
CODONML in paml version 4.10.10, 29 Jan 2026

----------------------------------------------
Phe F TTT | Ser S TCT | Tyr Y TAT | Cys C TGT
      TTC |       TCC |       TAC |       TGC
Leu L TTA |       TCA | *** * TAA | *** * TGA
      TTG |       TCG |       TAG | Trp W TGG
----------------------------------------------
Leu L CTT | Pro P CCT | His H CAT | Arg R CGT
      CTC |       CCC |       CAC |       CGC
      CTA |       CCA | Gln Q CAA |       CGA
      CTG |       CCG |       CAG |       CGG
----------------------------------------------
Ile I ATT | Thr T ACT | Asn N AAT | Ser S AGT
      ATC |       ACC |       AAC |       AGC
      ATA |       ACA | Lys K AAA | Arg R AGA
Met M ATG |       ACG |       AAG |       AGG
----------------------------------------------
Val V GTT | Ala A GCT | Asp D GAT | Gly G GGT
      GTC |       GCC |       GAC |       GGC
      GTA |       GCA | Glu E GAA |       GGA
      GTG |       GCG |       GAG |       GGG
----------------------------------------------
Nice code, uuh?
ns = 30  	ls = 918
Reading sequences, sequential format..
Reading seq # 1: Antrozous_pallidus       
Reading seq # 2: Eptesicus_fuscus       
Reading seq # 3: Erinaceus_europaeus       
Reading seq # 4: Ictidomys_tridecemlineatus       
Reading seq # 5: Marmota_flaviventris       
Reading seq # 6: Marmota_marmota       
Reading seq # 7: Marmota_monax       
Reading seq # 8: Myotis_lucifugus       
Reading seq # 9: Rhinolophus_ferrumequinum       
Reading seq #10: Urocitellus_parryii       
Reading seq #11: Ursus_americanus       
Reading seq #12: Ursus_arctos       
Reading seq #13: Callorhinus_ursinus       
Reading seq #14: Heterocephalus_glaber       
Reading seq #15: Homo_sapiens       
Reading seq #16: Lemmus_lemmus       
Reading seq #17: Microtus_ochrogaster       
Reading seq #18: Mus_musculus       
Reading seq #19: Mustela_erminea       
Reading seq #20: Mustela_putorius_furo       
Reading seq #21: Myodes_glareolus       
Reading seq #22: Neovison_vison       
Reading seq #23: Ochotona_princeps       
Reading seq #24: Oryctolagus_cuniculus       
Reading seq #25: Phoca_vitulina       
Reading seq #26: Pteropus_vampyrus       
Reading seq #27: Rattus_norvegicus       
Reading seq #28: Sorex_araneus       
Reading seq #29: Talpa_europaea       
Reading seq #30: Talpa_occidentalis       
Sequences read..
Counting site patterns..  0:00

Compressing,    302 patterns at    306 /    306 sites (100.0%),  0:00

Collecting fpatt[] & pose[],    302 patterns at    306 /    306 sites (100.0%),  0:00
1 ambiguous codons are seen in the data:
 ---
Counting codons..
NG distances for seqs.:
   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19  20  21  22  23  24  25  26  27  28  29  30

     3480 bytes for distance
   294752 bytes for conP
        0 bytes for fhK
  5000000 bytes for space

TREE #  1
(((((((18, 27), ((21, 17), 16)), 14), ((5, (6, 7)), (10, 4))), (24, 23)), 15), ((((2, 1, 8), (26, 9)), (((20, 19), 22), ((12, 11), (25, 13)))), ((28, (29, 30)), 3)));   MP score: -1
This is a rooted tree, without clock.  Check.

   1   41.407868
   2   38.590272
   3   38.440194
   4   38.413569
   5   35.805812
   6   35.791894
   7   35.790501
   8   35.605443
   9   35.572647
  10   35.572063
  11   35.571924
  12   35.571906
  4126528 bytes for conP, adjusted

1 node(s) used for scaling (Yang 2000 J Mol Evol 51:423-432):
 45

    0.054650    0.028161    0.033677    0.033444    0.110293    0.033355    0.095017    0.086177    0.074568    0.026613    0.055740    0.032622    0.080447    0.125610    0.139989    0.077965    0.033367    0.045593    0.070246    0.016751    0.020908    0.067741    0.075448    0.076421    0.089439    0.132461    0.138342    0.003511    0.077246    0.044905    0.146546    0.063398    0.106545    0.077056    0.030985    0.100725    0.117467    0.102385    0.100589    0.038099    0.043501    0.072715    0.023071    0.066818    0.109989    0.072096    0.053249    0.079793    0.050213    0.063960    0.164326    0.000000    0.188890    0.097101    0.026730    0.029293    0.210097    1.786666    0.990003

ntime & nrate & np:    57     2    59

Bounds (np=59):
   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000004   0.000100   0.000100
  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000  50.000000 999.000000 999.000000

np =    59
lnL0 = -9439.165163

Iterating by ming2
Initial: fx=  9439.165163
x=  0.05465  0.02816  0.03368  0.03344  0.11029  0.03335  0.09502  0.08618  0.07457  0.02661  0.05574  0.03262  0.08045  0.12561  0.13999  0.07796  0.03337  0.04559  0.07025  0.01675  0.02091  0.06774  0.07545  0.07642  0.08944  0.13246  0.13834  0.00351  0.07725  0.04490  0.14655  0.06340  0.10654  0.07706  0.03098  0.10072  0.11747  0.10239  0.10059  0.03810  0.04350  0.07271  0.02307  0.06682  0.10999  0.07210  0.05325  0.07979  0.05021  0.06396  0.16433  0.00000  0.18889  0.09710  0.02673  0.02929  0.21010  1.78667  0.99000

  1 h-m-p  0.0000 0.0000 2560.2883 ++     9284.179573  m 0.0000    64 | 1/59
  2 h-m-p  0.0000 0.0001 1961.2252 ++     9128.398856  m 0.0001   126 | 1/59
  3 h-m-p  0.0000 0.0000 36071.3630 ++     9124.985033  m 0.0000   188 | 1/59
  4 h-m-p  0.0000 0.0000 105332.7906 ++     9113.924697  m 0.0000   250 | 1/59
  5 h-m-p  0.0000 0.0000 75056.3114 ++     9109.932076  m 0.0000   312 | 1/59
  6 h-m-p  0.0000 0.0000 10869.9540 ++     9059.592547  m 0.0000   374 | 1/59
  7 h-m-p  0.0000 0.0000 17781.7706 ++     9014.311017  m 0.0000   436 | 2/59
  8 h-m-p  0.0000 0.0000 2323.2116 ++     9008.125584  m 0.0000   498 | 3/59
  9 h-m-p  0.0000 0.0001 5456.5815 ++     8787.859145  m 0.0001   560 | 3/59
 10 h-m-p  0.0000 0.0000 98941.4714 
h-m-p:      5.84719760e-23      2.92359880e-22      9.89414714e+04  8787.859145
..  | 3/59
 11 h-m-p  0.0000 0.0001 2481.3319 +YCCCC  8768.696768  4 0.0000   689 | 3/59
 12 h-m-p  0.0000 0.0000 1180.0515 ++     8752.885121  m 0.0000   751 | 4/59
 13 h-m-p  0.0000 0.0000 26422.2112 ++     8656.922984  m 0.0000   813 | 4/59
 14 h-m-p  0.0000 0.0000 12515.9085 ++     8517.808416  m 0.0000   875 | 4/59
 15 h-m-p  0.0000 0.0000 70362.3003 CYCCCC  8460.437579  5 0.0000   946 | 4/59
 16 h-m-p  0.0000 0.0000 842.9492 +YCCC  8454.708571  3 0.0000  1014 | 3/59
 17 h-m-p  0.0000 0.0000 1137.0341 YYYC   8453.829666  3 0.0000  1079 | 3/59
 18 h-m-p  0.0000 0.0001 365.5449 ++     8446.840217  m 0.0001  1141 | 3/59
 19 h-m-p -0.0000 -0.0000 497.8520 
h-m-p:     -0.00000000e+00     -0.00000000e+00      4.97852042e+02  8446.840217
..  | 3/59
 20 h-m-p  0.0000 0.0001 28718.4894 -CYYYCCCC  8443.231861  7 0.0000  1275 | 3/59
 21 h-m-p  0.0000 0.0000 576.1857 ++     8439.183800  m 0.0000  1337 | 4/59
 22 h-m-p  0.0000 0.0001 712.3863 +CYYCYCYC  8428.432511  7 0.0001  1411 | 4/59
 23 h-m-p  0.0000 0.0001 725.0710 +CYCCC  8422.115471  4 0.0001  1481 | 4/59
 24 h-m-p  0.0000 0.0001 376.7113 +YCCC  8418.968067  3 0.0001  1549 | 4/59
 25 h-m-p  0.0000 0.0001 729.2159 ++     8413.493858  m 0.0001  1611 | 4/59
 26 h-m-p  0.0001 0.0006 455.1465 +YCYC  8405.790043  3 0.0003  1678 | 4/59
 27 h-m-p  0.0001 0.0003 184.4415 CYCCC  8404.681001  4 0.0001  1747 | 4/59
 28 h-m-p  0.0002 0.0008 109.9195 CCCC   8403.856217  3 0.0002  1815 | 4/59
 29 h-m-p  0.0001 0.0006 250.8029 CC     8403.215711  1 0.0001  1879 | 4/59
 30 h-m-p  0.0001 0.0008 196.2223 YCCC   8402.045689  3 0.0002  1946 | 4/59
 31 h-m-p  0.0001 0.0005 210.7826 CCCC   8401.396362  3 0.0001  2014 | 4/59
 32 h-m-p  0.0002 0.0024 128.3738 YCCC   8400.517126  3 0.0004  2081 | 4/59
 33 h-m-p  0.0002 0.0014 233.7613 CCCC   8399.352941  3 0.0003  2149 | 4/59
 34 h-m-p  0.0006 0.0044 112.2930 YCCC   8398.766817  3 0.0004  2216 | 4/59
 35 h-m-p  0.0002 0.0008 179.4240 CCCC   8398.278458  3 0.0002  2284 | 4/59
 36 h-m-p  0.0004 0.0059  77.2934 CC     8397.723831  1 0.0006  2348 | 4/59
 37 h-m-p  0.0002 0.0009 161.5295 CCC    8397.313695  2 0.0002  2414 | 4/59
 38 h-m-p  0.0005 0.0048  72.5328 YC     8397.088233  1 0.0003  2477 | 4/59
 39 h-m-p  0.0004 0.0024  68.5198 CYC    8396.907268  2 0.0003  2542 | 4/59
 40 h-m-p  0.0004 0.0047  56.0891 CC     8396.779724  1 0.0003  2606 | 4/59
 41 h-m-p  0.0004 0.0043  39.5044 YC     8396.724578  1 0.0002  2669 | 4/59
 42 h-m-p  0.0003 0.0126  26.6923 CC     8396.666463  1 0.0004  2733 | 3/59
 43 h-m-p  0.0006 0.0200  16.9551 YC     8396.637366  1 0.0003  2796 | 3/59
 44 h-m-p  0.0002 0.0036  26.9853 YC     8396.591878  1 0.0004  2859 | 3/59
 45 h-m-p  0.0007 0.0054  13.9797 YC     8396.564800  1 0.0004  2922 | 3/59
 46 h-m-p  0.0004 0.0042  17.2246 CC     8396.529882  1 0.0005  2986 | 3/59
 47 h-m-p  0.0007 0.0050  12.1206 YC     8396.504349  1 0.0005  3049 | 3/59
 48 h-m-p  0.0003 0.0057  17.6956 C      8396.476485  0 0.0003  3111 | 3/59
 49 h-m-p  0.0006 0.0058  10.2518 CC     8396.431526  1 0.0007  3175 | 3/59
 50 h-m-p  0.0005 0.0037  15.2806 CC     8396.345456  1 0.0007  3239 | 3/59
 51 h-m-p  0.0004 0.0021  23.7953 CC     8396.190748  1 0.0006  3303 | 3/59
 52 h-m-p  0.0003 0.0016  24.4485 YC     8395.864135  1 0.0008  3366 | 3/59
 53 h-m-p  0.0002 0.0008  45.2047 +YCCC  8395.403168  3 0.0004  3434 | 3/59
 54 h-m-p  0.0000 0.0002  65.0467 ++     8394.772017  m 0.0002  3496 | 4/59
 55 h-m-p  0.0003 0.0030  37.7631 +YCCC  8393.574640  3 0.0009  3564 | 4/59
 56 h-m-p  0.0003 0.0014  66.5555 CCC    8392.893708  2 0.0003  3630 | 3/59
 57 h-m-p  0.0005 0.0031  41.2319 CC     8392.344793  1 0.0007  3694 | 3/59
 58 h-m-p  0.0003 0.0017  49.5965 CYC    8392.120505  2 0.0003  3759 | 3/59
 59 h-m-p  0.0005 0.0024  26.6691 YC     8392.034410  1 0.0003  3822 | 3/59
 60 h-m-p  0.0003 0.0028  27.3487 +YC    8391.867771  1 0.0008  3886 | 3/59
 61 h-m-p  0.0012 0.0059  11.4014 YC     8391.812011  1 0.0008  3949 | 3/59
 62 h-m-p  0.0008 0.0091  11.1014 CC     8391.762316  1 0.0007  4013 | 3/59
 63 h-m-p  0.0009 0.0103   8.0480 CC     8391.669134  1 0.0012  4077 | 3/59
 64 h-m-p  0.0011 0.0172   9.2302 CCC    8391.473303  2 0.0014  4143 | 3/59
 65 h-m-p  0.0010 0.0141  13.0456 CCC    8391.161837  2 0.0015  4209 | 3/59
 66 h-m-p  0.0016 0.0291  12.5191 YC     8391.050143  1 0.0012  4272 | 3/59
 67 h-m-p  0.0020 0.0160   7.6120 YC     8391.026804  1 0.0008  4335 | 3/59
 68 h-m-p  0.0020 0.0918   3.0390 C      8391.007998  0 0.0020  4397 | 3/59
 69 h-m-p  0.0025 0.0622   2.5068 +YC    8390.917487  1 0.0066  4461 | 3/59
 70 h-m-p  0.0020 0.0160   8.1585 CC     8390.721582  1 0.0028  4525 | 3/59
 71 h-m-p  0.0024 0.0256   9.5435 CY     8390.456255  1 0.0023  4589 | 3/59
 72 h-m-p  0.0014 0.0164  15.6678 CC     8390.203894  1 0.0014  4653 | 3/59
 73 h-m-p  0.0013 0.0064  11.2133 CC     8390.027463  1 0.0020  4717 | 3/59
 74 h-m-p  0.0006 0.0028  17.0961 YC     8389.904694  1 0.0013  4780 | 3/59
 75 h-m-p  0.0009 0.0047   8.2029 C      8389.879091  0 0.0009  4842 | 3/59
 76 h-m-p  0.0031 0.0290   2.4657 YC     8389.871017  1 0.0016  4905 | 3/59
 77 h-m-p  0.0033 0.2560   1.2065 YC     8389.845972  1 0.0054  4968 | 3/59
 78 h-m-p  0.0015 0.0601   4.3365 YC     8389.746514  1 0.0031  5031 | 3/59
 79 h-m-p  0.0034 0.0602   4.0611 YCC    8389.358510  2 0.0065  5096 | 3/59
 80 h-m-p  0.0054 0.0833   4.8758 YC     8389.330409  1 0.0022  5159 | 3/59
 81 h-m-p  0.1947 1.2229   0.0544 +YC    8389.058586  1 0.5217  5223 | 3/59
 82 h-m-p  1.6000 8.0000   0.0053 CC     8389.024364  1 1.5008  5343 | 3/59
 83 h-m-p  1.6000 8.0000   0.0024 YC     8389.016544  1 0.9545  5462 | 3/59
 84 h-m-p  1.2683 8.0000   0.0018 YC     8389.014548  1 1.0028  5581 | 3/59
 85 h-m-p  1.6000 8.0000   0.0004 Y      8389.014451  0 1.0510  5699 | 3/59
 86 h-m-p  1.6000 8.0000   0.0001 Y      8389.014445  0 1.1886  5817 | 3/59
 87 h-m-p  1.6000 8.0000   0.0000 C      8389.014444  0 1.5232  5935 | 3/59
 88 h-m-p  1.6000 8.0000   0.0000 Y      8389.014444  0 0.9324  6053 | 3/59
 89 h-m-p  1.3481 8.0000   0.0000 Y      8389.014444  0 0.5876  6171 | 3/59
 90 h-m-p  0.9867 8.0000   0.0000 Y      8389.014444  0 0.1648  6289 | 3/59
 91 h-m-p  0.1949 8.0000   0.0000 Y      8389.014444  0 0.0487  6407 | 3/59
 92 h-m-p  0.0515 8.0000   0.0000 Y      8389.014444  0 0.0515  6525 | 3/59
 93 h-m-p  0.0545 8.0000   0.0000 --------C  8389.014444  0 0.0000  6651
Out..
lnL  = -8389.014444
6652 lfun, 6652 eigenQcodon, 379164 P(t)

Time used:  7:01
