGATATTTAAGTCTGG
|
||||||
|
TTTTAAAGACCGAGGCTCAACCTCGGGAGTGGACTGGATACTGGATGTCTTGACCTCTGG
|
||||||
|
AGAGGTAACTGGAATTCCTGGTGTAGCGGTGGAATGCGTAGATACCAGGAGGAACACCAA
|
||||||
|
TGGCGAAGGCAAGTTACTGGACAGAAGGTGACGCTGAGGCGCGAAAGTGTGGGGAGCAAA
|
||||||
|
CCGGATTAGATACCCGGGTAGTCCACACCCTAAACGATGTACGTTGGCTAATGCTTGGCG
|
||||||
|
AAGCTAACGCGATAAACGTACCGCCTGGGAAGTACGGCCGCAAGGTTGAAACTCAAAGGA
|
||||||
|
ATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAA
|
||||||
|
CCTTACCAGGTCTTGACATGACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAG
|
||||||
|
ATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGCTTCCAGTTGCCGGGCACTCTGGA
|
||||||
|
GGGACTGCCTGTGCAGGAGGAAGGCGGGGATGACGTCTAGTCAGCATGGTCCTTACGTCC
|
||||||
|
TGGGCTACACACGTGCTACAATGGATAGGACAACGCGCAGCAAACATGTGAGTGTAAGCG
|
||||||
|
AATCGCTGAAACCTATCCCCAGTTCAGATCGGAGTCTGCAACTCGACTCCGTGAAGTTGG
|
||||||
|
AATCGCTAGTAATCGCGGGTCAGC-ATACCGCGGTGAATACGTTCCCGGGCCTTGTACAC
|
||||||
|
ACCGCCCGTCACACCATGGGAGTAGATTGCAGTTGAAAGACTGGGGTGAAGTCGTAACAA
|
||||||
|
GGTAACTGTACCG
|
||||||
|
>Thermotoga 1273 bp
|
||||||
|
CTCAGGGTGAACGCTGGCGGCGTGCCTAACACATGCAAGTCGAGCGGGGAGCGGCGGACG
|
||||||
|
GGTGAGTAACACGTGGGTAACCTGCCCTCCGGAGGGGGATAACCAGGGGAAACCCTGGCT
|
||||||
|
AATACCCCATACGCTCGAGGGGCCCGCGGCCCATCAGGTAGTTGGTGGGGTAACGGCCCA
|
||||||
|
CCAAGCCGACGACGGGTAGCCGGCCTGAGAGGGTGGTCGGCCACAGGGGCACTGAGACAC
|
||||||
|
GGGCCCCACTCCTACGGGAGGCAGCAGTGGGGAATCTTGGACAATGGGGGAAACCCTGAT
|
||||||
|
CCAGCGACGCCGCGTGCGGGACGAAGCCCTTCGGGGTGTAAACCGCTGTGGCGGGGGAAG
|
||||||
|
TGACGGTACCCCGCTAGGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGG
|
||||||
|
GGCAAGCGTTACCCGGATTTACTGGGCGTAAAGGGGGCGTAGGCGGCCTGGTGTGTCGGA
|
||||||
|
TGTGAAATCCCACGGCTCAACCGTGGGGCTGCATCCGAAACTACCAGGCTTGGGGGCGGT
|
||||||
|
AGAGGGAGACGGAACTGCCGGTGTAGGGGTGAAATCCGTAGATATCGGCAGGAACGCCGG
|
||||||
|
TGGGGAAGCCGGTCTCCTGGGCCGACCCCGACGCTGAGGCCCGAAAGCCAGGGGAGCAAA
|
||||||
|
CCGGATTAGATACCCGGGTAGTCCTGGCTGTAAACGATGCCCACTAGGTGTTCCGTGCTG
|
||||||
|
AAGCTAACGCGTTAAGTGGGCCGCCTGGGGAGTACGCCCGCAAGGGTGAAACTCAAAGGA
|
||||||
|
ATTGACGGGGGCCCGCACAAGCGGTGGAGCGTGTGGTTTAATTGGATGCTAAGCCAAGAA
|
||||||
|
CCTTACCAGGGCTTGACATGGCACAGGTGGTGCACGGCCGTCGTCAGCTCGTGCCGTGAG
|
||||||
|
GTGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTGCCCCTAGTTGCCGGGCACTCTAGG
|
||||||
|
GGGACTGCCGGCGCCGGAGGAAGGAGGGGATGACGTCAGGTACTCGTGCCCCTTATGCCC
|
||||||
|
TGGGCGACACACGCGCTACAATGGGCGGTACAATGGGTTGCGACCCCGCGAGGGGGAGCC
|
||||||
|
AATCCC-CAAAGCCGCCCTCAGTTCGGATCGCAGGCTGCAACCCGCCTGCGTGAAGCCGG
|
||||||
|
AATCGCTAGTAATCGCGGATCAGCCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACAC
|
||||||
|
ACCGCCCGTCACGCCACCCGAGTCGGGGGCTCCCGAAGGAGGGGGGCGAAGTCGTAACAA
|
||||||
|
GGTAGCCGTACCG
|
||||||
|
>Bacillus 1273 bp
|
||||||
|
CTCAGGACGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCGGACAGCGGCGGACG
|
||||||
|
GGTGAGTAACACGTGGGTAACCTGCCTGTAAGACTGGGATAACTCCGGGAAACCGGGGCT
|
||||||
|
AATACCGGATGGTTGTGATGGACCCGCGGCGCATTAGCTAGTTGGTGAGGTAACGGCTCA
|
||||||
|
CCAAGGCAACGATGCGTAGCCGACCTGAGAGGGTGATCGGCCACACTGGGACTGAGACAC
|
||||||
|
GGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGACGAAAGTCTGAC
|
||||||
|
GGAGCAACGCCGCGTGAGTGATGAAGGTTTTCGGATCGTAAAGCTCTGTTGTTAGGGAAG
|
||||||
|
TGACGGTACCTAACCAGGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGT
|
||||||
|
GGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTCGCAGGCGGTTTCTTAAGTCTGA
|
||||||
|
TGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGGAACTTGAGTGCAGA
|
||||||
|
AGAGGAGAGTGGAATTCCACGTGTAGCGGTGAAATGCGTAGAGATGTGGAGGAACACCAG
|
||||||
|
TGGCGAAGGCGACTCTCTGGTCTGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAA
|
||||||
|
CAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTTAGTGCTG
|
||||||
|
CAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGGTCGCAAGACTGAAACTCAAAGGA
|
||||||
|
ATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAA
|
||||||
|
CCTTACCAGGTCTTGACATCTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAG
|
||||||
|
ATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGATCTTAGTTGCCGGGCACTCTAAG
|
||||||
|
GTGACTGCCGGTGCCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGACC
|
||||||
|
TGGGCTACACACGTGCTACAATGGACAGAACAAAGGGCAGCGAAACCGCGAGGTTAAGCC
|
||||||
|
AATCCCACAAATCTGTTCTCAGTTCGGATCGCAGTCTGCAACTCGACTGCGTGAAGCTGG
|
||||||
|
AATCGCTAGTAATCGCGGATCAGC-ATGCCGCGGTGAATACGTTCCCGGGCCTTGTACAC
|
||||||
|
ACCGCCCGTCACACCACGAGAGTTTGTAACACCCGAAGGATTGGGGTGAAGTCGTAACAA
|
||||||
|
GGTAGCCGTATCG
|
||||||
|
>Thermus 1273 bp
|
||||||
|
CTCAGGGTGAACGCTGGCGGCGTGCCTAAGACATGCAAGTCGTGCGGGCAGCGGCGGACG
|
||||||
|
GGTGAGTAACGCGTGGGTGACCTACCCGGAAGAGGGGGACAACCCGGGGAAACTCGGGCT
|
||||||
|
AATCCCCCATGTGGACGATGGGCCCGCGTCCCATCAGCTAGTTGGTGGGGTAATGGCCCA
|
||||||
|
CCAAGGCGACGACGGGTAGCCGGTCTGAGAGGATGGCCGGCCACAGGGGCACTGAGACAC
|
||||||
|
GGGCCCCACTCCTACGGGAGGCAGCAGTTAGGAATCTTCCGCAATGGGCGCAAGCCTGAC
|
||||||
|
GGAGCGACGCCGCTTGGAGGAAGAAGCCCTTCGGGGTGTAAACTCCTGAACCCGGG-ACG
|
||||||
|
TGACGGTACCGGGGTAAGCGCCGGCCAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGG
|
||||||
|
CGCGAGCGTTACCCGGATTCACTGGGCGTAAAGGGCGTGTAGGCGGCCTGGGGCGTCCCA
|
||||||
|
TGTGAAAGACCACGGCTCAACCGTGGGGGAGCGTGGGATACGCTCAGGCTAGACGGTGGG
|
||||||
|
AGAGGGTGGTGGAATTCCCGGAGTAGCGGTGAAATGCGCAGATACCGGGAGGAACGCCGA
|
||||||
|
TGGCGAAGGCAGCCACCTGGTCCACCCGTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAA
|
||||||
|
CCGGATTAGATACCCGGGTAGTCCACGCCCTAAACGATGCGCGCTAGGTCTTGGGGGCCG
|
||||||
|
AAGCTAACGCGTTAAGCGCGCCGCCTGGGGAGTACGGCCGCAAGGCTGAAACTCAAAGGA
|
||||||
|
ATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAA
|
||||||
|
CCTTACCAGGCCTTGACATGGCACAGGTGCTGCATGGCCGTCGTCAGCTCGTGCCGTGAG
|
||||||
|
GTGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCCGCCGTTAGTTGCCGGGCACTCTAAC
|
||||||
|
GGGACTGCCCGCGCGGGAGGAAGGAGGGGACGACGTCTGGTCAGCATGGCCCTTACGGCC
|
||||||
|
TGGGCGACACACGTGCTACAATGCCC--TACAAAGCGATGCCACCCGGCAACGGGGAGCT
|
||||||
|
AATCGCAAAAAGGTGGGCCCAGTTCGGATTGGGGTCTGCAACCCGACCCCATGAAGCCGG
|
||||||
|
AATCGCTAGTAATCGCGGATCAGCCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACAC
|
||||||
|
ACCGCCCGTCACGCCATGGGAGCGGGCTCTACCCGAAGGACTGGGGCGAAGTCGTAACAA
|
||||||
|
GGTAGCTGTACCG
|
||||||
247
sample_data/thermus.tig
Normal file
247
sample_data/thermus.tig
Normal file
|
|
@ -0,0 +1,247 @@
|
||||||
|
#NEXUS
|
||||||
|
|
||||||
|
[This file contains data that has been analysed for site specific rates]
|
||||||
|
[using TIGER, developed by Carla Cummins in the laboratory of]
|
||||||
|
[Dr James McInerney, National University of Ireland, Maynooth]
|
||||||
|
|
||||||
|
|
||||||
|
[Histograms of number of sites in each category:]
|
||||||
|
[Bin1 |============================================================ |833 ]
|
||||||
|
[Bin2 | |0 ]
|
||||||
|
[Bin3 | |0 ]
|
||||||
|
[Bin4 | |0 ]
|
||||||
|
[Bin5 | |0 ]
|
||||||
|
[Bin6 |========= |116 ]
|
||||||
|
[Bin7 |======= |87 ]
|
||||||
|
[Bin8 |====== |72 ]
|
||||||
|
[Bin9 |======= |96 ]
|
||||||
|
[Bin10 |===== |69 ]
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
BEGIN TAXA;
|
||||||
|
Dimensions NTax = 5 ;
|
||||||
|
TaxLabels Aquifex1273bp Deinococcus1273bp Thermotoga1273bp Bacillus1273bp Thermus1273bp ;
|
||||||
|
END;
|
||||||
|
|
||||||
|
BEGIN CHARACTERS;
|
||||||
|
Dimensions nchar = 1273 ;
|
||||||
|
Format datatype = DNA gap = - interleave;
|
||||||
|
Matrix
|
||||||
|
|
||||||
|
Aquifex1273bp CTCAGCGCGAACGCTGGCGGCGTGCCTAACACATGCAAGTCGTGCGCAGAGCGGCAAACG
|
||||||
|
Deinococcus1273bp CTCAGGGTGAACGCTGGCGGCGTGCTTAAGACATGCAAGTCGAACGCGGAGTGGCGCACG
|
||||||
|
Thermotoga1273bp CTCAGGGTGAACGCTGGCGGCGTGCCTAACACATGCAAGTCGAGCGGGGAGCGGCGGACG
|
||||||
|
Bacillus1273bp CTCAGGACGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCGGACAGCGGCGGACG
|
||||||
|
Thermus1273bp CTCAGGGTGAACGCTGGCGGCGTGCCTAAGACATGCAAGTCGTGCGGGCAGCGGCGGACG
|
||||||
|
[Bin Numbers 111116791111111111111111161119111111111111961119111611161111]
|
||||||
|
[ 0 0 0 ]
|
||||||
|
|
||||||
|
|
||||||
|
Aquifex1273bp GGTGAGTAACACGTGGGTAACCTACCCCCAGGAGGGGGATAACCCCGGGAAACCGGGGCT
|
||||||
|
Deinococcus1273bp GGTGAGTAACACGTAACTGACCTACCCAGAAGTCATGAATAACTGGCCGAAAGGTCAGCT
|
||||||
|
Thermotoga1273bp GGTGAGTAACACGTGGGTAACCTGCCCTCCGGAGGGGGATAACCAGGGGAAACCCTGGCT
|
||||||
|
Bacillus1273bp GGTGAGTAACACGTGGGTAACCTGCCTGTAAGACTGGGATAACTCCGGGAAACCGGGGCT
|
||||||
|
Thermus1273bp GGTGAGTAACGCGTGGGTGACCTACCCGGAAGAGGGGGACAACCCGGGGAAACTCGGGCT
|
||||||
|
[Bin Numbers 111111111171116661811119117197816896161711181966111169116111]
|
||||||
|
[ 0 0 00 ]
|
||||||
|
|
||||||
|
|
||||||
|
Aquifex1273bp AATACCCCATAAAGCCGATGGGCCCGCGGCCCATCAGGTAGTTGGTGGGGTAACGGCCCA
|
||||||
|
Deinococcus1273bp AATACGTGATGTGGTGGATGGGGTTGCGTTCCATCAGCTGGTTGGTGGGGTAAAGGCCTA
|
||||||
|
Thermotoga1273bp AATACCCCATACGCTCGAGGGGCCCGCGGCCCATCAGGTAGTTGGTGGGGTAACGGCCCA
|
||||||
|
Bacillus1273bp AATACCGGATGGTTGTGATGGACCCGCGGCGCATTAGCTAGTTGGTGAGGTAACGGCTCA
|
||||||
|
Thermus1273bp AATCCCCCATGTGGACGATGGGCCCGCGTCCCATCAGCTAGTTGGTGGGGTAATGGCCCA
|
||||||
|
[Bin Numbers 111716981181991911711766611186711171181611111117111119111761]
|
||||||
|
[ 0 0 ]
|
||||||
|
|
||||||
|
|
||||||
|
Aquifex1273bp CCAAGCCTATGACGGGTAGCCGGCCTGAGAGGGTGGCCGGCCACAGCGGGACTGAGACAC
|
||||||
|
Deinococcus1273bp CCAAGGCGACGACGGATAGCCGGCCTGAGAGGGTGGCCGGCCACAGGGGCACTGAGACAC
|
||||||
|
Thermotoga1273bp CCAAGCCGACGACGGGTAGCCGGCCTGAGAGGGTGGTCGGCCACAGGGGCACTGAGACAC
|
||||||
|
Bacillus1273bp CCAAGGCAACGATGCGTAGCCGACCTGAGAGGGTGATCGGCCACACTGGGACTGAGACAC
|
||||||
|
Thermus1273bp CCAAGGCGACGACGGGTAGCCGGTCTGAGAGGATGGCCGGCCACAGGGGCACTGAGACAC
|
||||||
|
[Bin Numbers 111118191611717611111177111111117117911111111791191111111111]
|
||||||
|
[ ]
|
||||||
|
|
||||||
|
|
||||||
|
Aquifex1273bp GGCCCGCACCCCTACGGGGGGCAGCAGTGGGGAATCGTGGGCAATGGGCGAAAGCCTGAC
|
||||||
|
Deinococcus1273bp GGGTCCCACTCCTACGGGAGGCAGCAGTTAGGAATCTTCCACAATGGGCGCAAGCCTGAT
|
||||||
|
Thermotoga1273bp GGGCCCCACTCCTACGGGAGGCAGCAGTGGGGAATCTTGGACAATGGGGGAAACCCTGAT
|
||||||
|
Bacillus1273bp GGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGACGAAAGTCTGAC
|
||||||
|
Thermus1273bp GGGCCCCACTCCTACGGGAGGCAGCAGTTAGGAATCTTCCGCAATGGGCGCAAGCCTGAC
|
||||||
|
[Bin Numbers 119619711611111111611111111198111111618811111117718117711111]
|
||||||
|
[ 0 0]
|
||||||
|
|
||||||
|
|
||||||
|
Aquifex1273bp CCCGCGACGCCGCGTGGGGGAAGAAGCCCTGCGGGGTGTAAACCCCTGTCGGGGGGGACG
|
||||||
|
Deinococcus1273bp GGAGCGACGCCGCGTGAGGGATGAAGGTTTTCGGATCGTAAACCTCTGAATCTGGG-ACG
|
||||||
|
Thermotoga1273bp CCAGCGACGCCGCGTGCGGGACGAAGCCCTTCGGGGTGTAAACCGCTGTGGCGGGGGAAG
|
||||||
|
Bacillus1273bp GGAGCAACGCCGCGTGAGTGATGAAGGTTTTCGGATCGTAAAGCTCTGTTGTTAGGGAAG
|
||||||
|
Thermus1273bp GGAGCGACGCCGCTTGGAGGAAGAAGCCCTTCGGGGTGTAAACTCCTGAACCCGGG-ACG
|
||||||
|
[Bin Numbers 886117111111171117711111118881611188811111771111819997118191]
|
||||||
|
[ 0 0 0 0 ]
|
||||||
|
|
||||||
|
|
||||||
|
Aquifex1273bp TGACGGTACCCCCAGAGGGGACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGT
|
||||||
|
Deinococcus1273bp TGACGGTACCAGAGTAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGG
|
||||||
|
Thermotoga1273bp TGACGGTACCCCGCTAGGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGG
|
||||||
|
Bacillus1273bp TGACGGTACCTAACCAGGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGT
|
||||||
|
Thermus1273bp TGACGGTACCGGGGTAAGCGCCGGCCAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGG
|
||||||
|
[Bin Numbers 111111111119119181619111171111811111111111111111111111181119]
|
||||||
|
[ 0 00 0 ]
|
||||||
|
|
||||||
|
|
||||||
|
Aquifex1273bp CCCGAGCGTTGCGCGAAGTCACTGGGCGTAAAGCGTCCGCAGCCGGTCGGGTAAGCGGGA
|
||||||
|
Deinococcus1273bp TGCAAGCGTTACCCGGAATCACTGGGCGTAAAGGGCGTGTAGGCGGATATTTAAGTCTGG
|
||||||
|
Thermotoga1273bp GGCAAGCGTTACCCGGATTTACTGGGCGTAAAGGGGGCGTAGGCGGCCTGGTGTGTCGGA
|
||||||
|
Bacillus1273bp GGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTCGCAGGCGGTTTCTTAAGTCTGA
|
||||||
|
Thermus1273bp CGCGAGCGTTACCCGGATTCACTGGGCGTAAAGGGCGTGTAGGCGGCCTGGGGCGTCCCA
|
||||||
|
[Bin Numbers 161911111197611611191711111111111619981911611118198799166976]
|
||||||
|
[ 0 0 0 0 ]
|
||||||
|
|
||||||
|
|
||||||
|
Aquifex1273bp TGTCAAAGCCCACGGCTCAACCGTGGAATGGCATCCCGAACTGCCCGACTTGAGGCACGC
|
||||||
|
Deinococcus1273bp TTTTAAAGACCGAGGCTCAACCTCGGGAGTGGACTGGATACTGGATGTCTTGACCTCTGG
|
||||||
|
Thermotoga1273bp TGTGAAATCCCACGGCTCAACCGTGGGGCTGCATCCGAAACTACCAGGCTTGGGGGCGGT
|
||||||
|
Bacillus1273bp TGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGGAACTTGAGTGCAGA
|
||||||
|
Thermus1273bp TGTGAAAGACCACGGCTCAACCGTGGGGGAGCGTGGGATACGCTCAGGCTAGACGGTGGG
|
||||||
|
[Bin Numbers 161111178119611111111169119191767698668117999171117178919111]
|
||||||
|
[ 0 0 0 0 0 0 0 0]
|
||||||
|
|
||||||
|
|
||||||
|
Aquifex1273bp CCGGGCAGGCGGAATTCCCGGGGTAGCGGTGAAATGCGTAGATCTCGGGAGGAACACCGA
|
||||||
|
Deinococcus1273bp AGAGGTAACTGGAATTCCTGGTGTAGCGGTGGAATGCGTAGATACCAGGAGGAACACCAA
|
||||||
|
Thermotoga1273bp AGAGGGAGACGGAACTGCCGGTGTAGGGGTGAAATCCGTAGATATCGGCAGGAACGCCGG
|
||||||
|
Bacillus1273bp AGAGGAGAGTGGAATTCCACGTGTAGCGGTGAAATGCGTAGAGATGTGGAGGAACACCAG
|
||||||
|
Thermus1273bp AGAGGGTGGTGGAATTCCCGGAGTAGCGGTGAAATGCGCAGATACCGGGAGGAACGCCGA
|
||||||
|
[Bin Numbers 666111181811117171971911117111161117117111768791711111191189]
|
||||||
|
[ 00 0 ]
|
||||||
|
|
||||||
|
|
||||||
|
Aquifex1273bp AGGGGAAGCCAGCCTGCTGGGGCTGTCCTGACGGTCAGGGACGAAAGCCGGGGGAGCGAA
|
||||||
|
Deinococcus1273bp TGGCGAAGGCAAGTTACTGGACAGAAGGTGACGCTGAGGCGCGAAAGTGTGGGGAGCAAA
|
||||||
|
Thermotoga1273bp TGGGGAAGCCGGTCTCCTGGGCCGACCCCGACGCTGAGGCCCGAAAGCCAGGGGAGCAAA
|
||||||
|
Bacillus1273bp TGGCGAAGGCGACTCTCTGGTCTGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAA
|
||||||
|
Thermus1273bp TGGCGAAGGCAGCCACCTGGTCCACCCGTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAA
|
||||||
|
[Bin Numbers 611811118198181111111699119871111616111991111116891111111911]
|
||||||
|
[ 0 00 0 00 ]
|
||||||
|
|
||||||
|
|
||||||
|
Aquifex1273bp CCGGATTAGATACCCGGGTAGTCCCGGCCGTAAACCATGGGCGCTAGGGCTGCAGGCTCG
|
||||||
|
Deinococcus1273bp CCGGATTAGATACCCGGGTAGTCCACACCCTAAACGATGTACGTTGGCTAATGCTTGGCG
|
||||||
|
Thermotoga1273bp CCGGATTAGATACCCGGGTAGTCCTGGCTGTAAACGATGCCCACTAGGTGTTCCGTGCTG
|
||||||
|
Bacillus1273bp CAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTTAGTGCTG
|
||||||
|
Thermus1273bp CCGGATTAGATACCCGGGTAGTCCACGCCCTAAACGATGCGCGCTAGGTCTTGGGGGCCG
|
||||||
|
[Bin Numbers 171111111111111711111111986178111116111117761676616691696191]
|
||||||
|
[ 00 0 0 0 ]
|
||||||
|
|
||||||
|
|
||||||
|
Aquifex1273bp CAGCTAACGCGTTAAGCGCCCCGCCTGGGGAGTACGGGCGCAAGCCTGAAACTCAAAGGA
|
||||||
|
Deinococcus1273bp AAGCTAACGCGATAAACGTACCGCCTGGGAAGTACGGCCGCAAGGTTGAAACTCAAAGGA
|
||||||
|
Thermotoga1273bp AAGCTAACGCGTTAAGTGGGCCGCCTGGGGAGTACGCCCGCAAGGGTGAAACTCAAAGGA
|
||||||
|
Bacillus1273bp CAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGGTCGCAAGACTGAAACTCAAAGGA
|
||||||
|
Thermus1273bp AAGCTAACGCGTTAAGCGCGCCGCCTGGGGAGTACGGCCGCAAGGCTGAAACTCAAAGGA
|
||||||
|
[Bin Numbers 911111111176111677111111111116111111791111119111111111111111]
|
||||||
|
[ 00 0 ]
|
||||||
|
|
||||||
|
|
||||||
|
Aquifex1273bp ATTGGCGGGGGCCCGCACAACCGGTGGAGCGTCTGGTTCAATTCGATGCTAACCGAAGAA
|
||||||
|
Deinococcus1273bp ATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAA
|
||||||
|
Thermotoga1273bp ATTGACGGGGGCCCGCACAAGCGGTGGAGCGTGTGGTTTAATTGGATGCTAAGCCAAGAA
|
||||||
|
Bacillus1273bp ATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAA
|
||||||
|
Thermus1273bp ATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAA
|
||||||
|
[Bin Numbers 111161111111111111116111111111816111116111171181181861711111]
|
||||||
|
[ ]
|
||||||
|
|
||||||
|
|
||||||
|
Aquifex1273bp CCTTACCCGGGCTTGACATGGCACAGGTGGTGCATGGCCGTCGTCAGCTCGTGTCGTGAG
|
||||||
|
Deinococcus1273bp CCTTACCAGGTCTTGACATGACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAG
|
||||||
|
Thermotoga1273bp CCTTACCAGGGCTTGACATGGCACAGGTGGTGCACGGCCGTCGTCAGCTCGTGCCGTGAG
|
||||||
|
Bacillus1273bp CCTTACCAGGTCTTGACATCTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAG
|
||||||
|
Thermus1273bp CCTTACCAGGCCTTGACATGGCACAGGTGCTGCATGGCCGTCGTCAGCTCGTGCCGTGAG
|
||||||
|
[Bin Numbers 111111161191111111179711111118111171178111111111111119111111]
|
||||||
|
[ ]
|
||||||
|
|
||||||
|
|
||||||
|
Aquifex1273bp ATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTGCCCCTAGTTGCTGAGCACTCTAGG
|
||||||
|
Deinococcus1273bp ATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGCTTCCAGTTGCCGGGCACTCTGGA
|
||||||
|
Thermotoga1273bp GTGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTGCCCCTAGTTGCCGGGCACTCTAGG
|
||||||
|
Bacillus1273bp ATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGATCTTAGTTGCCGGGCACTCTAAG
|
||||||
|
Thermus1273bp GTGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCCGCCGTTAGTTGCCGGGCACTCTAAC
|
||||||
|
[Bin Numbers 911111111111111111111111111111111871789161111116161111111619]
|
||||||
|
[ 0 0 ]
|
||||||
|
|
||||||
|
|
||||||
|
Aquifex1273bp GGGACCGCCGGCGCCGGAGGAAGGGGGGGATGACGTCAGGTCAGTATGCCCTTTATGCCC
|
||||||
|
Deinococcus1273bp GGGACTGCCTGTGCAGGAGGAAGGCGGGGATGACGTCTAGTCAGCATGGTCCTTACGTCC
|
||||||
|
Thermotoga1273bp GGGACTGCCGGCGCCGGAGGAAGGAGGGGATGACGTCAGGTACTCGTGCCCCTTATGCCC
|
||||||
|
Bacillus1273bp GTGACTGCCGGTGCCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGACC
|
||||||
|
Thermus1273bp GGGACTGCCCGCGCGGGAGGAAGGAGGGGACGACGTCTGGTCAGCATGGCCCTTACGGCC
|
||||||
|
[Bin Numbers 171116111918119111111111111111711111188717796711861611181111]
|
||||||
|
[ 0 0 ]
|
||||||
|
|
||||||
|
|
||||||
|
Aquifex1273bp GGGGCCACACAGGCGCTACAGTGGCCGGGACAATGGGAAGCGACCCCGCAAGGGGGAGCT
|
||||||
|
Deinococcus1273bp TGGGCTACACACGTGCTACAATGGATAGGACAACGCGCAGCAAACATGTGAGTGTAAGCG
|
||||||
|
Thermotoga1273bp TGGGCGACACACGCGCTACAATGGGCGGTACAATGGGTTGCGACCCCGCGAGGGGGAGCC
|
||||||
|
Bacillus1273bp TGGGCTACACACGTGCTACAATGGACAGAACAAAGGGCAGCGAAACCGCGAGGTTAAGCC
|
||||||
|
Thermus1273bp TGGGCGACACACGTGCTACAATGCCC--TACAAAGCGATGCCACCCGGCAACGGGGAGCT
|
||||||
|
[Bin Numbers 611111111116181111116117169711111118119119187691691767881111]
|
||||||
|
[ 0 0 0 0 0 0]
|
||||||
|
|
||||||
|
|
||||||
|
Aquifex1273bp AATCCCAGAAACCCGGTCATGGTGCGGATTGGGGGCTGAAACTCGCCCCCATGAAGCCGG
|
||||||
|
Deinococcus1273bp AATCGCTGAAACCTATCCCCAGTTCAGATCGGAGTCTGCAACTCGACTCCGTGAAGTTGG
|
||||||
|
Thermotoga1273bp AATCCC-CAAAGCCGCCCTCAGTTCGGATCGCAGGCTGCAACCCGCCTGCGTGAAGCCGG
|
||||||
|
Bacillus1273bp AATCCCACAAATCTGTTCTCAGTTCGGATCGCAGTCTGCAACTCGACTGCGTGAAGCTGG
|
||||||
|
Thermus1273bp AATCGCAAAAAGGTGGGCCCAGTTCGGATTGGGGTCTGCAACCCGACCCCATGAAGCCGG
|
||||||
|
[Bin Numbers 111181111111786111166116161119199181116111911819919111116811]
|
||||||
|
[ 00 0 00 0 ]
|
||||||
|
|
||||||
|
|
||||||
|
Aquifex1273bp AATCGGTAGTAACGGGGTATCAGCGATGTCCCCGTGAATACGTTCTCGGGCCTTGCACAC
|
||||||
|
Deinococcus1273bp AATCGCTAGTAATCGCGGGTCAGC-ATACCGCGGTGAATACGTTCCCGGGCCTTGTACAC
|
||||||
|
Thermotoga1273bp AATCGCTAGTAATCGCGGATCAGCCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACAC
|
||||||
|
Bacillus1273bp AATCGCTAGTAATCGCGGATCAGC-ATGCCGCGGTGAATACGTTCCCGGGCCTTGTACAC
|
||||||
|
Thermus1273bp AATCGCTAGTAATCGCGGATCAGCCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACAC
|
||||||
|
[Bin Numbers 111116111111661616611111111661616111111111111611111111161111]
|
||||||
|
[ 0 ]
|
||||||
|
|
||||||
|
|
||||||
|
Aquifex1273bp ACCGCCCGTCACGCCACGGAAGTCGGTCCGGCCGGAAGGACTGGGGCGAAGTCGTAACAA
|
||||||
|
Deinococcus1273bp ACCGCCCGTCACACCATGGGAGTAGATTGCAGTTGAAAGACTGGGGTGAAGTCGTAACAA
|
||||||
|
Thermotoga1273bp ACCGCCCGTCACGCCACCCGAGTCGGGGGCTCCCGAAGGAGGGGGGCGAAGTCGTAACAA
|
||||||
|
Bacillus1273bp ACCGCCCGTCACACCACGAGAGTTTGTAACACCCGAAGGATTGGGGTGAAGTCGTAACAA
|
||||||
|
Thermus1273bp ACCGCCCGTCACGCCATGGGAGCGGGCTCTACCCGAAGGACTGGGGCGAAGTCGTAACAA
|
||||||
|
[Bin Numbers 111111111111811187961171769119966111161197111181111111111111]
|
||||||
|
[ 0 00 0 ]
|
||||||
|
|
||||||
|
|
||||||
|
Aquifex1273bp GGTAGCCGTAGGG
|
||||||
|
Deinococcus1273bp GGTAACTGTACCG
|
||||||
|
Thermotoga1273bp GGTAGCCGTACCG
|
||||||
|
Bacillus1273bp GGTAGCCGTATCG
|
||||||
|
Thermus1273bp GGTAGCTGTACCG
|
||||||
|
[Bin Numbers 1111618111961]
|
||||||
|
[ ]
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
;
|
||||||
|
END;
|
||||||
|
|
||||||
|
BEGIN PAUP;
|
||||||
|
Charset Bin1 = 1 2 3 4 5 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 27 28 29 31 32 33 34 35 36 37 38 39 40 41 42 45 46 50 51 53 54 55 58 59 60 61 62 63 64 65 66 67 68 69 70 72 73 74 78 80 81 82 83 85 86 92 97 99 101 102 103 109 110 111 112 118 119 120 121 122 123 125 129 130 137 138 140 141 146 147 148 152 153 154 156 157 159 161 162 163 164 165 166 167 169 170 171 172 173 175 176 177 180 181 182 183 184 185 187 189 191 192 194 197 198 199 200 201 202 205 206 207 208 209 210 211 212 214 215 218 219 220 221 222 223 224 225 228 229 231 232 233 234 235 236 237 238 239 240 241 242 245 248 249 251 252 253 254 255 256 257 258 260 261 262 263 264 265 266 267 268 271 272 273 274 275 276 278 282 283 284 285 286 287 290 292 293 296 297 298 299 304 305 307 308 309 310 311 312 313 315 316 320 321 323 324 325 326 330 332 333 334 338 339 340 341 342 346 347 348 355 356 358 360 361 362 363 364 365 366 367 368 369 370 376 378 382 383 384 385 387 388 389 390 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 417 418 419 423 425 426 427 428 429 430 434 435 437 439 441 443 444 445 446 447 448 449 450 451 452 453 455 459 461 462 464 465 466 475 481 483 485 486 487 490 491 494 495 496 497 498 499 500 501 502 505 506 520 521 529 530 532 539 544 545 551 552 553 554 556 558 561 563 564 565 566 568 569 570 571 573 574 575 577 578 580 581 582 588 590 591 592 593 594 595 597 598 602 603 605 606 607 608 610 617 618 619 620 630 631 632 633 635 637 638 639 642 643 644 645 646 647 651 652 653 654 655 656 657 659 660 661 663 664 665 666 667 668 669 670 671 672 673 674 675 677 678 679 680 681 682 683 684 688 691 692 693 694 695 697 698 699 705 720 722 723 724 725 726 727 728 729 730 733 734 735 741 742 743 744 745 746 747 748 749 751 752 753 754 755 756 759 760 761 762 763 764 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 802 803 804 805 806 807 808 809 810 812 814 815 816 817 818 820 821 822 823 825 826 828 829 831 834 836 837 838 839 840 841 842 843 844 845 846 847 849 850 852 853 854 855 856 857 858 859 863 864 865 866 867 868 869 871 872 873 874 876 877 880 881 882 883 884 885 886 887 888 889 890 891 892 893 895 896 897 898 899 900 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 936 942 943 944 945 946 947 949 951 952 953 954 955 956 957 961 963 964 965 967 968 969 971 973 974 976 977 978 979 980 981 982 983 984 986 987 988 989 990 992 993 994 995 996 997 1001 1007 1008 1011 1013 1014 1015 1017 1019 1020 1022 1023 1024 1025 1027 1028 1029 1030 1031 1033 1035 1036 1037 1038 1039 1040 1042 1043 1050 1051 1052 1053 1055 1057 1060 1061 1063 1068 1071 1077 1078 1079 1081 1082 1083 1084 1086 1089 1090 1091 1098 1102 1103 1105 1107 1108 1109 1111 1114 1116 1117 1118 1120 1121 1122 1124 1125 1127 1130 1132 1133 1134 1135 1136 1139 1140 1141 1142 1143 1144 1145 1147 1148 1149 1150 1151 1152 1155 1157 1160 1161 1162 1163 1164 1166 1167 1170 1172 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1187 1188 1189 1190 1191 1192 1193 1194 1195 1197 1198 1199 1200 1201 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1214 1215 1216 1221 1222 1235 1236 1237 1239 1240 1243 1244 1245 1246 1248 1249 1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 1266 1268 1269 1270 1273;
|
||||||
|
Charset Bin6 = 6 26 44 52 56 75 76 77 93 96 98 107 108 113 117 126 143 144 145 150 160 179 190 196 244 250 259 277 303 331 379 422 433 436 454 463 476 477 480 482 493 503 512 514 517 518 541 542 543 572 584 601 622 634 636 648 687 696 704 706 708 709 711 712 715 717 732 736 750 785 801 813 819 833 848 941 948 950 958 966 1005 1010 1012 1021 1032 1041 1046 1066 1069 1073 1095 1100 1101 1104 1106 1119 1137 1146 1153 1154 1156 1158 1159 1168 1169 1171 1173 1186 1196 1220 1226 1232 1233 1238 1265 1272;
|
||||||
|
Charset Bin7 = 7 71 87 90 100 124 139 142 151 155 168 178 193 195 203 204 213 216 226 247 288 289 294 295 306 314 318 319 343 344 354 386 432 442 472 479 488 511 513 522 527 531 533 555 557 560 567 576 579 583 586 589 629 662 676 689 702 703 707 731 737 738 757 824 835 860 862 875 878 935 937 962 991 1000 1002 1003 1006 1044 1048 1065 1072 1074 1093 1218 1223 1225 1242;
|
||||||
|
Charset Bin8 = 79 91 94 104 128 131 149 158 186 270 279 280 291 301 302 327 328 329 335 336 337 349 357 377 391 416 458 468 471 489 516 519 534 548 550 585 599 604 609 612 614 628 649 686 690 811 827 830 832 870 879 934 938 972 998 999 1009 1016 1034 1056 1064 1075 1076 1085 1094 1115 1126 1138 1213 1217 1247 1267;
|
||||||
|
Charset Bin9 = 8 30 43 48 84 89 95 106 114 127 133 134 136 174 188 217 227 230 243 246 269 351 352 353 359 372 375 381 420 424 431 440 456 457 460 470 473 474 478 492 504 507 509 515 523 524 525 535 537 559 562 587 596 600 611 623 624 627 640 641 650 658 685 713 716 719 721 758 765 851 861 894 901 939 960 970 975 1004 1047 1059 1062 1067 1070 1110 1112 1113 1123 1128 1129 1131 1219 1227 1230 1231 1241 1271;
|
||||||
|
Charset Bin10 = 47 49 57 88 105 115 116 132 135 281 300 317 322 345 350 371 373 374 380 421 438 467 469 484 508 510 526 528 536 538 540 546 547 549 613 615 616 621 625 626 700 701 710 714 718 739 740 766 940 959 985 1018 1026 1045 1049 1054 1058 1080 1087 1088 1092 1096 1097 1099 1165 1224 1228 1229 1234;
|
||||||
|
END;
|
||||||
|
[START TIME: 12 : 19 : 33 ]
|
||||||
|
[FINISH TIME: 12 : 19 : 33 ]
|
||||||
380
tiger
Normal file
380
tiger
Normal file
|
|
@ -0,0 +1,380 @@
|
||||||
|
#!/usr/bin/env python
|
||||||
|
|
||||||
|
#*********TIGER v1.02*************
|
||||||
|
|
||||||
|
#...read in options...
|
||||||
|
import time
|
||||||
|
lt_S = time.localtime()
|
||||||
|
import sys
|
||||||
|
import random
|
||||||
|
import re
|
||||||
|
from tiger_fns_102 import *
|
||||||
|
options = sys.argv
|
||||||
|
|
||||||
|
formRate = 0
|
||||||
|
formSort = 0
|
||||||
|
binNo = 10
|
||||||
|
file = ""
|
||||||
|
rate_file = ""
|
||||||
|
write_rates = False
|
||||||
|
numbered = False
|
||||||
|
|
||||||
|
doPTP = False
|
||||||
|
rands = 100
|
||||||
|
pval = 0.05
|
||||||
|
|
||||||
|
write_pvals = False
|
||||||
|
pval_file = ""
|
||||||
|
|
||||||
|
unknown = ["?"]
|
||||||
|
|
||||||
|
if len(options) < 2:
|
||||||
|
printHelp()
|
||||||
|
sys.exit(0)
|
||||||
|
|
||||||
|
for opt in range(len(options)):
|
||||||
|
if options[opt] == "-in":
|
||||||
|
file_name = options[opt + 1]
|
||||||
|
try:
|
||||||
|
file = open(file_name)
|
||||||
|
except IOError:
|
||||||
|
print "File \"" + file_name + "\" not found..."
|
||||||
|
sys.exit(0)
|
||||||
|
|
||||||
|
elif options[opt] == "-b":
|
||||||
|
binNo = int(options[opt + 1])
|
||||||
|
|
||||||
|
elif options[opt] == "-f":
|
||||||
|
formOpts = options[opt + 1].split(",")
|
||||||
|
if "r" in formOpts:
|
||||||
|
formRate = 1
|
||||||
|
if "s" in formOpts:
|
||||||
|
formSort = 1
|
||||||
|
if "c" in formOpts:
|
||||||
|
numbered = True
|
||||||
|
|
||||||
|
elif options[opt] == "-v":
|
||||||
|
print "TIGER version 1.02"
|
||||||
|
sys.exit(0)
|
||||||
|
|
||||||
|
elif options[opt] == "-rl":
|
||||||
|
write_rates = True
|
||||||
|
try:
|
||||||
|
rate_file = options[opt+1]
|
||||||
|
if rate_file[0] == "-":
|
||||||
|
print "\n\nPlease specify file name for -rl option.\n\n"
|
||||||
|
sys.exit(0)
|
||||||
|
except IndexError:
|
||||||
|
print "\n\nPlease specify file name for -rl option.\n\n"
|
||||||
|
sys.exit(0)
|
||||||
|
|
||||||
|
elif options[opt] == "-pl":
|
||||||
|
write_pvals = True
|
||||||
|
try:
|
||||||
|
pval_file = options[opt+1]
|
||||||
|
if pval_file[0] == "-":
|
||||||
|
print "\n\nPlease specify file name for -pl option.\n\n"
|
||||||
|
sys.exit(0)
|
||||||
|
except IndexError:
|
||||||
|
print "\n\nPlease specify file name for -pl option.\n\n"
|
||||||
|
sys.exit(0)
|
||||||
|
|
||||||
|
elif options[opt] == "-ptp":
|
||||||
|
doPTP = True
|
||||||
|
|
||||||
|
elif options[opt] == "-z":
|
||||||
|
rands = int(options[opt+1])
|
||||||
|
|
||||||
|
elif options[opt] == "-p":
|
||||||
|
pval = float(options[opt+1])
|
||||||
|
|
||||||
|
elif options[opt] == "-u":
|
||||||
|
unknown = options[opt+1].split(",")
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
if not file:
|
||||||
|
print "No file specified (-in option)"
|
||||||
|
sys.exit(0)
|
||||||
|
|
||||||
|
|
||||||
|
#Parse .aln file
|
||||||
|
names = []
|
||||||
|
seqs = []
|
||||||
|
if ">" in file.readline():
|
||||||
|
tmp = FastaParse(file_name)
|
||||||
|
else:
|
||||||
|
print """
|
||||||
|
*******************************
|
||||||
|
File not in correct format!
|
||||||
|
TIGER accepts FastA format.
|
||||||
|
*******************************
|
||||||
|
"""
|
||||||
|
sys.exit(0)
|
||||||
|
|
||||||
|
import re
|
||||||
|
names = tmp[0]
|
||||||
|
for x, nm in (enumerate(names)):
|
||||||
|
names[x] = re.sub(" ", "", nm)
|
||||||
|
seqs = tmp[1]
|
||||||
|
|
||||||
|
lns = [len(l) for l in seqs]
|
||||||
|
lns.sort()
|
||||||
|
if lns[0] != lns[-1]:
|
||||||
|
print "\n\nUneven sequence lengths. Ensure sequences have been aligned!\n\n"
|
||||||
|
sys.exit(0)
|
||||||
|
|
||||||
|
|
||||||
|
datatype = DNAdetect(seqs[0])
|
||||||
|
|
||||||
|
#Create array of site patterns
|
||||||
|
patterns = []
|
||||||
|
sites = []
|
||||||
|
comp_Pats = []
|
||||||
|
comp_Sites = []
|
||||||
|
for i in range(len(seqs[0])):
|
||||||
|
sites.append("".join([j[i] for j in seqs]))
|
||||||
|
patterns.append(getPattern(sites[-1], unknown))
|
||||||
|
if patterns[-1] not in comp_Pats:
|
||||||
|
comp_Pats.append(patterns[-1])
|
||||||
|
comp_Sites.append(sites[-1])
|
||||||
|
|
||||||
|
|
||||||
|
#Compare character patterns and score
|
||||||
|
ranks = range(len(patterns))
|
||||||
|
comp_ranks = []
|
||||||
|
keep = []
|
||||||
|
br = ""
|
||||||
|
if doPTP:
|
||||||
|
comp_disagree = []
|
||||||
|
disagree = range(len(patterns))
|
||||||
|
|
||||||
|
for aa, patA in enumerate(comp_Pats):
|
||||||
|
if re.search("\|", patA):
|
||||||
|
cfl = scoreConflict(aa, patA, patterns)
|
||||||
|
comp_ranks.append(1.0 - cfl)
|
||||||
|
else:
|
||||||
|
comp_ranks.append(1.0)
|
||||||
|
|
||||||
|
if doPTP:
|
||||||
|
dis = 0
|
||||||
|
for z in range(rands):
|
||||||
|
patJ = jumblePattern(comp_Sites[aa], unknown)
|
||||||
|
scr = scoreConflict(aa, patJ, patterns)
|
||||||
|
#check if site has higher conflict score than original site
|
||||||
|
if scr >= (1.0 - comp_ranks[aa]):
|
||||||
|
dis += 1
|
||||||
|
|
||||||
|
dis = float(dis)/float(rands)
|
||||||
|
comp_disagree.append(dis)
|
||||||
|
|
||||||
|
|
||||||
|
i = -1
|
||||||
|
try:
|
||||||
|
while 1:
|
||||||
|
i = patterns.index(patA, i + 1)
|
||||||
|
ranks[i] = comp_ranks[aa]
|
||||||
|
if doPTP:
|
||||||
|
disagree[i] = comp_disagree[aa]
|
||||||
|
except ValueError:
|
||||||
|
pass
|
||||||
|
|
||||||
|
#Output total alignment score to file alnRate.txt
|
||||||
|
if write_rates:
|
||||||
|
handle = open(rate_file, 'w')
|
||||||
|
handle.write("\n".join([str(r) for r in ranks]))
|
||||||
|
handle.close()
|
||||||
|
|
||||||
|
if write_pvals and not doPTP:
|
||||||
|
outF.write("-ptp option not selected. No p-values to write!")
|
||||||
|
|
||||||
|
|
||||||
|
#Find significant sites
|
||||||
|
if doPTP:
|
||||||
|
sig_dis = []
|
||||||
|
for x in range(len(disagree)):
|
||||||
|
if disagree[x] < pval:
|
||||||
|
sig_dis.append(x+1)
|
||||||
|
|
||||||
|
if write_pvals:
|
||||||
|
outF = open(pval_file, 'w')
|
||||||
|
for d in range(len(disagree)):
|
||||||
|
outF.write(str(disagree[d]))
|
||||||
|
if (d+1) in sig_dis:
|
||||||
|
outF.write(" *")
|
||||||
|
outF.write("\n")
|
||||||
|
|
||||||
|
|
||||||
|
#BINNING
|
||||||
|
maxRank = max(ranks)
|
||||||
|
minRank = min(ranks)
|
||||||
|
|
||||||
|
binStr = []
|
||||||
|
for numb, r in enumerate(ranks):
|
||||||
|
if 1 > 0:
|
||||||
|
binParts = []
|
||||||
|
for mult in range(binNo + 1):
|
||||||
|
binParts.append(minRank + (((maxRank - minRank)/binNo)*mult))
|
||||||
|
binParts.reverse()
|
||||||
|
for bin in range(1, len(binParts)):
|
||||||
|
if r < binParts[bin - 1] and r >= binParts[bin]:
|
||||||
|
binStr.append(str(bin))
|
||||||
|
break
|
||||||
|
elif round(r, 5) == round(maxRank, 5):
|
||||||
|
binStr.append("1")
|
||||||
|
break
|
||||||
|
|
||||||
|
|
||||||
|
#Make names equal lengths
|
||||||
|
filler = " "*20
|
||||||
|
filled_names = names[:]
|
||||||
|
for n, nm in enumerate(names):
|
||||||
|
nm_r = re.sub("[\s]+", "_", nm)
|
||||||
|
if len(nm_r) > 20:
|
||||||
|
filled_names[n] = nm_r[1] + "_" + nm_r[-18:]
|
||||||
|
else:
|
||||||
|
filled_names[n] = nm_r+ filler[:(20 -len(nm_r))]
|
||||||
|
|
||||||
|
|
||||||
|
#print in correct format.... :(
|
||||||
|
print "#NEXUS\n\n[This file contains data that has been analysed for site specific rates]"
|
||||||
|
print "[using TIGER, developed by Carla Cummins in the laboratory of]"
|
||||||
|
print "[Dr James McInerney, National University of Ireland, Maynooth]\n\n"
|
||||||
|
|
||||||
|
print "[Histograms of number of sites in each category:]"
|
||||||
|
Hnames = []
|
||||||
|
counts = []
|
||||||
|
for b in range(binNo):
|
||||||
|
Hnames.append("Bin" + str(b+1) + "\t")
|
||||||
|
counts.append(binStr.count(str(b+1)))
|
||||||
|
histogram(counts, Hnames)
|
||||||
|
|
||||||
|
print "\n\n"
|
||||||
|
|
||||||
|
print "\n\n\nBEGIN TAXA;"
|
||||||
|
print "\tDimensions NTax = ", len(seqs), ";"
|
||||||
|
print "\tTaxLabels ", " ".join(filled_names), ";\nEND;\n"
|
||||||
|
|
||||||
|
print "BEGIN CHARACTERS;"
|
||||||
|
print "\tDimensions nchar = ", len(seqs[0]), ";"
|
||||||
|
print "\tFormat datatype = ", datatype, " gap = - interleave;\nMatrix\n"
|
||||||
|
|
||||||
|
|
||||||
|
sorted = range(len(seqs[0]))
|
||||||
|
if formSort == 1:
|
||||||
|
sorted = range(len(ranks))
|
||||||
|
sr = ranks[:]
|
||||||
|
sr.sort()
|
||||||
|
sr.reverse()
|
||||||
|
s = 0
|
||||||
|
sortD = {}
|
||||||
|
for x in range(len(ranks)):
|
||||||
|
ind = sr.index(ranks[x])
|
||||||
|
sortD[x] = ind
|
||||||
|
sorted[ind] = x
|
||||||
|
sr[ind] = "|"
|
||||||
|
|
||||||
|
print sortD
|
||||||
|
|
||||||
|
|
||||||
|
if doPTP:
|
||||||
|
sig_sorted = []
|
||||||
|
for d in sig_dis:
|
||||||
|
sig_sorted.append(sortD[d-1]+1)
|
||||||
|
sig_dis = sig_sorted
|
||||||
|
|
||||||
|
for xy in range(0, len(seqs[0]), 60):
|
||||||
|
for xz in range(len(seqs)):
|
||||||
|
ln = filled_names[xz] + "\t"
|
||||||
|
|
||||||
|
if len(seqs[xz][xy:]) < 60:
|
||||||
|
for i in sorted[xy:]:
|
||||||
|
ln = ln + seqs[xz][i].upper()
|
||||||
|
else:
|
||||||
|
for j in sorted[xy:xy+60]:
|
||||||
|
ln = ln + seqs[xz][j].upper()
|
||||||
|
|
||||||
|
print ln
|
||||||
|
|
||||||
|
if formRate == 0:
|
||||||
|
for x in range(len(str(binNo))):
|
||||||
|
if x == 0:
|
||||||
|
bnls = "[Bin Numbers \t"
|
||||||
|
else:
|
||||||
|
bnls = "[" + filler + "\t"
|
||||||
|
|
||||||
|
for y in range(xy, (xy + 60)):
|
||||||
|
if y < len(binStr):
|
||||||
|
if len(binStr[sorted[y]]) - 1 < x:
|
||||||
|
bnls = bnls + " "
|
||||||
|
else:
|
||||||
|
s = sorted[y]
|
||||||
|
bnls = bnls + str(binStr[s])[x]
|
||||||
|
else:
|
||||||
|
break
|
||||||
|
print bnls + "]"
|
||||||
|
|
||||||
|
else:
|
||||||
|
for c in range(5):
|
||||||
|
if c == 0:
|
||||||
|
rtls = "[Rank Values \t"
|
||||||
|
else:
|
||||||
|
rtls = "[" + filler + "\t"
|
||||||
|
for d in range(xy, (xy + 60)):
|
||||||
|
if d < len(ranks):
|
||||||
|
if len(str(ranks[sorted[d]])) - 1 < c:
|
||||||
|
rtls = rtls + " "
|
||||||
|
else:
|
||||||
|
rtls = rtls + str(ranks[sorted[d]])[c]
|
||||||
|
else:
|
||||||
|
break
|
||||||
|
print rtls + "]"
|
||||||
|
|
||||||
|
if numbered:
|
||||||
|
digits = len(str(len(sorted)))
|
||||||
|
srted = sorted[:]
|
||||||
|
for sn, sv in enumerate(srted):
|
||||||
|
if len(str(sv)) < digits:
|
||||||
|
srted[sn] = str(sv) + " "*(digits-len(str(sv)))
|
||||||
|
for c in range(digits):
|
||||||
|
if c == 0:
|
||||||
|
colnms = "[Column Numbers \t"
|
||||||
|
else:
|
||||||
|
colnms = "[" + filler + "\t"
|
||||||
|
nms = [str(n)[c] for n in srted[xy:xy+60]]
|
||||||
|
colnms += "".join(nms)
|
||||||
|
print colnms + "]"
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
print "\n"
|
||||||
|
print "\n"
|
||||||
|
|
||||||
|
print ";\nEND;\n\nBEGIN PAUP;"
|
||||||
|
if formSort:
|
||||||
|
lower_bound = 1
|
||||||
|
for c in range(1, binNo + 1):
|
||||||
|
amt = binStr.count(str(c))
|
||||||
|
if amt > 0:
|
||||||
|
charset = "\tCharset Bin" + str(c) + " = "
|
||||||
|
upper_bound = lower_bound + (binStr.count(str(c))) - 1
|
||||||
|
charset = charset + str(lower_bound) + "-" + str(upper_bound) + ";"
|
||||||
|
lower_bound = upper_bound + 1
|
||||||
|
print charset
|
||||||
|
else:
|
||||||
|
for x in range(1, binNo + 1):
|
||||||
|
tmpL = []
|
||||||
|
if str(x) in binStr:
|
||||||
|
for y in range(len(binStr)):
|
||||||
|
if str(binStr[y]) == str(x):
|
||||||
|
tmpL.append(str(y + 1))
|
||||||
|
print "\tCharset Bin" + str(x) + " = ", " ".join(tmpL) + ";"
|
||||||
|
|
||||||
|
if doPTP:
|
||||||
|
print "\tCharset Sig_Disagreement = " + " ".join([str(i) for i in sig_dis]) + ";"
|
||||||
|
|
||||||
|
print "END;"
|
||||||
|
|
||||||
|
lt_F = time.localtime()
|
||||||
|
print "[START TIME:", lt_S[3], ":", lt_S[4],":", lt_S[5], "]"
|
||||||
|
print "[FINISH TIME:", lt_F[3], ":", lt_F[4],":", lt_F[5], "]"
|
||||||
229
tiger_fns_102.py
Normal file
229
tiger_fns_102.py
Normal file
|
|
@ -0,0 +1,229 @@
|
||||||
|
#!/usr/bin/env python
|
||||||
|
|
||||||
|
import re
|
||||||
|
|
||||||
|
# DEFINE FUNCTIONS
|
||||||
|
|
||||||
|
def shared(x, y):
|
||||||
|
sh = 0
|
||||||
|
grX = x.split("|")
|
||||||
|
grY = y.split("|")
|
||||||
|
|
||||||
|
for i in range(len(grX)):
|
||||||
|
grX[i] = set(grX[i].split(","))
|
||||||
|
for j in range(len(grY)):
|
||||||
|
grY[j] = set(grY[j].split(","))
|
||||||
|
|
||||||
|
|
||||||
|
for xXx in grX:
|
||||||
|
for yYy in grY:
|
||||||
|
if xXx.issubset(yYy):
|
||||||
|
sh += 1
|
||||||
|
break
|
||||||
|
|
||||||
|
return sh
|
||||||
|
|
||||||
|
def scoreConflict(indA, patA, patterns):
|
||||||
|
vrai = True
|
||||||
|
|
||||||
|
dividand = 0
|
||||||
|
|
||||||
|
pg = patA.split("|")
|
||||||
|
score = 0.0
|
||||||
|
pats2 = patterns[:]
|
||||||
|
overall_rank = 0.0
|
||||||
|
conflict_score = 0.0
|
||||||
|
del pats2[indA]
|
||||||
|
for bb, patB in enumerate(pats2):
|
||||||
|
if re.search("\|", patB):
|
||||||
|
dividand += 1
|
||||||
|
compB = patB.split("|")
|
||||||
|
scB = 0.0
|
||||||
|
for group in compB:
|
||||||
|
cont = 1
|
||||||
|
if vrai:
|
||||||
|
tax = group.split(",")
|
||||||
|
ch1 = tax[0]
|
||||||
|
for gp in pg:
|
||||||
|
if ch1 in gp:
|
||||||
|
for ch2 in tax[1:]:
|
||||||
|
if ch2 not in gp and cont:
|
||||||
|
scB = scB + 1.0
|
||||||
|
cont = 0
|
||||||
|
score += (scB/len(compB))
|
||||||
|
|
||||||
|
conflict_score = score/dividand
|
||||||
|
|
||||||
|
return conflict_score
|
||||||
|
|
||||||
|
def uniqify(seq):
|
||||||
|
seen = {}
|
||||||
|
result = []
|
||||||
|
for item in seq:
|
||||||
|
if item in seen : continue
|
||||||
|
seen[item] = 1
|
||||||
|
result.append(item)
|
||||||
|
return result
|
||||||
|
|
||||||
|
|
||||||
|
def getPattern(site, unknown):
|
||||||
|
considered = []
|
||||||
|
pattern = []
|
||||||
|
for x in range(len(site)):
|
||||||
|
if site[x] not in unknown:
|
||||||
|
if site[x] in considered:
|
||||||
|
pattern[considered.index(site[x])].append(str(x))
|
||||||
|
else:
|
||||||
|
considered.append(site[x])
|
||||||
|
pattern.append([str(x)])
|
||||||
|
|
||||||
|
|
||||||
|
patStr = "|".join([",".join(g) for g in pattern])
|
||||||
|
|
||||||
|
return patStr
|
||||||
|
|
||||||
|
|
||||||
|
def jumblePattern(site, unknown):
|
||||||
|
import random
|
||||||
|
|
||||||
|
siteJ = ""
|
||||||
|
while site:
|
||||||
|
pos = random.randrange(len(site))
|
||||||
|
siteJ += site[pos]
|
||||||
|
site = site[:pos] + site[(pos+1):]
|
||||||
|
|
||||||
|
return getPattern(siteJ, unknown)
|
||||||
|
|
||||||
|
|
||||||
|
def DNAdetect(seq):
|
||||||
|
seq = seq.upper()
|
||||||
|
oLen = float(len(seq))
|
||||||
|
seq_C = ""
|
||||||
|
|
||||||
|
seq_C = seq.replace("A", "")
|
||||||
|
seq_C = seq_C.replace("C", "")
|
||||||
|
seq_C = seq_C.replace("G", "")
|
||||||
|
seq_C = seq_C.replace("T", "")
|
||||||
|
|
||||||
|
nLen = float(len(seq_C))
|
||||||
|
perc = (nLen/oLen)*100
|
||||||
|
|
||||||
|
if perc < 20.0:
|
||||||
|
return "DNA"
|
||||||
|
else:
|
||||||
|
seq_C = seq.replace("0", "")
|
||||||
|
seq_C = seq_C.replace("1", "")
|
||||||
|
if len(seq_C) == 0:
|
||||||
|
return "standard"
|
||||||
|
else:
|
||||||
|
return "protein"
|
||||||
|
|
||||||
|
|
||||||
|
def histogram(num_list, name_list):
|
||||||
|
upper = float(max(num_list))
|
||||||
|
pad = len(str(upper))
|
||||||
|
parts = []
|
||||||
|
for i in range(1,61):
|
||||||
|
parts.append((upper/60)*i)
|
||||||
|
|
||||||
|
for m, n in enumerate(num_list):
|
||||||
|
pr = name_list[m] + "|"
|
||||||
|
low = 0.0
|
||||||
|
if n == 0:
|
||||||
|
pr = pr + " "*61
|
||||||
|
for p, hi in enumerate(parts):
|
||||||
|
if n > low and n <= hi:
|
||||||
|
pr = pr + "="*(p+1) + (" "*(60 - p))
|
||||||
|
break
|
||||||
|
low = hi
|
||||||
|
print "[" + pr + "|" + str(n) + " "*(pad-len(str(n))) + "]"
|
||||||
|
|
||||||
|
|
||||||
|
def FastaParse(file_name):
|
||||||
|
file = open(file_name)
|
||||||
|
names = []
|
||||||
|
seqs = []
|
||||||
|
for line in file:
|
||||||
|
if ">" in line:
|
||||||
|
names.append(line[1:].strip())
|
||||||
|
seqs.append("")
|
||||||
|
else:
|
||||||
|
seqs[-1] += line.strip()
|
||||||
|
|
||||||
|
ret = [names, seqs]
|
||||||
|
return ret
|
||||||
|
|
||||||
|
|
||||||
|
def printHelp():
|
||||||
|
print """
|
||||||
|
****************
|
||||||
|
TIGER Help:
|
||||||
|
****************
|
||||||
|
|
||||||
|
TIGER: Tree-Independent Generation of Evolutionary Rates
|
||||||
|
|
||||||
|
(Developed by Carla Cummins in the lab of James Mc Inerney, NUI Maynooth, Co. Kildare, Ireland)
|
||||||
|
|
||||||
|
-Options:
|
||||||
|
|
||||||
|
-in Specify input file. File must be in FastA format and must be aligned prior.
|
||||||
|
Datasets with uneven sequence lengths will return an error.
|
||||||
|
|
||||||
|
-v Returns current TIGER version.
|
||||||
|
|
||||||
|
-f Changes output formatting options.
|
||||||
|
-f s: sorts sites depending on their agreement score
|
||||||
|
-f r: displays rank values rather than bin numbers
|
||||||
|
-f s,r: displays sorted ranks (*Be sure to put only a "," NO SPACE!)
|
||||||
|
|
||||||
|
Default prints bin numbers unsorted.
|
||||||
|
|
||||||
|
-b Set the number of bins to be used.
|
||||||
|
-b <int>: Sites will be placed into <int> number of bins. <int> is a whole number.
|
||||||
|
|
||||||
|
Default is 10
|
||||||
|
|
||||||
|
-rl A list of the rate at each site may be optionally written to a specified
|
||||||
|
file.
|
||||||
|
-rl <file.txt> : writes list of the rates at each site to file.txt.
|
||||||
|
|
||||||
|
-ptp Specifies that a PTP test should be run. *Note: this option has a huge
|
||||||
|
effect on running time!
|
||||||
|
|
||||||
|
-z Number of randomisations to be used for the PTP test.
|
||||||
|
-z <int>: each site will be randomised <int> times. <int> is a whole number.
|
||||||
|
|
||||||
|
Default is 100
|
||||||
|
|
||||||
|
-p Specify p-value which denotes significance in PTP test.
|
||||||
|
-p <float>: site will be denoted as significant if p-value is better than <float>.
|
||||||
|
<float> is a floating point number.
|
||||||
|
|
||||||
|
Default is 0.05
|
||||||
|
|
||||||
|
-pl Write a list of p-values to a specified file.
|
||||||
|
-pl <file.txt>: writes list of p-values for each site to file.txt.
|
||||||
|
|
||||||
|
-u Specify unknown characters in the alignment. Unknown characters are omitted from
|
||||||
|
site patterns and so are not considered in the analysis.
|
||||||
|
-u ?,-,*: defines ?, - and * as unknown characters. (*Be sure to put only a comma
|
||||||
|
between characters, NO SPACE!!)
|
||||||
|
|
||||||
|
Default is ? only
|
||||||
|
|
||||||
|
|
||||||
|
-Examples:
|
||||||
|
|
||||||
|
1. ./TIGER -in ExampleFile.aln -f s,r -v -rl rate_list.txt
|
||||||
|
|
||||||
|
This will run the software on "ExampleFile.aln", with sorted ranks included in the output.
|
||||||
|
The variability measure for each site will be displayed and a list of the rates at (unsorted)
|
||||||
|
sites will be written to the file "rate_list.txt".
|
||||||
|
|
||||||
|
2. ./TIGER -in ExampleFile.aln -ptp -r 1000 -p 0.01 -u ?,*
|
||||||
|
|
||||||
|
This will run the software on the file "ExampleFile.aln" with a PTP test. Sites will be
|
||||||
|
randomised 1,000 times and pass the test if their p-value is <0.01. All ? and * characters
|
||||||
|
encountered in the alignment will be ommitted from the analysis.
|
||||||
|
|
||||||
|
"""
|
||||||
BIN
tiger_fns_102.pyc
Executable file
BIN
tiger_fns_102.pyc
Executable file
Binary file not shown.
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Reference in a new issue