
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 = 25  	ls = 918
Reading sequences, sequential format..
Reading seq # 1: Antrozous_pallidus       
Reading seq # 2: Eptesicus_fuscus       
Reading seq # 3: Erinaceus_europaeus       
Reading seq # 4: Myotis_lucifugus       
Reading seq # 5: Rhinolophus_ferrumequinum       
Reading seq # 6: Ursus_americanus       
Reading seq # 7: Ursus_arctos       
Reading seq # 8: Callorhinus_ursinus       
Reading seq # 9: Heterocephalus_glaber       
Reading seq #10: Homo_sapiens       
Reading seq #11: Lemmus_lemmus       
Reading seq #12: Microtus_ochrogaster       
Reading seq #13: Mus_musculus       
Reading seq #14: Mustela_erminea       
Reading seq #15: Mustela_putorius_furo       
Reading seq #16: Myodes_glareolus       
Reading seq #17: Neovison_vison       
Reading seq #18: Ochotona_princeps       
Reading seq #19: Oryctolagus_cuniculus       
Reading seq #20: Phoca_vitulina       
Reading seq #21: Pteropus_vampyrus       
Reading seq #22: Rattus_norvegicus       
Reading seq #23: Sorex_araneus       
Reading seq #24: Talpa_europaea       
Reading seq #25: 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

     2400 bytes for distance
   294752 bytes for conP
        0 bytes for fhK
  5000000 bytes for space

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

   1   24.179144
   2   20.406485
   3   19.968323
   4   19.935993
   5   19.930247
   6   19.930065
   7   19.930057
  3389648 bytes for conP, adjusted

1 node(s) used for scaling (Yang 2000 J Mol Evol 51:423-432):
 35

    0.000000    0.034243    0.050010    0.168843    0.058272    0.095691    0.093870    0.079268    0.057113    0.067969    0.051682    0.034179    0.167841    0.110689    0.090267    0.137771    0.155118    0.020454    0.058618    0.046455    0.194053    0.071649    0.084520    0.089630    0.066888    0.128042    0.125318    0.104343    0.099301    0.021818    0.025742    0.041606    0.035699    0.041146    0.067113    0.056712    0.033367    0.072505    0.049152    0.052792    0.185673    0.007410    0.244491    0.173596    0.009459    0.047002    0.214725    1.985931    0.151477

ntime & nrate & np:    47     2    49

Bounds (np=49):
   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 999.000000 999.000000

np =    49
lnL0 = -8084.515107

Iterating by ming2
Initial: fx=  8084.515107
x=  0.00000  0.03424  0.05001  0.16884  0.05827  0.09569  0.09387  0.07927  0.05711  0.06797  0.05168  0.03418  0.16784  0.11069  0.09027  0.13777  0.15512  0.02045  0.05862  0.04646  0.19405  0.07165  0.08452  0.08963  0.06689  0.12804  0.12532  0.10434  0.09930  0.02182  0.02574  0.04161  0.03570  0.04115  0.06711  0.05671  0.03337  0.07250  0.04915  0.05279  0.18567  0.00741  0.24449  0.17360  0.00946  0.04700  0.21472  1.98593  0.15148

  1 h-m-p  0.0000 0.0001 1322.4469 ++     7967.374599  m 0.0001    54 | 0/49
  2 h-m-p  0.0000 0.0000 29865.9728 ++     7953.791747  m 0.0000   106 | 0/49
  3 h-m-p  0.0000 0.0000 12530.8630 +CYYYYC  7940.902414  5 0.0000   165 | 0/49
  4 h-m-p  0.0000 0.0000 3922.4597 ++     7925.346900  m 0.0000   217 | 1/49
  5 h-m-p  0.0000 0.0001 898.6218 ++     7891.487676  m 0.0001   269 | 1/49
  6 h-m-p  0.0000 0.0000 6434.5424 +YCCC  7878.846169  3 0.0000   327 | 1/49
  7 h-m-p  0.0000 0.0001 534.5075 ++     7868.049634  m 0.0001   379 | 1/49
  8 h-m-p  0.0001 0.0003 739.9957 +YYYCC  7845.606183  4 0.0002   437 | 1/49
  9 h-m-p  0.0000 0.0001 577.0352 +YCCC  7840.308267  3 0.0001   495 | 1/49
 10 h-m-p  0.0002 0.0010 136.4091 CCC    7838.471052  2 0.0003   551 | 1/49
 11 h-m-p  0.0003 0.0014 134.6494 CCC    7837.157223  2 0.0003   607 | 1/49
 12 h-m-p  0.0003 0.0015 132.5991 YCC    7836.516526  2 0.0002   662 | 1/49
 13 h-m-p  0.0003 0.0018  76.1828 CYC    7836.056542  2 0.0003   717 | 1/49
 14 h-m-p  0.0002 0.0020 100.6876 CCC    7835.547636  2 0.0003   773 | 1/49
 15 h-m-p  0.0003 0.0018 119.3261 YCC    7835.194081  2 0.0002   828 | 1/49
 16 h-m-p  0.0003 0.0063  82.8321 YC     7834.611956  1 0.0006   881 | 1/49
 17 h-m-p  0.0003 0.0015 171.5536 YCC    7834.262153  2 0.0002   936 | 1/49
 18 h-m-p  0.0003 0.0023 102.1102 CCC    7833.749236  2 0.0005   992 | 1/49
 19 h-m-p  0.0003 0.0017 141.9591 YCC    7833.485350  2 0.0002  1047 | 1/49
 20 h-m-p  0.0003 0.0055  94.7202 CCC    7833.131580  2 0.0004  1103 | 1/49
 21 h-m-p  0.0005 0.0030  90.3701 YC     7832.918046  1 0.0003  1156 | 1/49
 22 h-m-p  0.0003 0.0033  85.5334 CC     7832.705994  1 0.0003  1210 | 1/49
 23 h-m-p  0.0007 0.0137  38.0468 YC     7832.592471  1 0.0005  1263 | 1/49
 24 h-m-p  0.0007 0.0113  24.8584 YC     7832.536260  1 0.0004  1316 | 1/49
 25 h-m-p  0.0004 0.0053  26.3374 YC     7832.503780  1 0.0003  1369 | 1/49
 26 h-m-p  0.0009 0.0553   7.7788 CC     7832.467535  1 0.0011  1423 | 1/49
 27 h-m-p  0.0009 0.0294   9.9639 YC     7832.436212  1 0.0007  1476 | 1/49
 28 h-m-p  0.0009 0.0409   7.4139 CC     7832.371389  1 0.0013  1530 | 1/49
 29 h-m-p  0.0011 0.0208   8.5934 CC     7832.182415  1 0.0017  1584 | 1/49
 30 h-m-p  0.0011 0.0165  12.8672 +YC    7830.849765  1 0.0036  1638 | 1/49
 31 h-m-p  0.0012 0.0069  38.4509 CCCC   7827.138033  3 0.0019  1696 | 1/49
 32 h-m-p  0.0004 0.0019 106.1954 CYC    7825.078966  2 0.0004  1751 | 1/49
 33 h-m-p  0.0003 0.0017  62.1113 YCCC   7823.276853  3 0.0007  1808 | 1/49
 34 h-m-p  0.0006 0.0029  67.8245 CC     7821.968792  1 0.0007  1862 | 1/49
 35 h-m-p  0.0008 0.0039  29.3391 CCC    7821.701251  2 0.0007  1918 | 1/49
 36 h-m-p  0.0011 0.0055  18.5102 YCC    7821.610675  2 0.0007  1973 | 1/49
 37 h-m-p  0.0009 0.0097  13.9889 CC     7821.556381  1 0.0008  2027 | 1/49
 38 h-m-p  0.0012 0.0347  10.0226 YC     7821.526339  1 0.0009  2080 | 1/49
 39 h-m-p  0.0045 0.1475   1.9594 CC     7821.502003  1 0.0036  2134 | 1/49
 40 h-m-p  0.0025 0.1197   2.8789 YC     7821.412111  1 0.0041  2187 | 1/49
 41 h-m-p  0.0028 0.0389   4.2372 +YYYC  7820.176567  3 0.0109  2243 | 1/49
 42 h-m-p  0.0006 0.0029  33.6996 +YCCC  7818.233817  3 0.0017  2301 | 1/49
 43 h-m-p  0.0012 0.0062  20.1654 YCC    7818.068906  2 0.0008  2356 | 1/49
 44 h-m-p  0.0016 0.0280   9.7513 CC     7818.014807  1 0.0013  2410 | 1/49
 45 h-m-p  0.0041 0.1454   3.1214 YC     7818.011517  1 0.0007  2463 | 1/49
 46 h-m-p  0.0023 0.1467   0.9580 YC     7818.010438  1 0.0014  2516 | 1/49
 47 h-m-p  0.0051 1.5146   0.2575 +CC    7817.991887  1 0.0256  2619 | 1/49
 48 h-m-p  0.0018 0.1257   3.6120 YC     7817.935799  1 0.0030  2720 | 1/49
 49 h-m-p  0.0027 0.0729   4.0180 YC     7817.767885  1 0.0052  2773 | 1/49
 50 h-m-p  0.0037 0.0445   5.6850 CC     7817.745797  1 0.0013  2827 | 1/49
 51 h-m-p  0.1965 1.9071   0.0377 YCC    7817.614288  2 0.4321  2882 | 1/49
 52 h-m-p  1.6000 8.0000   0.0048 CC     7817.541938  1 1.8342  2984 | 1/49
 53 h-m-p  1.6000 8.0000   0.0028 CC     7817.490570  1 2.0203  3086 | 1/49
 54 h-m-p  1.5197 8.0000   0.0037 CC     7817.478287  1 1.4054  3188 | 1/49
 55 h-m-p  1.6000 8.0000   0.0013 CC     7817.474691  1 1.9421  3290 | 1/49
 56 h-m-p  1.6000 8.0000   0.0008 C      7817.472869  0 1.7897  3390 | 1/49
 57 h-m-p  1.6000 8.0000   0.0006 C      7817.472513  0 1.4287  3490 | 1/49
 58 h-m-p  1.6000 8.0000   0.0003 C      7817.472341  0 2.1422  3590 | 1/49
 59 h-m-p  1.6000 8.0000   0.0002 +C     7817.471771  0 6.4966  3691 | 1/49
 60 h-m-p  1.6000 8.0000   0.0006 C      7817.471406  0 1.8740  3791 | 1/49
 61 h-m-p  1.6000 8.0000   0.0004 Y      7817.471341  0 1.1033  3891 | 1/49
 62 h-m-p  1.6000 8.0000   0.0001 C      7817.471334  0 1.3818  3991 | 1/49
 63 h-m-p  1.6000 8.0000   0.0000 C      7817.471332  0 1.6500  4091 | 1/49
 64 h-m-p  1.6000 8.0000   0.0000 C      7817.471332  0 1.5457  4191 | 1/49
 65 h-m-p  1.6000 8.0000   0.0000 Y      7817.471332  0 1.0314  4291 | 1/49
 66 h-m-p  0.8718 8.0000   0.0000 Y      7817.471332  0 1.8342  4391 | 1/49
 67 h-m-p  1.6000 8.0000   0.0000 Y      7817.471332  0 0.6558  4491 | 1/49
 68 h-m-p  0.2966 8.0000   0.0000 +C     7817.471332  0 1.0424  4592 | 1/49
 69 h-m-p  1.3137 8.0000   0.0000 ++     7817.471332  m 8.0000  4692 | 1/49
 70 h-m-p  1.6000 8.0000   0.0000 -----Y  7817.471332  0 0.0004  4797
Out..
lnL  = -7817.471332
4798 lfun, 4798 eigenQcodon, 225506 P(t)

Time used:  2:17
