Supplemental results for CODEML (seqf: algn  treef: tree)


dN/dS for site classes (K=3)

p:   0.49161  0.37297  0.13542
w:   0.15802  1.00000  3.33823

Naive Empirical Bayes (NEB) probabilities for 3 classes& postmean_w & P(w>1)
Loxodonta_africana used as reference

   1 M   0.99832 0.00168 0.00000 ( 1)  0.159  0.000
   2 A   0.29194 0.70548 0.00258 ( 2)  0.760  0.003
   3 R   0.99871 0.00129 0.00000 ( 1)  0.159  0.000
   4 Y   0.99704 0.00296 0.00000 ( 1)  0.161  0.000
   5 R   0.08653 0.91336 0.00012 ( 2)  0.927  0.000
   6 C   0.99995 0.00005 0.00000 ( 1)  0.158  0.000
   7 C   0.99993 0.00007 0.00000 ( 1)  0.158  0.000
   8 R   0.99915 0.00085 0.00000 ( 1)  0.159  0.000
   9 S   0.99999 0.00001 0.00000 ( 1)  0.158  0.000
  10 R   0.00000 0.06341 0.93659 ( 3)  3.190  0.937
  11 *   0.49161 0.37297 0.13542 ( 1)  0.903  0.135
  12 *   0.49161 0.37297 0.13542 ( 1)  0.903  0.135
  13 S   1.00000 0.00000 0.00000 ( 1)  0.158  0.000
  14 R   0.68108 0.31889 0.00003 ( 1)  0.427  0.000
  15 S   1.00000 0.00000 0.00000 ( 1)  0.158  0.000
  16 R   0.99516 0.00484 0.00000 ( 1)  0.162  0.000
  17 C   1.00000 0.00000 0.00000 ( 1)  0.158  0.000
  18 *   0.85866 0.13657 0.00478 ( 1)  0.288  0.005
  19 *   0.25644 0.55077 0.19279 ( 2)  1.235  0.193
  20 R   0.10791 0.89209 0.00000 ( 2)  0.909  0.000
  21 S   0.98344 0.01656 0.00000 ( 1)  0.172  0.000
  22 R   0.01294 0.98403 0.00304 ( 2)  0.996  0.003
  23 *   0.49161 0.37297 0.13542 ( 1)  0.903  0.135
  24 *   0.49161 0.37297 0.13542 ( 1)  0.903  0.135
  25 *   0.49161 0.37297 0.13542 ( 1)  0.903  0.135
  26 R   0.99463 0.00537 0.00000 ( 1)  0.163  0.000
  27 R   0.01874 0.92299 0.05828 ( 2)  1.120  0.058
  28 R   0.58834 0.41166 0.00000 ( 1)  0.505  0.000
  29 S   0.00050 0.99245 0.00705 ( 2)  1.016  0.007
  30 H   0.00000 0.99987 0.00013 ( 2)  1.000  0.000
  31 *   0.49161 0.37297 0.13542 ( 1)  0.903  0.135
  32 R   0.01796 0.97004 0.01201 ( 2)  1.013  0.012
  33 R   0.72852 0.26829 0.00320 ( 1)  0.394  0.003
  34 R   0.99944 0.00056 0.00000 ( 1)  0.158  0.000
  35 R   0.99953 0.00047 0.00000 ( 1)  0.158  0.000
  36 R   0.56490 0.43507 0.00003 ( 1)  0.524  0.000
  37 S   0.00000 0.99994 0.00005 ( 2)  1.000  0.000
  38 C   0.00000 0.99844 0.00156 ( 2)  1.004  0.002
  39 R   0.04218 0.95537 0.00246 ( 2)  0.970  0.002
  40 S   0.03583 0.96382 0.00035 ( 2)  0.971  0.000
  41 R   0.09563 0.90295 0.00142 ( 2)  0.923  0.001
  42 R   0.86539 0.13461 0.00000 ( 1)  0.271  0.000
  43 R   0.00000 0.70321 0.29679 ( 2)  1.694  0.297
  44 *   0.00006 0.06922 0.93072 ( 3)  3.176  0.931
  45 *   0.00000 0.00338 0.99662 ( 3)  3.330  0.997
  46 R   0.00017 0.97454 0.02529 ( 2)  1.059  0.025
  47 C   1.00000 0.00000 0.00000 ( 1)  0.158  0.000
  48 C   0.99983 0.00017 0.00000 ( 1)  0.158  0.000
  49 *   0.82935 0.16728 0.00337 ( 1)  0.310  0.003
  50 *   0.86761 0.13120 0.00118 ( 1)  0.272  0.001
  51 R   0.98059 0.01941 0.00000 ( 1)  0.174  0.000
  52 R   0.93316 0.06684 0.00000 ( 1)  0.214  0.000
  53 R   0.01731 0.98265 0.00004 ( 2)  0.986  0.000
  54 H   0.93438 0.06562 0.00000 ( 1)  0.213  0.000
  55 R   0.00000 0.00679 0.99321 ( 3)  3.322  0.993
  56 *   0.00000 0.00000 1.00000 ( 3)  3.338  1.000
  57 *   0.00000 0.11487 0.88513 ( 3)  3.070  0.885
  58 *   0.00179 0.74711 0.25110 ( 2)  1.586  0.251
  59 *   0.00000 0.29396 0.70604 ( 3)  2.651  0.706
  60 *   0.06229 0.93763 0.00008 ( 2)  0.948  0.000
  61 *   0.86512 0.13488 0.00000 ( 1)  0.272  0.000
  62 *   0.00000 0.99776 0.00224 ( 2)  1.005  0.002
  63 *   0.76843 0.21237 0.01920 ( 1)  0.398  0.019
  64 *   0.03583 0.44867 0.51551 ( 3)  2.175  0.516
  65 *   0.49161 0.37297 0.13542 ( 1)  0.903  0.135

Positively selected sites

	Prob(w>1)  mean w

    10 R      0.937         3.190
    44 *      0.931         3.176
    45 *      0.997**       3.330
    55 R      0.993**       3.322
    56 *      1.000**       3.338
    57 *      0.885         3.070
    59 *      0.706         2.651
    64 *      0.516         2.175


lnL = -3284.673112

Bayes Empirical Bayes (BEB) probabilities for 3 classes (class)& postmean_w
Loxodonta_africana used as reference

   1 M   0.99826 0.00174 0.00000 ( 1)  0.153 +-  0.037
   2 A   0.27538 0.72070 0.00392 ( 2)  0.774 +-  0.403
   3 R   0.99864 0.00136 0.00000 ( 1)  0.152 +-  0.033
   4 Y   0.99672 0.00328 0.00000 ( 1)  0.154 +-  0.050
   5 R   0.07801 0.92154 0.00045 ( 2)  0.935 +-  0.230
   6 C   0.99995 0.00005 0.00000 ( 1)  0.151 +-  0.012
   7 C   0.99993 0.00007 0.00000 ( 1)  0.151 +-  0.013
   8 R   0.99906 0.00094 0.00000 ( 1)  0.152 +-  0.028
   9 S   0.99999 0.00001 0.00000 ( 1)  0.151 +-  0.011
  10 R   0.00000 0.11261 0.88739 ( 3)  3.188 +-  0.875
  11 *   0.47772 0.37785 0.14443 ( 1)  0.953 +-  1.123
  12 *   0.47772 0.37785 0.14443 ( 1)  0.953 +-  1.123
  13 S   1.00000 0.00000 0.00000 ( 1)  0.151 +-  0.011
  14 R   0.65141 0.34849 0.00010 ( 1)  0.447 +-  0.405
  15 S   1.00000 0.00000 0.00000 ( 1)  0.151 +-  0.011
  16 R   0.99483 0.00517 0.00000 ( 1)  0.156 +-  0.062
  17 C   1.00000 0.00000 0.00000 ( 1)  0.151 +-  0.011
  18 *   0.85183 0.14303 0.00514 ( 1)  0.289 +-  0.370
  19 *   0.24322 0.55384 0.20294 ( 2)  1.294 +-  1.169
  20 R   0.08943 0.91057 0.00000 ( 2)  0.925 +-  0.241
  21 S   0.98042 0.01958 0.00000 ( 1)  0.168 +-  0.118
  22 R   0.01148 0.98365 0.00486 ( 2)  1.000 +-  0.163
  23 *   0.47772 0.37785 0.14443 ( 1)  0.953 +-  1.123
  24 *   0.47772 0.37785 0.14443 ( 1)  0.953 +-  1.123
  25 *   0.47772 0.37785 0.14443 ( 1)  0.953 +-  1.123
  26 R   0.99426 0.00574 0.00000 ( 1)  0.156 +-  0.065
  27 R   0.01681 0.92146 0.06173 ( 2)  1.124 +-  0.566
  28 R   0.55900 0.44097 0.00003 ( 1)  0.526 +-  0.421
  29 S   0.00048 0.98869 0.01082 ( 2)  1.020 +-  0.204
  30 H   0.00001 0.99921 0.00078 ( 2)  1.001 +-  0.045
  31 *   0.47772 0.37785 0.14443 ( 1)  0.953 +-  1.123
  32 R   0.01634 0.96567 0.01798 ( 2)  1.020 +-  0.284
  33 R   0.71276 0.28355 0.00370 ( 1)  0.403 +-  0.419
  34 R   0.99941 0.00059 0.00000 ( 1)  0.152 +-  0.023
  35 R   0.99951 0.00049 0.00000 ( 1)  0.152 +-  0.022
  36 R   0.53344 0.46645 0.00011 ( 1)  0.548 +-  0.424
  37 S   0.00001 0.99952 0.00047 ( 2)  1.001 +-  0.034
  38 C   0.00000 0.99487 0.00512 ( 2)  1.008 +-  0.120
  39 R   0.03746 0.95858 0.00395 ( 2)  0.976 +-  0.203
  40 S   0.03141 0.96777 0.00082 ( 2)  0.975 +-  0.156
  41 R   0.08467 0.91303 0.00231 ( 2)  0.933 +-  0.255
  42 R   0.84538 0.15461 0.00000 ( 1)  0.282 +-  0.307
  43 R   0.00000 0.72190 0.27809 ( 2)  1.650 +-  1.072
  44 *   0.00005 0.07436 0.92559 ( 3)  3.339 +-  0.823
  45 *   0.00000 0.00469 0.99531 ( 3)  3.511 +-  0.531
  46 R   0.00017 0.96813 0.03170 ( 2)  1.064 +-  0.366
  47 C   1.00000 0.00000 0.00000 ( 1)  0.151 +-  0.011
  48 C   0.99980 0.00020 0.00000 ( 1)  0.151 +-  0.016
  49 *   0.82116 0.17515 0.00370 ( 1)  0.311 +-  0.370
  50 *   0.86075 0.13789 0.00136 ( 1)  0.272 +-  0.312
  51 R   0.97916 0.02084 0.00000 ( 1)  0.169 +-  0.122
  52 R   0.91616 0.08384 0.00000 ( 1)  0.222 +-  0.235
  53 R   0.01526 0.98454 0.00020 ( 2)  0.988 +-  0.105
  54 H   0.92195 0.07805 0.00000 ( 1)  0.217 +-  0.228
  55 R   0.00000 0.01763 0.98237 ( 3)  3.461 +-  0.564
  56 *   0.00000 0.00000 1.00000 ( 3)  3.525 +-  0.515
  57 *   0.00000 0.16570 0.83430 ( 3)  3.055 +-  0.996
  58 *   0.00159 0.75271 0.24570 ( 2)  1.583 +-  1.048
  59 *   0.00000 0.37365 0.62635 ( 3)  2.504 +-  1.203
  60 *   0.05529 0.94438 0.00033 ( 2)  0.954 +-  0.195
  61 *   0.84701 0.15298 0.00000 ( 1)  0.281 +-  0.306
  62 *   0.00000 0.99162 0.00838 ( 2)  1.014 +-  0.151
  63 *   0.75894 0.22058 0.02048 ( 1)  0.405 +-  0.560
  64 *   0.03263 0.44612 0.52125 ( 3)  2.280 +-  1.337
  65 *   0.47772 0.37785 0.14443 ( 1)  0.953 +-  1.123

Positively selected sites

	Prob(w>1)  mean w

    10 R      0.887         3.188 +- 0.875
    44 *      0.926         3.339 +- 0.823
    45 *      0.995**       3.511 +- 0.531
    55 R      0.982*        3.461 +- 0.564
    56 *      1.000**       3.525 +- 0.515
    57 *      0.834         3.055 +- 0.996
    59 *      0.626         2.504 +- 1.203
    64 *      0.521         2.280 +- 1.337

