forester/aptx/aptx_example_files/cu_zn_superoxide_dismutase.nex

   1 NEXUS
   2 BEGIN TAXA;
   3   DIMENSIONS ntax=26;
   4   TAXLABELS  O_volvulus_AAB64227.1 O_volvulus_AAB64226.1 C_elegans_AAF39759.1 C_elegans_AAA83577.1
   5     S_cerevisiae_CAA89634.1 C_albicans_AAC12872.1 S_pombe_CAB57444.1 N_crassa_AAA63780.1 M_musculus_AAA40121.1
   6     C_capitata_AAA57249.1 D_virilis_CAA32060.1 D_erecta_AAF23595.1 D_orena_AAF23594.1 D_teissieri_AAF23599.1
   7     D_yakuba_AAF23598.1 D_melanogaster_AAF50095.1 D_mauritiana_AAF23597.1 D_sechellia_AAF23596.1
   8     D_simulans_CAA33720.1 Z_mays_AAB49913.1 O_sativa_AAC14464.1 O_sativa_AAC14465.1 A_thaliana_AAF99769.1
   9     P_tremuloides_AAD01605.1 A_thaliana_BAB09468.1 A_thaliana_AAD29823.2;
  10 END;
  11 BEGIN CHARACTERS;
  12   DIMENSIONS ntax=26 nchar=30;
  13   FORMAT  datatype=protein gap=- missing=?;
  14   CHARLABELS 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112
  15     113 114 115 116 117 118 119 120;
  16   MATRIX
  17     M_musculus_AAA40121.1       QGTIHFEQKASGE--PVVLSGQITGLTE-G
  18     C_capitata_AAA57249.1       KGTVHFEQQDAKS--PVLVTGEVNGLAK-G
  19     N_crassa_AAA63780.1         KGTVIFEQESESA--PTTITYDISGNDPNA
  20        --stuff deleted here--
  21     D_simulans_CAA33720.1       KGTVFFEQESSGT--PVKVSGEVCGLAK-G
  22     S_cerevisiae_CAA89634.1     SGVVKFEQASESE--PTTVSYEIAGNSPNA
  23     S_pombe_CAB57444.1          SGVVTFEQVDQNS--QVSVIVDLVGNDANA;
  24 END;
  25 BEGIN ASSUMPTIONS;
  26   WTSET MySoapWeights  (VECTOR) = 1 1 1 1 1 1 1 1 0.83 0.8 0.8 0.8 0.8 0.8 0.71 0.71 1 1 1 1 1 1 1 1
  27     1 1 1 1 1 1;
  28 END;
  29 BEGIN TREES;
  30   TREE "Cu-Zn Superoxide Dismutase" = (((((O_volvulus_AAB64227.1:0.31741,O_volvulus_AAB64226.1:0.13498):
  31     0.20268[1],(C_elegans_AAF39759.1:0.14579,C_elegans_AAA83577.1:0.27311):0.2533[1]):0.12655[0.98],
  32     ((S_cerevisiae_CAA89634.1:0.28255,C_albicans_AAC12872.1:0.25631):0.08358[0.91],(S_pombe_CAB57444.1:
  33     0.3159,N_crassa_AAA63780.1:0.1635):0.11954[0.97]):0.17514[1]):0.08988[0.77],(M_musculus_AAA40121.1:
  34     0.49149,(C_capitata_AAA57249.1:0.18945,(D_virilis_CAA32060.1:0.11453,(((D_erecta_AAF23595.1:0.00661,
  35     D_orena_AAF23594.1:0.00769):0.00497[0.92],(D_teissieri_AAF23599.1:0.004,D_yakuba_AAF23598.1:0.01012):
  36     0.0073[0.87]):0.01271[0.88],(((D_melanogaster_AAF50095.1:0.00836,D_mauritiana_AAF23597.1:0.00552):
  37     0.00203[0.28],D_sechellia_AAF23596.1:0.01103):0.00398[0.7],D_simulans_CAA33720.1:0.00595):0.00739[0.75]):
  38     0.11795[1]):0.11754[1]):0.12932[1]):0.10326[1]):0.0712[0.9],(((((Z_mays_AAB49913.1:0.05142,
  39     O_sativa_AAC14464.1:0.09031):0.02799[0.98],O_sativa_AAC14465.1:0.06915):0.05245[0.99],
  40     (A_thaliana_AAF99769.1:0.17064,P_tremuloides_AAD01605.1:0.1075):0.08023[1]):0.08596[1],
  41     A_thaliana_BAB09468.1:0.46052):0.06401[0.75],A_thaliana_AAD29823.2:0.42442):0.14252[0.94]);
  42 END;