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thermus.nex
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#NEXUS
[!*************************************************************]
[!*Test data file containing Ribosomal RNA sequences. *]
[!*These sequences have opposing base compositional biases *]
[!*that have the ability to confound phylogenetic analyses *]
[!*Using the appropriate methods of phylogenetic analysis, it *]
[!*is possible to reconstruct the correct set of relationships*]
[!* *]
[!*The inclusion of T_ruber will facilitate easier phylogeny *]
[!*reconstruction. This taxon is included in an effort to *]
[!*demonstrate the effectiveness of adequate taxon sampling *]
[!* *]
[!*Remove the first taxon (T_ruber) from initial analyses *]
[!*and include it in subsequent analyses in order to see the *]
[!*effect of taxon sampling. *]
[!* *]
[!* *]
[!*Save this file to your computer as text and use it in *]
[!*conjunction with the PAUP program *]
[!* *]
[!*************************************************************]
Begin data;
Dimensions ntax=6 nchar=1273;
Format datatype=nucleotide gap=- missing=? matchchar=. interleave;
Matrix
T_ruber CTCAGGGTGAACGCTGGCGGTATGCCTAAGACATGCAAGTCGAACGGGCA
Aquifex CTCAGCGCGAACGCTGGCGGCGTGCCTAACACATGCAAGTCGTGCGCAGA
Deinococcus CTCAGGGTGAACGCTGGCGGCGTGCTTAAGACATGCAAGTCGAACGCGGA
Thermotoga CTCAGGGTGAACGCTGGCGGCGTGCCTAACACATGCAAGTCGAGCGGGGA
Bacillus CTCAGGACGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCGGACA
Thermus CTCAGGGTGAACGCTGGCGGCGTGCCTAAGACATGCAAGTCGTGCGGGCA
T_ruber GTGGCGGACGGGTGAGTAACACGTAGGTGACCTACCCCAAAGTCTGGGAC
Aquifex GCGGCAAACGGGTGAGTAACACGTGGGTAACCTACCCCCAGGAGGGGGAT
Deinococcus GTGGCGCACGGGTGAGTAACACGTAACTGACCTACCCAGAAGTCATGAAT
Thermotoga GCGGCGGACGGGTGAGTAACACGTGGGTAACCTGCCCTCCGGAGGGGGAT
Bacillus GCGGCGGACGGGTGAGTAACACGTGGGTAACCTGCCTGTAAGACTGGGAT
Thermus GCGGCGGACGGGTGAGTAACGCGTGGGTGACCTACCCGGAAGAGGGGGAC
T_ruber AACTAGGAGAAATCTTAGCTAATCCTGGATGTGGACGATGGGCCTGCGGC
Aquifex AACCCCGGGAAACCGGGGCTAATACCCCATAAAGCCGATGGGCCCGCGGC
Deinococcus AACTGGCCGAAAGGTCAGCTAATACGTGATGTGGTGGATGGGGTTGCGTT
Thermotoga AACCAGGGGAAACCCTGGCTAATACCCCATACGCTCGAGGGGCCCGCGGC
Bacillus AACTCCGGGAAACCGGGGCTAATACCGGATGGTTGTGATGGACCCGCGGC
Thermus AACCCGGGGAAACTCGGGCTAATCCCCCATGTGGACGATGGGCCCGCGTC
T_ruber GCATCAGGTAGTTGGTGGGGTAATGGCCTACCAAGCCGACGACGCGTAGC
Aquifex CCATCAGGTAGTTGGTGGGGTAACGGCCCACCAAGCCTATGACGGGTAGC
Deinococcus CCATCAGCTGGTTGGTGGGGTAAAGGCCTACCAAGGCGACGACGGATAGC
Thermotoga CCATCAGGTAGTTGGTGGGGTAACGGCCCACCAAGCCGACGACGGGTAGC
Bacillus GCATTAGCTAGTTGGTGAGGTAACGGCTCACCAAGGCAACGATGCGTAGC
Thermus CCATCAGCTAGTTGGTGGGGTAATGGCCCACCAAGGCGACGACGGGTAGC
T_ruber TGGTCTGAGAGGACGATCAGCCACAGGGGTACTGAGACACGGACCCCACT
Aquifex CGGCCTGAGAGGGTGGCCGGCCACAGCGGGACTGAGACACGGCCCGCACC
Deinococcus CGGCCTGAGAGGGTGGCCGGCCACAGGGGCACTGAGACACGGGTCCCACT
Thermotoga CGGCCTGAGAGGGTGGTCGGCCACAGGGGCACTGAGACACGGGCCCCACT
Bacillus CGACCTGAGAGGGTGATCGGCCACACTGGGACTGAGACACGGCCCAGACT
Thermus CGGTCTGAGAGGATGGCCGGCCACAGGGGCACTGAGACACGGGCCCCACT
T_ruber CCTACGGGAGGCAGCAGTTAGGAATCTTCCGCAATGGGCGAAAGCCTGAC
Aquifex CCTACGGGGGGCAGCAGTGGGGAATCGTGGGCAATGGGCGAAAGCCTGAC
Deinococcus CCTACGGGAGGCAGCAGTTAGGAATCTTCCACAATGGGCGCAAGCCTGAT
Thermotoga CCTACGGGAGGCAGCAGTGGGGAATCTTGGACAATGGGGGAAACCCTGAT
Bacillus CCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGACGAAAGTCTGAC
Thermus CCTACGGGAGGCAGCAGTTAGGAATCTTCCGCAATGGGCGCAAGCCTGAC
T_ruber GGAGCGATACCGCTTGAAGGACGAAGCCCTTCGGGGTGTAAACTTCTGAA
Aquifex CCCGCGACGCCGCGTGGGGGAAGAAGCCCTGCGGGGTGTAAACCCCTGTC
Deinococcus GGAGCGACGCCGCGTGAGGGATGAAGGTTTTCGGATCGTAAACCTCTGAA
Thermotoga CCAGCGACGCCGCGTGCGGGACGAAGCCCTTCGGGGTGTAAACCGCTGTG
Bacillus GGAGCAACGCCGCGTGAGTGATGAAGGTTTTCGGATCGTAAAGCTCTGTT
Thermus GGAGCGACGCCGCTTGGAGGAAGAAGCCCTTCGGGGTGTAAACTCCTGAA
T_ruber CTCGGG-ACGTGACGGTACCGAGGTAAGCACCGGCTAACTCCGTGCCAGC
Aquifex GGGGGGGACGTGACGGTACCCCCAGAGGGGACGGCTAACTACGTGCCAGC
Deinococcus TCTGGG-ACGTGACGGTACCAGAGTAAGCACCGGCTAACTCCGTGCCAGC
Thermotoga GCGGGGGAAGTGACGGTACCCCGCTAGGCCCCGGCTAACTACGTGCCAGC
Bacillus GTTAGGGAAGTGACGGTACCTAACCAGGCCACGGCTAACTACGTGCCAGC
Thermus CCCGGG-ACGTGACGGTACCGGGGTAAGCGCCGGCCAACTCCGTGCCAGC
T_ruber AGCCGCGGTAATACGGAGGGTGCGAGCGTTACCCGGATTTACTGGGTGTA
Aquifex AGCCGCGGTAATACGTAGGTCCCGAGCGTTGCGCGAAGTCACTGGGCGTA
Deinococcus AGCCGCGGTAATACGGAGGGTGCAAGCGTTACCCGGAATCACTGGGCGTA
Thermotoga AGCCGCGGTAATACGTAGGGGGCAAGCGTTACCCGGATTTACTGGGCGTA
Bacillus AGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTA
Thermus AGCCGCGGTAATACGGAGGGCGCGAGCGTTACCCGGATTCACTGGGCGTA
T_ruber AAGGGCGTGTAGGCGGTCTCTCAAGTCCGATGCTAAAGACCGAAGCTCAA
Aquifex AAGCGTCCGCAGCCGGTCGGGTAAGCGGGATGTCAAAGCCCACGGCTCAA
Deinococcus AAGGGCGTGTAGGCGGATATTTAAGTCTGGTTTTAAAGACCGAGGCTCAA
Thermotoga AAGGGGGCGTAGGCGGCCTGGTGTGTCGGATGTGAAATCCCACGGCTCAA
Bacillus AAGGGCTCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAA
Thermus AAGGGCGTGTAGGCGGCCTGGGGCGTCCCATGTGAAAGACCACGGCTCAA
T_ruber CTTCGGGGGTGCGTTGGATACTGTGAGGCTAGACGGTCGGAGAGGGTAGC
Aquifex CCGTGGAATGGCATCCCGAACTGCCCGACTTGAGGCACGCCCGGGCAGGC
Deinococcus CCTCGGGAGTGGACTGGATACTGGATGTCTTGACCTCTGGAGAGGTAACT
Thermotoga CCGTGGGGCTGCATCCGAAACTACCAGGCTTGGGGGCGGTAGAGGGAGAC
Bacillus CCGGGGAGGGTCATTGGAAACTGGGGAACTTGAGTGCAGAAGAGGAGAGT
Thermus CCGTGGGGGAGCGTGGGATACGCTCAGGCTAGACGGTGGGAGAGGGTGGT
T_ruber GGAATTTCCGGAGTAGCGGTGAAATGCGCAGATACCGGAAGGAACGCCAA
Aquifex GGAATTCCCGGGGTAGCGGTGAAATGCGTAGATCTCGGGAGGAACACCGA
Deinococcus GGAATTCCTGGTGTAGCGGTGGAATGCGTAGATACCAGGAGGAACACCAA
Thermotoga GGAACTGCCGGTGTAGGGGTGAAATCCGTAGATATCGGCAGGAACGCCGG
Bacillus GGAATTCCACGTGTAGCGGTGAAATGCGTAGAGATGTGGAGGAACACCAG
Thermus GGAATTCCCGGAGTAGCGGTGAAATGCGCAGATACCGGGAGGAACGCCGA
T_ruber TAGCGAAAGCAGCTACCTGGACGATTTGTGACGCTGAGGCGCGAAAGCGT
Aquifex AGGGGAAGCCAGCCTGCTGGGGCTGTCCTGACGGTCAGGGACGAAAGCCG
Deinococcus TGGCGAAGGCAAGTTACTGGACAGAAGGTGACGCTGAGGCGCGAAAGTGT
Thermotoga TGGGGAAGCCGGTCTCCTGGGCCGACCCCGACGCTGAGGCCCGAAAGCCA
Bacillus TGGCGAAGGCGACTCTCTGGTCTGTAACTGACGCTGAGGAGCGAAAGCGT
Thermus TGGCGAAGGCAGCCACCTGGTCCACCCGTGACGCTGAGGCGCGAAAGCGT
T_ruber GGGGAGCAAACCGGATTAGATACCCGGGTAGTCCACGCCCTAAACGATGA
Aquifex GGGGAGCGAACCGGATTAGATACCCGGGTAGTCCCGGCCGTAAACCATGG
Deinococcus GGGGAGCAAACCGGATTAGATACCCGGGTAGTCCACACCCTAAACGATGT
Thermotoga GGGGAGCAAACCGGATTAGATACCCGGGTAGTCCTGGCTGTAAACGATGC
Bacillus GGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGA
Thermus GGGGAGCAAACCGGATTAGATACCCGGGTAGTCCACGCCCTAAACGATGC
T_ruber GTGCTGGGTGTTGGGTGCCGTAGCTAACGCGTTAAGCACTCCACCTGGGA
Aquifex GCGCTAGGGCTGCAGGCTCGCAGCTAACGCGTTAAGCGCCCCGCCTGGGG
Deinococcus ACGTTGGCTAATGCTTGGCGAAGCTAACGCGATAAACGTACCGCCTGGGA
Thermotoga CCACTAGGTGTTCCGTGCTGAAGCTAACGCGTTAAGTGGGCCGCCTGGGG
Bacillus GTGCTAAGTGTTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGG
Thermus GCGCTAGGTCTTGGGGGCCGAAGCTAACGCGTTAAGCGCGCCGCCTGGGG
T_ruber AGTACGGTCGCAAGACTGAAACTCAAAGGAATTGACGGGGGCCCGCACAA
Aquifex AGTACGGGCGCAAGCCTGAAACTCAAAGGAATTGGCGGGGGCCCGCACAA
Deinococcus AGTACGGCCGCAAGGTTGAAACTCAAAGGAATTGACGGGGGCCCGCACAA
Thermotoga AGTACGCCCGCAAGGGTGAAACTCAAAGGAATTGACGGGGGCCCGCACAA
Bacillus AGTACGGTCGCAAGACTGAAACTCAAAGGAATTGACGGGGGCCCGCACAA
Thermus AGTACGGCCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAA
T_ruber GCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGCAGAACCTTACCAGG
Aquifex CCGGTGGAGCGTCTGGTTCAATTCGATGCTAACCGAAGAACCTTACCCGG
Deinococcus GCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCAGG
Thermotoga GCGGTGGAGCGTGTGGTTTAATTGGATGCTAAGCCAAGAACCTTACCAGG
Bacillus GCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCAGG
Thermus GCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCAGG
T_ruber TCTTGACATCAGACAGGTGCTGCATGGTCGTCGTCAGCTCGTGTCGTGAG
Aquifex GCTTGACATGGCACAGGTGGTGCATGGCCGTCGTCAGCTCGTGTCGTGAG
Deinococcus TCTTGACATGACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAG
Thermotoga GCTTGACATGGCACAGGTGGTGCACGGCCGTCGTCAGCTCGTGCCGTGAG
Bacillus TCTTGACATCTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAG
Thermus CCTTGACATGGCACAGGTGCTGCATGGCCGTCGTCAGCTCGTGCCGTGAG
T_ruber ATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTGTTGCTAGTTGCCGG
Aquifex ATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTGCCCCTAGTTGCTGA
Deinococcus ATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGCTTCCAGTTGCCGG
Thermotoga GTGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTGCCCCTAGTTGCCGG
Bacillus ATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGATCTTAGTTGCCGG
Thermus GTGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCCGCCGTTAGTTGCCGG
T_ruber GCACTCTAGCGAGACTGCCTACGTAGGAGGAAGGCGGGGATGACGTCTGA
Aquifex GCACTCTAGGGGGACCGCCGGCGCCGGAGGAAGGGGGGGATGACGTCAGG
Deinococcus GCACTCTGGAGGGACTGCCTGTGCAGGAGGAAGGCGGGGATGACGTCTAG
Thermotoga GCACTCTAGGGGGACTGCCGGCGCCGGAGGAAGGAGGGGATGACGTCAGG
Bacillus GCACTCTAAGGTGACTGCCGGTGCCGGAGGAAGGTGGGGATGACGTCAAA
Thermus GCACTCTAACGGGACTGCCCGCGCGGGAGGAAGGAGGGGACGACGTCTGG
T_ruber TCCGCATGGCCCTTACGACCTGGGCGACACACGTGCTACAATGCCTGCCA
Aquifex TCAGTATGCCCTTTATGCCCGGGGCCACACAGGCGCTACAGTGGCCGGGA
Deinococcus TCAGCATGGTCCTTACGTCCTGGGCTACACACGTGCTACAATGGATAGGA
Thermotoga TACTCGTGCCCCTTATGCCCTGGGCGACACACGCGCTACAATGGGCGGTA
Bacillus TCATCATGCCCCTTATGACCTGGGCTACACACGTGCTACAATGGACAGAA
Thermus TCAGCATGGCCCTTACGGCCTGGGCGACACACGTGCTACAATGCCC--TA
T_ruber CAAAGCGCTGCGACCCGGTAACGGGAAGCCAATCGCACAAAAGCAGGCTC
Aquifex CAATGGGAAGCGACCCCGCAAGGGGGAGCTAATCCCAGAAACCCGGTCAT
Deinococcus CAACGCGCAGCAAACATGTGAGTGTAAGCGAATCGCTGAAACCTATCCCC
Thermotoga CAATGGGTTGCGACCCCGCGAGGGGGAGCCAATCCC-CAAAGCCGCCCTC
Bacillus CAAAGGGCAGCGAAACCGCGAGGTTAAGCCAATCCCACAAATCTGTTCTC
Thermus CAAAGCGATGCCACCCGGCAACGGGGAGCTAATCGCAAAAAGGTGGGCCC
T_ruber AGTTCGGATTGGGGTCTGCAACTCGACCCCATGAAGCCGGAATCGCTAGT
Aquifex GGTGCGGATTGGGGGCTGAAACTCGCCCCCATGAAGCCGGAATCGGTAGT
Deinococcus AGTTCAGATCGGAGTCTGCAACTCGACTCCGTGAAGTTGGAATCGCTAGT
Thermotoga AGTTCGGATCGCAGGCTGCAACCCGCCTGCGTGAAGCCGGAATCGCTAGT
Bacillus AGTTCGGATCGCAGTCTGCAACTCGACTGCGTGAAGCTGGAATCGCTAGT
Thermus AGTTCGGATTGGGGTCTGCAACCCGACCCCATGAAGCCGGAATCGCTAGT
T_ruber AATCGCGGATCAGCCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACAC
Aquifex AACGGGGTATCAGCGATGTCCCCGTGAATACGTTCTCGGGCCTTGCACAC
Deinococcus AATCGCGGGTCAGC-ATACCGCGGTGAATACGTTCCCGGGCCTTGTACAC
Thermotoga AATCGCGGATCAGCCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACAC
Bacillus AATCGCGGATCAGC-ATGCCGCGGTGAATACGTTCCCGGGCCTTGTACAC
Thermus AATCGCGGATCAGCCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACAC
T_ruber ACCGCCCGTCAAGCCATGGGAGTGGGTTTTGCCTGAAGGACTGGGGCTAA
Aquifex ACCGCCCGTCACGCCACGGAAGTCGGTCCGGCCGGAAGGACTGGGGCGAA
Deinococcus ACCGCCCGTCACACCATGGGAGTAGATTGCAGTTGAAAGACTGGGGTGAA
Thermotoga ACCGCCCGTCACGCCACCCGAGTCGGGGGCTCCCGAAGGAGGGGGGCGAA
Bacillus ACCGCCCGTCACACCACGAGAGTTTGTAACACCCGAAGGATTGGGGTGAA
Thermus ACCGCCCGTCACGCCATGGGAGCGGGCTCTACCCGAAGGACTGGGGCGAA
T_ruber GTCGTAACAAGGTAGCTGTACCG
Aquifex GTCGTAACAAGGTAGCCGTAGGG
Deinococcus GTCGTAACAAGGTAACTGTACCG
Thermotoga GTCGTAACAAGGTAGCCGTACCG
Bacillus GTCGTAACAAGGTAGCCGTATCG
Thermus GTCGTAACAAGGTAGCTGTACCG
;
End;