
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 = 29  	ls = 918
Reading sequences, sequential format..
Reading seq # 1: Antrozous_pallidus       
Reading seq # 2: Eptesicus_fuscus       
Reading seq # 3: Ictidomys_tridecemlineatus       
Reading seq # 4: Marmota_flaviventris       
Reading seq # 5: Marmota_marmota       
Reading seq # 6: Marmota_monax       
Reading seq # 7: Myotis_lucifugus       
Reading seq # 8: Rhinolophus_ferrumequinum       
Reading seq # 9: Urocitellus_parryii       
Reading seq #10: Ursus_americanus       
Reading seq #11: Ursus_arctos       
Reading seq #12: Callorhinus_ursinus       
Reading seq #13: Heterocephalus_glaber       
Reading seq #14: Homo_sapiens       
Reading seq #15: Lemmus_lemmus       
Reading seq #16: Microtus_ochrogaster       
Reading seq #17: Mus_musculus       
Reading seq #18: Mustela_erminea       
Reading seq #19: Mustela_putorius_furo       
Reading seq #20: Myodes_glareolus       
Reading seq #21: Neovison_vison       
Reading seq #22: Ochotona_princeps       
Reading seq #23: Oryctolagus_cuniculus       
Reading seq #24: Phoca_vitulina       
Reading seq #25: Pteropus_vampyrus       
Reading seq #26: Rattus_norvegicus       
Reading seq #27: Sorex_araneus       
Reading seq #28: Talpa_europaea       
Reading seq #29: Talpa_occidentalis       
Sequences read..
Counting site patterns..  0:00

Compressing,    301 patterns at    306 /    306 sites (100.0%),  0:00

Collecting fpatt[] & pose[],    301 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

     3248 bytes for distance
   293776 bytes for conP
        0 bytes for fhK
  5000000 bytes for space

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

   1   44.967579
   2   42.638658
   3   42.415118
   4   42.402581
   5   42.402184
   6   30.849676
   7   16.960254
   8   15.464758
   9   15.028371
  10   14.280188
  11   13.571507
  12   13.410566
  13    9.919933
  14    9.767140
  15    9.654357
  16    9.654245
  17  1975211.462968
  18    9.654285
  19    9.654242
  20    9.650704
  21    9.539396
  22    9.539285
  23    9.492837
  24    9.466834
  25    9.466217
  26    9.466214
  27    9.466214
  28    9.466199
  29    9.462737
  30    9.416697
  31    9.160998
  32    9.160747
  33    9.158242
  34    9.158136
  35    9.158030
  36    9.157971
  37  1540781.022596
  38    9.177203
  39    9.157178
  40    9.156386
  41    9.156352
  42    9.156352
  43  2054315.778765
  44  1174783.260536
  45    9.156446
  46    9.156346
  47  1300831.305046
  48    9.207223
  49    9.156344
  3965976 bytes for conP, adjusted

    0.001717    0.029847    0.038816    0.018217    0.197888    0.053520    0.095406    0.116941    0.109367    0.040311    0.052317    0.046497    0.052095    0.205691    0.190632    0.053065    0.016138    0.026230    0.034260    0.047175    0.032265    0.036125    0.032553    0.119579    0.105009    0.194973    0.200150    0.000001    0.104079    0.011918    0.213707    0.087606    0.096894    0.089832    0.017302    0.158488    0.143960    0.113716    0.109629    0.026429    0.028063    0.010206    0.040561    0.032082    0.110118    0.009873    0.007449    0.048414    0.030051    0.043213    0.204081    0.364854    0.182661    0.011972    0.033116    2.356533    0.162904

ntime & nrate & np:    55     2    57

Bounds (np=57):
   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 999.000000 999.000000

np =    57
lnL0 = -8061.161455

Iterating by ming2
Initial: fx=  8061.161455
x=  0.00172  0.02985  0.03882  0.01822  0.19789  0.05352  0.09541  0.11694  0.10937  0.04031  0.05232  0.04650  0.05209  0.20569  0.19063  0.05307  0.01614  0.02623  0.03426  0.04718  0.03227  0.03612  0.03255  0.11958  0.10501  0.19497  0.20015  0.00000  0.10408  0.01192  0.21371  0.08761  0.09689  0.08983  0.01730  0.15849  0.14396  0.11372  0.10963  0.02643  0.02806  0.01021  0.04056  0.03208  0.11012  0.00987  0.00745  0.04841  0.03005  0.04321  0.20408  0.36485  0.18266  0.01197  0.03312  2.35653  0.16290

  1 h-m-p  0.0000 0.0000 2021.2077 ++     8026.907796  m 0.0000    62 | 1/57
  2 h-m-p  0.0000 0.0001 1036.3405 ++     7993.276686  m 0.0001   122 | 2/57
  3 h-m-p  0.0000 0.0000 6911.2059 ++     7983.272515  m 0.0000   182 | 3/57
  4 h-m-p  0.0000 0.0000 1708.7750 +CYYYYC  7963.888409  5 0.0000   249 | 3/57
  5 h-m-p  0.0000 0.0000 1690.9980 +YYYYC  7961.595532  4 0.0000   314 | 3/57
  6 h-m-p  0.0000 0.0000 1653.3713 +YCCC  7950.936395  3 0.0000   380 | 3/57
  7 h-m-p  0.0001 0.0003 1034.2057 YCCC   7937.557515  3 0.0001   445 | 3/57
  8 h-m-p  0.0001 0.0005 325.1084 YCCC   7929.906463  3 0.0002   510 | 3/57
  9 h-m-p  0.0001 0.0003 268.9475 +YCCC  7926.689160  3 0.0002   576 | 3/57
 10 h-m-p  0.0002 0.0011 216.7465 CCC    7924.802801  2 0.0002   640 | 3/57
 11 h-m-p  0.0001 0.0003 170.4263 CYCCC  7924.068628  4 0.0001   707 | 3/57
 12 h-m-p  0.0002 0.0011  81.8773 CCC    7923.426649  2 0.0003   771 | 3/57
 13 h-m-p  0.0003 0.0023  82.6231 CCC    7922.957790  2 0.0003   835 | 3/57
 14 h-m-p  0.0003 0.0020  90.9743 CCC    7922.628401  2 0.0002   899 | 3/57
 15 h-m-p  0.0003 0.0036  77.6596 CC     7922.329577  1 0.0003   961 | 3/57
 16 h-m-p  0.0004 0.0021  56.8962 YCC    7922.151612  2 0.0003  1024 | 3/57
 17 h-m-p  0.0005 0.0048  31.9496 YC     7922.059488  1 0.0003  1085 | 3/57
 18 h-m-p  0.0004 0.0033  29.6580 CC     7921.988804  1 0.0003  1147 | 3/57
 19 h-m-p  0.0005 0.0087  19.1964 CC     7921.914492  1 0.0005  1209 | 3/57
 20 h-m-p  0.0003 0.0092  34.6688 +YC    7921.721367  1 0.0007  1271 | 3/57
 21 h-m-p  0.0004 0.0034  62.6563 CCC    7921.503647  2 0.0004  1335 | 3/57
 22 h-m-p  0.0004 0.0048  64.0575 YC     7921.045672  1 0.0008  1396 | 3/57
 23 h-m-p  0.0003 0.0037 159.1465 CCC    7920.461746  2 0.0004  1460 | 3/57
 24 h-m-p  0.0005 0.0023  95.8360 CYC    7920.068396  2 0.0004  1523 | 3/57
 25 h-m-p  0.0004 0.0022  94.5679 CCC    7919.503380  2 0.0006  1587 | 3/57
 26 h-m-p  0.0006 0.0031 103.1494 YCC    7919.091595  2 0.0004  1650 | 3/57
 27 h-m-p  0.0004 0.0043  94.1050 CC     7918.660512  1 0.0004  1712 | 3/57
 28 h-m-p  0.0006 0.0035  69.0041 YCC    7918.347159  2 0.0004  1775 | 3/57
 29 h-m-p  0.0004 0.0038  66.8392 CCC    7917.783803  2 0.0006  1839 | 3/57
 30 h-m-p  0.0005 0.0027  57.4327 YC     7917.414424  1 0.0004  1900 | 3/57
 31 h-m-p  0.0006 0.0035  42.3485 YYC    7917.016187  2 0.0005  1962 | 3/57
 32 h-m-p  0.0005 0.0034  42.0004 CCC    7916.435360  2 0.0005  2026 | 3/57
 33 h-m-p  0.0006 0.0033  38.3768 CCCC   7914.903499  3 0.0010  2092 | 3/57
 34 h-m-p  0.0002 0.0008 126.2639 +YCCC  7912.319717  3 0.0004  2158 | 3/57
 35 h-m-p  0.0002 0.0009 136.8302 YCCCC  7909.589587  4 0.0004  2225 | 3/57
 36 h-m-p  0.0001 0.0005 144.3777 YCCCC  7908.094665  4 0.0002  2292 | 3/57
 37 h-m-p  0.0001 0.0004 149.9945 CYCCC  7907.248035  4 0.0001  2359 | 3/57
 38 h-m-p  0.0001 0.0004  64.4245 YCCCC  7907.002045  4 0.0001  2426 | 3/57
 39 h-m-p  0.0002 0.0032  42.2029 YC     7906.778831  1 0.0004  2487 | 3/57
 40 h-m-p  0.0009 0.0101  16.6110 YC     7906.719941  1 0.0005  2548 | 3/57
 41 h-m-p  0.0006 0.0074  13.0878 YC     7906.689421  1 0.0004  2609 | 3/57
 42 h-m-p  0.0006 0.0138   8.8674 YC     7906.624362  1 0.0011  2670 | 3/57
 43 h-m-p  0.0012 0.0290   8.2856 CC     7906.462868  1 0.0017  2732 | 3/57
 44 h-m-p  0.0009 0.0091  16.1190 CCC    7905.960946  2 0.0015  2796 | 3/57
 45 h-m-p  0.0005 0.0081  48.4031 YC     7904.506797  1 0.0011  2857 | 3/57
 46 h-m-p  0.0008 0.0083  65.9220 YCCC   7901.671414  3 0.0014  2922 | 3/57
 47 h-m-p  0.0011 0.0057  61.4348 YCC    7900.450051  2 0.0008  2985 | 3/57
 48 h-m-p  0.0023 0.0192  22.6551 CC     7900.304029  1 0.0006  3047 | 3/57
 49 h-m-p  0.0019 0.0738   7.7807 YC     7900.261149  1 0.0015  3108 | 3/57
 50 h-m-p  0.0048 0.3015   2.3776 CC     7900.255965  1 0.0010  3170 | 3/57
 51 h-m-p  0.0019 0.5809   1.3033 +CC    7900.208099  1 0.0088  3233 | 3/57
 52 h-m-p  0.0038 0.1532   2.9948 YC     7899.972681  1 0.0068  3294 | 3/57
 53 h-m-p  0.0020 0.0230  10.1822 CCC    7899.167351  2 0.0032  3358 | 3/57
 54 h-m-p  0.0013 0.0083  25.8063 CC     7898.352080  1 0.0014  3420 | 3/57
 55 h-m-p  0.0018 0.0193  19.7280 YC     7898.184536  1 0.0009  3481 | 3/57
 56 h-m-p  0.0143 0.2784   1.2262 YC     7898.181758  1 0.0025  3542 | 3/57
 57 h-m-p  0.0457 2.6055   0.0658 ++YYC  7897.826306  2 0.6160  3606 | 3/57
 58 h-m-p  1.6000 8.0000   0.0129 YC     7897.646324  1 1.2213  3721 | 3/57
 59 h-m-p  0.9902 8.0000   0.0159 C      7897.585723  0 1.0077  3835 | 3/57
 60 h-m-p  0.9445 8.0000   0.0169 YC     7897.558263  1 0.6366  3950 | 3/57
 61 h-m-p  1.6000 8.0000   0.0043 C      7897.543619  0 1.5271  4064 | 3/57
 62 h-m-p  1.6000 8.0000   0.0015 C      7897.538838  0 1.5138  4178 | 3/57
 63 h-m-p  1.3140 8.0000   0.0017 CC     7897.536158  1 1.6502  4294 | 3/57
 64 h-m-p  1.6000 8.0000   0.0007 Y      7897.535734  0 1.2781  4408 | 3/57
 65 h-m-p  1.6000 8.0000   0.0002 C      7897.535578  0 1.7227  4522 | 3/57
 66 h-m-p  1.2712 8.0000   0.0003 C      7897.535491  0 1.8302  4636 | 3/57
 67 h-m-p  1.6000 8.0000   0.0002 C      7897.535454  0 1.7599  4750 | 3/57
 68 h-m-p  1.6000 8.0000   0.0001 C      7897.535446  0 1.5681  4864 | 3/57
 69 h-m-p  1.6000 8.0000   0.0000 C      7897.535444  0 1.6107  4978 | 3/57
 70 h-m-p  1.6000 8.0000   0.0000 C      7897.535443  0 1.8048  5092 | 3/57
 71 h-m-p  1.6000 8.0000   0.0000 C      7897.535443  0 1.6926  5206 | 3/57
 72 h-m-p  1.6000 8.0000   0.0000 C      7897.535443  0 1.3616  5320 | 3/57
 73 h-m-p  1.6000 8.0000   0.0000 C      7897.535443  0 1.3398  5434 | 3/57
 74 h-m-p  1.6000 8.0000   0.0000 Y      7897.535443  0 0.8411  5548 | 3/57
 75 h-m-p  1.2538 8.0000   0.0000 Y      7897.535443  0 0.3135  5662 | 3/57
 76 h-m-p  0.2802 8.0000   0.0000 ---C   7897.535443  0 0.0011  5779
Out..
lnL  = -7897.535443
5780 lfun, 5780 eigenQcodon, 317900 P(t)

Time used:  3:11
