perl/etc/WoodyMiaoLin/DistMCMC/test_seq.nex

   1 #NEXUS
   2 BEGIN DATA;
   3 Dimensions ntax=8 nchar=1140;
   4 Format datatype=DNA gap=- missing=?;
   5 Matrix
   6 NC_003426       ATGACCAACATCCGAAAAACCCACCCATTAGCTAAAATCATCAACAACTCACTTATTGATCTCCCAACACCATCAAATATCTCAGCATGATGAAACTTCGGATCTCTCCTCGGAGTATGTTTAGTACTACAAATTCTAACGGGCCTATTTCTAGCCATACACTACACATCAGATACAACTACAGCCTTTTCATCAATCACCCATATTTGCCGAGATGTTCACTACGGATGAATTATCCGATACATACATGCTAACGGAGCTTCCATGTTCTTTATCTGCCTGTTCATGCACGTAGGACGGGGTCTGTACTATGGCTCATACCTACTCTCAGAAACATGAAACATTGGCATTATCCTCCTATTTACAGTTATAGCCACCGCATTCATAGGATATGTCCTGCCCTGAGGCCAAATATCCTTCTGAGGAGCAACTGTTATCACCAACCTCCTATCAGCCATCCCCTATATTGGAACAGACCTAGTAGAATGGATCTGAGGGGGCTTTTCTGTGAATAAGGCAACTCTGACACGATTCTTTGCCTTCCACTTTATTCTTCCATTCATCATCTTGACACTAGCAGCAGTCCACCTATTATTCCTACACGAAACAGGATCTAATAACCCCTCTGGAATCCCATCTGACTCAGACAAAATCCCATTTCATCCATATTATACAATTAAAGACGCCCTAGGCGCCCTACTTTTCATCCTAGCCCTAACAACTCTAGTCCTATTCTCGCCTGACCTACTAGGAGATCCCGATAACTACACCCCCGCAAACCCACTGAGCACCCCACCCCACATCAAACCTGAATGATATTTTCTATTTGCCTACGCTATTCTACGGTCCATCCCCAACAAACTAGGAGGAGTGCTAGCACTAATTTTCTCTATCCTAATCCTAGCTATTATCCCCCTTCTACACACATCCAAGCAACGAGGAATAATGTTCCGACCCCTAAGCCAATGCCTATTCTGACTTCTAGTAGCAGACCTACTAACACTAACATGAATCGGAGGGCAACCAGTAGAACACCCCTTTATCATTATCGGCCAGTTGGCCTCTATCCTCTACTTCACAATCCTCCTAGTGCTCATGCCTATCGCTGGGATCATTGAAAATAACCTCTCAAAATGAAGA
   7 NC_003427       ATGACCAACATCCGAAAAACCCACCCATTAGCTAAAATCATCAACAACTCATTTATTGACCTTCCAACACCATCAAACATCTCAGCATGATGAAACTTTGGATCCCTCCTCGGAGTATGTTTAATCCTACAGATTCTAACAGGCCTGTTCCTAGCCATACACTATACATCAGACACAACCACAGCTTTTTCATCAGTCACCCACATTTGCCGAGACGTTCACTACGGATGAGTTATCCGATATGTACATGCAAATGGAGCCTCCATCTTCTTTATCTGCCTATTTATGCACGTAGGACGGGGCCTGTACTATGGCTCATACCTATTCTCAGAAACATGAAACATCGGCATCATTCTCCTATTTACAGTTATAGCCACCGCATTTATAGGATACGTCCTACCCTGAGGCCAAATGTCCTTCTGAGGAGCGACTGTCATCACCAATCTACTATCAGCCATTCCCTACATCGGAACGGACCTGGTAGAATGAATCTGAGGGGGCTTTTCCGTAGATAAGGCGACTCTAACACGATTCTTTGCTTTCCACTTTATTCTCCCGTTCATCATCCTAGCACTAGCAGCAGTCCATCTATTGTTCCTACACGAAACAGGATCCAACAACCCCTCTGGAATCCCATCTGACTCAGACAAAATCCCATTCCATCCATACTATACAATTAAGGATATCTTAGGCGCCCTACTTCTCGCCCTAACCTTAGCAACCCTAGTCCTATTCTCGCCCGACTTACTAGGAGACCCTGATAACTATACCCCCGCAAATCCACTGAGCACTCCACCCCACATCAAACCCGAGTGGTACTTTCTATTTGCCTACGCTATCCTACGATCCATCCCTAATAAACTAGGAGGAGTACTAGCACTAATTTTCTCCATTCTAATCCTAGCCATCATTCCTCTCCTACACACGTCCAAACAACGAGGAATGATATTCCGACCCCTAAGCCAATGCCTATTTTGACTTCTAGTAGCAGACCTACTAACACTAACATGAATTGGAGGACAACCAGTAGAACATCCCTTCATTATTATCGGACAACTAGCCTCCATTCTCTACTTTACAATCCTCCTAGTACTTATACCCGTCGCTGGAATTATTGAAAACAACCTCTTAAAGTGGAGA
   8 NC_003428       ATGACCAACATCCGAAAAACCCACCCATTAGCTAAAATCATCAACAACTCATTTATTGATCTTCCAACACCATCAAACATCTCAGCATGATGAAACTTTGGATCCCTCCTTGGAGTGTGTTTAATTCTACAGATTCTAACAGGCCTGTTTCTAGCCATACACTATACATCAGACACAACCACAGCTTTTTCATCAGTCACCCACATTTGCCGAGACGTTCACTACGGGTGAGTTATCCGATATGTACATGCAAATGGAGCCTCCATGTTCTTTATCTGCCTATTCATGCACGTAGGACGGGGCCTGTACTATGGCTCATACCTATTCTCAGAAACATGAAACATTGGCATTATTCTCCTATTTACAGTTATAGCCACCGCATTTATAGGATACGTCCTACCCTGAGGCCAAATGTCCTTCTGAGGAGCGACTGTCATCACCAATCTACTATCGGCCATTCCCTATATCGGAACGGACCTGGTAGAATGAATCTGAGGGGGCTTTTCCGTAGATAAAGCGACTCTAACACGATTCTTTGCTTTCCACTTTATTCTCCCGTTCATCATCCTAGCACTAGCAGCAGTCCACCTATTGTTCCTACACGAAACAGGATCCAACAACCCCTCTGGAATCCCATCTGACTCAGACAAAATCCCATTCCATCCATACTATACAATTAAGGATATTCTAGGCGCCCTACTTCTCACCCTAGCCTTAGCAACCCTAGTCCTATTCTCGCCCGACTTACTAGGAGACCCTGATAACTATATCCCCGCAAATCCACTGAGCACCCCACCCCACATCAAACCCGAGTGGTACTTTCTATTTGCCTACGCTATCCTACGATCCATCCCTAATAAACTAGGAGGAGTACTAGCACTAATTTTCTCCATTCTAATCCTAGCCCTCATTCCTCTTCTACACACGTCCAAACAACGAGGAATGATATTCCGGCCCCTAAGCCAATGCCTATTTTGACTTCTAGTAGCAGACCTACTAACACTAACATGAATTGGAGGACAACCAGTAGAACACCCCTTCATTATTATCGGACAACTAGCCTCCATTCTCTACTTTACAATCCTCCTAGTACTCATACCCATCGCTGGAATTATTGAAAACAACCTCTTAAAGTGGAGA
   9 NC_009331       ATGACCAACATCCGAAAAACCCACCCATTAGCCAAAATCATCAACAACTCACTCATTGATCTCCCAGCACCATCAAATATCTCAGCATGATGAAACTTTGGATCCCTCCTCGGAGTATGCCTAATCCTACAGATTCTGACAGGCCTATTTCTAGCTATACACTACACATCAGACGCGACTACAGCCTTTTCATCAGTCGCCCATATTTGCCGAGACGTCCATTACGGATGAATTATCCGATACATACATGCAAACGGAGCCTCCATGTTCTTCATCTGCCTATTCATACACGTAGGACGGGGCTTGTATTATGGCTCATACCTACTCTCAGAAACATGAAACATTGGCATCATCCTCCTATTTACAGTTATAGCCACCGCATTCATAGGATACGTCCTACCCTGAGGCCAAATATCCTTCTGAGGAGCGACTGTCATTACCAACCTCCTATCAGCCATTCCCTATATTGGAACGGACCTAGTAGAGTGAATCTGAGGGGGCTTTTCCGTAGATAAAGCAACCCTAACACGATTCTTTGCTTTCCACTTTATCCTTCCGTTTATCATCCTAGCACTAGCAGCAGTCCACCTATTGTTCCTACACGAAACAGGATCCAACAACCCCTCTGGAATCCCATCCGACTCGGACAAAATCCCATTCCACCCATACTATACAATTAAGGACGCCCTAGGCGCCCTACTTCTCATTCTAGCCCTAGCAACTCTAGTTCTATTCTCGCCCGACTTACTAGGAGACCCTGACAACTATACCCCCGCAAACCCACTGAGCACCCCGCCCCACATCAAGCCCGAGTGATACTTTTTATTTGCTTACGCTATCCTACGATCCATCCCCAACAAACTAGGAGGAGTACTAGCGCTAATTTTCTCTATCCTAATCCTAGCCATTATCCCCCTTCTACACACATCCAAACAACGAGGAATAATGTTCCGACCCCTAAGCCAATGCCTATTTTGACTCCTAGTAGCAGACCTACTAACACTAACATGAATCGGAGGACAACCAGTAGATCATCCCTTCACCATTATCGGACAGCTAGCCTCCATCCTCTACTTCACAATCCTCCTGGTGCTCATGCCCATCGCTGGAATCATTGAAAACAACCTCTCAAAATGAAGA
  10 NC_009968       ATGACCAACATCCGAAAAACCCACCCATTAGCTAAAATCATTAACAACTCACTTATTGACCTCCCAGCACCATCAAACATCTCGGCGTGATGAAACTTCGGATCCCTCCTCGGAGTATGCTTAATCCTACAGATTATGACAGGCCTATTTCTAGCCATACACTATACATCAGACACAACCACAGCCTTTTCATCAATCACTCATATCTGCCGAGACGTTCACTACGGATGAATTATCCGATATATACATGCAAACGGAGCCTCCATGTTCTTTATCTGCCTATTCATGCACGTAGGACGGGGTCTGTACTATGGCTCGTACCTATTCTCAGAAACATGAAACATCGGTATTATCCTCCTATTTACAGTTATAGCCACCGCATTTATAGGATACGTCCTACCCTGAGGCCAAATGTCCTTCTGAGGAGCAACTGTCATTACCAATCTCTTATCAGCCATCCCCTATATTGGAACGGACCTAGTAGAATGAGTCTGAGGGGGCTTTTCCGTAGACAAAGCAACTCTAACACGATTCTTTGCCTTCCACTTTATCCTTCCGTTCATCATCTTGGCACTAACAGCGGTCCACCTATTATTCCTACACGAAACAGGGTCCAACAATCCCTCTGGAATCCCATCTGACTCAGACAAAATCCCATTTCACCCGTACTATACAATTAAGGACATCCTAGGCGCCCTACTTCTTACCCTAGCCCTAACAACCCTAGTTCTATTCTCGCCCGACTTACTAGGAGACCCTGACAACTACATCCCCGCAAATCCATTGAGCACCCCACCCCACATCAAACCCGAATGGTACTTTCTATTTGCCTACGCTATCCTACGATCCATTCCCAACAAACTAGGAGGAGTACTAGCTCTAGTCTTCTCTATCCTAATCCTAGCCATTATCCCCCTCTTACACACATCCAAGCAACGAGGAATGATATTCCGACCTCTGAGCCAATGCCTATTTTGACTCCTAGTAGCAGACCTACTAACACTAACATGAATTGGAGGACAACCAGTAGAACATCCCTTTACCATTATCGGACAACTAGCCTCCATTCTCTATTTCATAATCTTCCTAGTATTCATACCCATCGCTGGAATTATTGAAAATAACCTCTCAAAATGAAGA
  11 NC_009970       ATGACCAACATCCGAAAAACCCACCCACTAGCTAAAATCATTAACAACTCACTCATTGACCTCCCAGCACCATCAAACATCTCAGCATGATGGAACTTCGGATCCCTCCTCGGAGTGTGCTTAATTCTACAAATTCTAACAGGCCTATTTCTAGCCATACACTATACATCAGACACAACCACAGCCTTTTCATCAGTCACCCATATTTGTCGAGACGTCCACTACGGATGAATCATCCGATATATACATGCAAACGGGGCCTCCATATTCTTTATCTGCCTATTCATGCACGTAGGACGGGGTCTGTACTATGGCTCATACCTATTCTCGGAGACATGAAACACTGGCATTATTCTCCTATTTACAGTCATAGCCACCGCATTCATAGGATACGTCCTACCCTGAGGCCAAATGTCCTTCTGAGGAGCGACTGTCATCACCAATCTACTATCAGCCATTCCCTATATTGGAACGGACCTAGTAGAATGAATCTGAGGGGGGTTTTCCGTAGACAAGGCGACTCTAACACGATTCTTTGCCTTCCACTTTATCCTTCCATTTATCATCCTAGCATTGGTAATAGTCCACCTATTGTTCCTACATGAAACAGGATCTAACAACCCCTCTGGAATCCCATCCAACTCAGACAAAATCCCATTTCACCCATACTATACAATTAAAGATATTATAGGCGCCTTACTTCTCATCCTAGCCCTGGCAACCCTAGTCCTATTCTCACCCGACTTACTAGGAGACCCCGACAACTACACCCCTGCAAACCCACTGAGCACCCCACCCCACATCAAACCCGAGTGGTACTTTCTATTTGCCTACGCTATCCTACGATCCATCCCCAATAAACTAGGAGGGGTACTAGCACTAATTCTCTCCATCCTAATCCTAGCTATCATTCCCCTTCTACATACATCCAAACAACGAGGAATGATATTCCGGCCCCTAAGCCAATGCCTATTTTGACTCCTAGTAGCAGACCTACTAACACTTACATGAATCGGAGGACAACCAGTAGAATATCCCTTCATCACTATTGGACAACTAGCCTCCATCCTCTACTTCATAATCCTCCTAGTACTCATGCCCATCGCCGGAATCATTGAAAACAATCTCTCAAAGTGAAGA
  12 NC_011117       ATGACCAACATCCGAAAAACCCATCCATTAGCCAAAATCATCAACAACTCACTCATTGATCTCCCAGCACCATCAAATATCTCAGCATGATGAAACTTTGGATCCCTCCTCGGAGTATGCCTAATCCTACAGATTCTGACAGGCCTATTTCTAGCTATACACTACACATCAGACGCGACTACAGCCTTTTCATCAGTCGCCCATATTTGCCGAGACGTCCATTACGGATGAATTATCCGATACATACATGCAAACGGAGCCTCCATGTTCTTCATCTGCCTATTCATACACGTAGGACGGGGCTTGTATTATGGCTCATACCTACTCTCAGAAACATGAAACATTGGCATCATCCTCCTATTTACAGTTATAGCCACCGCATTCATAGGATACGTCCTACCCTGAGGCCAAATATCCTTCTGAGGAGCGACTGTCATTACCAACCTCCTATCAGCCATTCCCTATATTGGAACGGATCTAGTAGAGTGAATCTGAGGGGGCTTTTCCGTAGATAAAGCAACCCTAACACGATTCTTTGCTTTCCACTTTATCCTTCCATTTATCATCCTAGCACTAGCAGCAGTTCATCTATTGTTCCTACACGAAACAGGATCCAACAACCCCTCTGGAATCCCATCCGACTCAGACAAAATCCCATTCCACCCATACTATGCAATTAAGGACGCCCTAGGCGCCCTACTTCTCATTCTAGCCCTAGCAACTCTAGTTCTATTCTCGCCCGATTTACTAGGAGACCCTGACAACTATACCCCCGCAAACCCACTGAGCACCCCGCCCCACATCAAGCCCGAGTGATACTTTCTATTTGCTTACGCTATCCTACGATCCATCCCCAACAAACTAGGAGGAGTACTAGCGCTAATCTTCTCTATCCTAATCCTAGCCATTATCCCCCTTCTACACACATCCAAACAACGAGGAATAATGTTCCGACCCCTAAGCCAATGCCTATTTTGACTCCTAGTAGCAGACCTACTAACACTAACATGAATCGGAGGACAACCAGTAGAACATCCCTTCACCATTATCGGACAGCTAGCCTCCATCCTCTACTTCACAATCCTCCTGGTGCTCATGCCCATCGCTGGAATCATTGAAAACAACCTCTCAAAATGAAGA
  13 NC_011118       ATGACCAACATCCGAAAAACTCATCCATTAGCCAAAATCATCAACAACTCACTCATTGATCTCCCAGCACCATCAAATATCTCAGCATGATGAAACTTTGGATCCCTCCTCGGAGTATGCCTAATCCTACAGATTCTGACAGGCCTATTTCTAGCTATACACTACACATCAGACGCGACTACAGCCTTTTCATCAGTCGCCCATATTTGCCGAGACGTCCATTACGGATGAATTATCCGATACATACATGCAAACGGAGCCTCCATGTTCTTCATCTGCCTATTCATACACGTAGGACGGGGCTTGTATTATGGCTCATATCTACTCTCAGAAACATGAAACATTGGCATCATCCTCCTATTTACAGTTATAGCCACCGCATTCATAGGATACGTCCTACCCTGAGGCCAAATATCCTTCTGAGGAGCGACTGTCATTACCAACCTCCTATCAGCCATTCCCTATATTGGAACGGACCTAGTAGAGTGAATCTGAGGGGGCTTTTCCGTAGATAAAGCAACCCTAACACGATTCTTTGCTTTCCACTTTATCCTTCCATTTATCATCCTAGCACTAGCAGCAGTTCATCTATTGTTCCTACACGAAACAGGATCCAACAACCCCTCTGGAATCCCATCCGACTCGGACAAAATCCCATTCCACCCATACTACACAATTAAGGACGCCCTATGGGCCCTACTTCTCATTCTAGCCCTAGCAACTCTAGTTCTATTCTCGCCCGACTTGCTAGGAGACCCCGACAACTATACCCCCGCAAACCCACTGAGCACCCCGCCCCACATCAAGCCCGAGTGATACTTTTTATTTGCTTACGCTATCCTACGATCCATCCCCAACAAACTAGGAGGAGTACTAGCGCTAATCTTCTCTATCCTAATCCTAGCCATTATCCCCCTTCTACACACATCCAAACAACGAGGAATAATGTTCCGACCCCTAAGCCAATGCCTATTTTGACTCCTAGTAGCAGACCTACTAACACTAACATGAATCGGAGGACAACCAGTAGAACATCCCTTCACCATTATCGGACAGCTAGCCTCCATCCTCTACTTCACAATCCTCCTGGTGCTCATGCCCATCGCTGGAATCATTGAAAACAACCTCTCAAAATGAAGA
  14 ;
  15 END;
  16
  17 begin paup;
  18 set autoclose=yes increase=auto warntree=no warnreset=no;
  19
  20 set criterion=distance;
  21 dset distance=jc;
  22 showdist;
  23
  24 dset distance=k2p;
  25 showdist;
  26
  27 dset distance=jc rates=gamma shape=1;
  28 showdist;
  29
  30 dset distance=jc rates=gamma shape=0.6;
  31 showdist;
  32
  33 dset distance=jc rates=gamma shape=0.2;
  34 showdist;
  35
  36 dset distance=k2p rates=gamma shape=1;
  37 showdist;
  38
  39 dset distance=k2p rates=gamma shape=0.6;
  40 showdist;
  41
  42 dset distance=k2p rates=gamma shape=0.2;
  43 showdist;
  44
  45 quit;
  46 end;