
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

2 branch types are in tree. Stop if wrong.
Tree is 
(((((((Mus_musculus, Rattus_norvegicus), ((Myodes_glareolus, Microtus_ochrogaster), Lemmus_lemmus)), Heterocephalus_glaber), ((Marmota_flaviventris #1, (Marmota_marmota #1, Marmota_monax #1)), (Urocitellus_parryii #1, Ictidomys_tridecemlineatus #1))), (Oryctolagus_cuniculus, Ochotona_princeps)), Homo_sapiens), ((((Eptesicus_fuscus #1, Antrozous_pallidus #1, Myotis_lucifugus #1), (Pteropus_vampyrus, Rhinolophus_ferrumequinum #1)), (((Mustela_putorius_furo, Mustela_erminea), Neovison_vison), ((Ursus_arctos #1, Ursus_americanus #1), (Phoca_vitulina, Callorhinus_ursinus)))), (Sorex_araneus, (Talpa_europaea, Talpa_occidentalis))));

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   29.916357
   2   29.048225
   3   28.780368
   4   28.771944
   5   28.771101
   6   28.144478
   7   26.232239
   8   25.804412
   9   25.794378
  10   25.793625
  11   25.718535
  12   25.585523
  13   25.453222
  14   25.411547
  15   23.690831
  16   23.652143
  17   23.646985
  18   23.645761
  19   23.645598
  20   23.645211
  21   23.643580
  22   23.643558
  23   23.643340
  24   23.640440
  25   23.636574
  26   23.585118
  27   23.584901
  28   23.584900
  29  1472597.837399
  30  1776601.007307
  31  1299423.847573
  32  1234718.389869
  33  1504676.713370
  34   23.900149
  35   23.584900
  3965976 bytes for conP, adjusted

    0.000000    0.036904    0.061272    0.020384    0.139321    0.040729    0.095997    0.072869    0.062249    0.037422    0.046511    0.051607    0.070558    0.193688    0.190570    0.064624    0.028553    0.029096    0.019954    0.053197    0.026884    0.049242    0.042695    0.118097    0.094274    0.118908    0.155449    0.004751    0.072869    0.014628    0.182421    0.064793    0.088278    0.085605    0.032255    0.146422    0.119402    0.068246    0.087092    0.041473    0.049363    0.055931    0.019213    0.067172    0.076250    0.013923    0.024350    0.028567    0.057483    0.041049    0.154354    0.235625    0.124700    0.042477    0.040338    0.169924    0.132513    0.178750

ntime & nrate & np:    55     3    58

Bounds (np=58):
   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   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 999.000000

np =    58
lnL0 = -9172.428627

Iterating by ming2
Initial: fx=  9172.428627
x=  0.00000  0.03690  0.06127  0.02038  0.13932  0.04073  0.09600  0.07287  0.06225  0.03742  0.04651  0.05161  0.07056  0.19369  0.19057  0.06462  0.02855  0.02910  0.01995  0.05320  0.02688  0.04924  0.04269  0.11810  0.09427  0.11891  0.15545  0.00475  0.07287  0.01463  0.18242  0.06479  0.08828  0.08560  0.03225  0.14642  0.11940  0.06825  0.08709  0.04147  0.04936  0.05593  0.01921  0.06717  0.07625  0.01392  0.02435  0.02857  0.05748  0.04105  0.15435  0.23562  0.12470  0.04248  0.04034  0.16992  0.13251  0.17875

  1 h-m-p  0.0000 0.0000 3928.1210 ++     8697.923244  m 0.0000    63 | 1/58
  2 h-m-p  0.0000 0.0000 1505.9653 ++     8661.144676  m 0.0000   124 | 2/58
  3 h-m-p  0.0000 0.0000 772.5675 ++     8648.091456  m 0.0000   185 | 3/58
  4 h-m-p  0.0000 0.0003 509.8125 +YYCC  8634.609200  3 0.0002   251 | 3/58
  5 h-m-p  0.0000 0.0002 213.2842 +YYCCC  8632.350435  4 0.0001   319 | 3/58
  6 h-m-p  0.0001 0.0023 175.3974 CYC    8631.095260  2 0.0001   383 | 3/58
  7 h-m-p  0.0002 0.0009 107.7322 CCCC   8629.752914  3 0.0003   450 | 3/58
  8 h-m-p  0.0002 0.0010  95.5176 CCC    8628.842126  2 0.0003   515 | 3/58
  9 h-m-p  0.0004 0.0022  47.4376 CCCC   8627.135696  3 0.0007   582 | 3/58
 10 h-m-p  0.0002 0.0012  78.3100 +YCCC  8622.375408  3 0.0007   649 | 3/58
 11 h-m-p  0.0002 0.0009 190.2482 YCYC   8614.714121  3 0.0004   714 | 3/58
 12 h-m-p  0.0001 0.0007 161.3344 +YYYCC  8595.574873  4 0.0005   781 | 3/58
 13 h-m-p  0.0001 0.0003 386.5204 +CYYCYCCC  8567.518118  7 0.0002   854 | 3/58
 14 h-m-p  0.0000 0.0000 702.0183 +YYYYYCCCC  8564.339459  8 0.0000   927 | 3/58
 15 h-m-p  0.0000 0.0000 2772.3815 ++     8561.868570  m 0.0000   988 | 3/58
 16 h-m-p -0.0000 -0.0000 309.6473 
h-m-p:     -9.20538906e-23     -4.60269453e-22      3.09647325e+02  8561.868570
..  | 3/58
 17 h-m-p  0.0000 0.0001 2005.9042 ++     8355.120199  m 0.0001  1107 | 3/58
 18 h-m-p  0.0000 0.0000 194249.9138 +YCYCCC  8295.017654  5 0.0000  1177 | 3/58
 19 h-m-p  0.0000 0.0001 4530.8610 YCCC   8253.504312  3 0.0001  1243 | 3/58
 20 h-m-p  0.0000 0.0001 920.5424 +CYCYYYC  8215.334247  6 0.0001  1313 | 3/58
 21 h-m-p  0.0000 0.0000 5566.6626 ++     8185.949381  m 0.0000  1374 | 3/58
 22 h-m-p  0.0000 0.0000 5638.7092 +YYYCCC  8147.228996  5 0.0000  1443 | 3/58
 23 h-m-p  0.0000 0.0000 7150.8439 ++     8130.547626  m 0.0000  1504 | 3/58
 24 h-m-p  0.0000 0.0000 1975.2924 
h-m-p:      1.84905148e-21      9.24525739e-21      1.97529239e+03  8130.547626
..  | 3/58
 25 h-m-p  0.0000 0.0001 1169.1671 ++     8057.731468  m 0.0001  1623 | 3/58
 26 h-m-p  0.0000 0.0000 14261.5485 +CCCC  8049.730684  3 0.0000  1691 | 3/58
 27 h-m-p  0.0000 0.0000 1152.9086 +YYYCYCYC  8036.574144  7 0.0000  1763 | 3/58
 28 h-m-p  0.0000 0.0000 4856.0870 ++     8020.455751  m 0.0000  1824 | 3/58
 29 h-m-p  0.0000 0.0000 1409.2413 
h-m-p:      7.54612559e-22      3.77306279e-21      1.40924126e+03  8020.455751
..  | 3/58
 30 h-m-p  0.0000 0.0001 784.0431 +YCYCCC  7993.707152  5 0.0001  1953 | 3/58
 31 h-m-p  0.0000 0.0000 1789.9160 +YYYCC  7985.865259  4 0.0000  2020 | 3/58
 32 h-m-p  0.0000 0.0000 729.8931 +YYYYCYCCC  7982.321091  8 0.0000  2093 | 3/58
 33 h-m-p  0.0000 0.0000 1016.4697 +YYYYC  7975.032745  4 0.0000  2159 | 3/58
 34 h-m-p  0.0000 0.0001 853.5146 +YCCC  7969.914788  3 0.0000  2226 | 3/58
 35 h-m-p  0.0000 0.0001 594.5714 YCYCCC  7965.143520  5 0.0001  2295 | 3/58
 36 h-m-p  0.0000 0.0001 569.1430 YCCCC  7962.412055  4 0.0001  2363 | 3/58
 37 h-m-p  0.0000 0.0005 855.1205 +YCYYCC  7934.806187  5 0.0004  2433 | 3/58
 38 h-m-p  0.0000 0.0001 7287.2040 YCCCC  7919.511081  4 0.0000  2501 | 3/58
 39 h-m-p  0.0000 0.0001 507.5677 +YYCCC  7915.968917  4 0.0001  2569 | 3/58
 40 h-m-p  0.0000 0.0002 710.7702 YCCC   7913.163369  3 0.0001  2635 | 3/58
 41 h-m-p  0.0000 0.0002 530.4492 YCYC   7911.542576  3 0.0001  2700 | 3/58
 42 h-m-p  0.0000 0.0002 376.5671 YC     7909.589491  1 0.0001  2762 | 3/58
 43 h-m-p  0.0002 0.0010 152.0827 CCCC   7908.367761  3 0.0002  2829 | 3/58
 44 h-m-p  0.0002 0.0013 154.1719 CCC    7906.941365  2 0.0003  2894 | 3/58
 45 h-m-p  0.0003 0.0014 113.8026 YYC    7906.394429  2 0.0002  2957 | 3/58
 46 h-m-p  0.0002 0.0021 130.1766 CYC    7905.940414  2 0.0002  3021 | 3/58
 47 h-m-p  0.0002 0.0013 106.4600 YCC    7905.680039  2 0.0002  3085 | 3/58
 48 h-m-p  0.0004 0.0023  41.2842 YCC    7905.533242  2 0.0003  3149 | 3/58
 49 h-m-p  0.0003 0.0039  43.9533 YC     7905.449120  1 0.0002  3211 | 3/58
 50 h-m-p  0.0003 0.0020  33.7239 YC     7905.405410  1 0.0002  3273 | 3/58
 51 h-m-p  0.0002 0.0056  25.5339 CC     7905.368468  1 0.0003  3336 | 3/58
 52 h-m-p  0.0002 0.0053  33.4977 CC     7905.341150  1 0.0002  3399 | 3/58
 53 h-m-p  0.0003 0.0067  18.8037 CC     7905.315834  1 0.0003  3462 | 3/58
 54 h-m-p  0.0003 0.0072  20.3873 CC     7905.281678  1 0.0004  3525 | 3/58
 55 h-m-p  0.0009 0.0123  10.5052 YC     7905.260073  1 0.0006  3587 | 3/58
 56 h-m-p  0.0005 0.0157  11.9793 CC     7905.239540  1 0.0005  3650 | 3/58
 57 h-m-p  0.0004 0.0127  12.9777 CC     7905.219467  1 0.0004  3713 | 3/58
 58 h-m-p  0.0007 0.0758   6.7495 YC     7905.150921  1 0.0017  3775 | 3/58
 59 h-m-p  0.0005 0.0026  21.3908 YCC    7905.103537  2 0.0003  3839 | 3/58
 60 h-m-p  0.0004 0.0181  16.6760 +YC    7904.918613  1 0.0010  3902 | 3/58
 61 h-m-p  0.0007 0.0101  26.0491 CCC    7904.566878  2 0.0009  3967 | 3/58
 62 h-m-p  0.0009 0.0043  26.7601 YCCC   7903.541472  3 0.0015  4033 | 3/58
 63 h-m-p  0.0005 0.0032  77.7277 YCC    7901.341691  2 0.0010  4097 | 3/58
 64 h-m-p  0.0005 0.0026  68.5724 YCCC   7899.351664  3 0.0010  4163 | 3/58
 65 h-m-p  0.0005 0.0027  47.3679 CCC    7898.775342  2 0.0006  4228 | 3/58
 66 h-m-p  0.0002 0.0009  82.2131 YCCC   7898.274589  3 0.0003  4294 | 3/58
 67 h-m-p  0.0009 0.0082  28.3953 CYC    7897.997996  2 0.0009  4358 | 3/58
 68 h-m-p  0.0005 0.0072  50.8172 CCC    7897.786858  2 0.0005  4423 | 3/58
 69 h-m-p  0.0013 0.0223  18.2989 YC     7897.691543  1 0.0009  4485 | 3/58
 70 h-m-p  0.0011 0.0140  14.8219 YC     7897.655131  1 0.0006  4547 | 3/58
 71 h-m-p  0.0013 0.0355   6.8228 YC     7897.639658  1 0.0009  4609 | 3/58
 72 h-m-p  0.0015 0.0444   4.1745 YC     7897.633739  1 0.0009  4671 | 3/58
 73 h-m-p  0.0025 0.1289   1.4478 YC     7897.631677  1 0.0011  4733 | 3/58
 74 h-m-p  0.0005 0.1205   3.0619 YC     7897.626219  1 0.0011  4795 | 3/58
 75 h-m-p  0.0028 0.2297   1.2178 YC     7897.597289  1 0.0061  4857 | 3/58
 76 h-m-p  0.0016 0.1257   4.5482 +CC    7897.399096  1 0.0055  4921 | 3/58
 77 h-m-p  0.0011 0.0338  22.3803 YC     7896.996933  1 0.0019  4983 | 3/58
 78 h-m-p  0.0021 0.0192  20.4278 YC     7896.735203  1 0.0016  5045 | 3/58
 79 h-m-p  0.0046 0.0503   7.2891 YC     7896.713702  1 0.0009  5107 | 3/58
 80 h-m-p  0.0020 0.0783   3.2721 YC     7896.708921  1 0.0010  5169 | 3/58
 81 h-m-p  0.0020 0.2054   1.6041 YC     7896.707337  1 0.0012  5231 | 3/58
 82 h-m-p  0.0033 0.5986   0.5610 C      7896.705316  0 0.0034  5292 | 3/58
 83 h-m-p  0.0015 0.4323   1.2488 +YC    7896.693608  1 0.0046  5410 | 3/58
 84 h-m-p  0.0031 0.1743   1.8483 +YC    7896.505620  1 0.0212  5473 | 3/58
 85 h-m-p  0.0024 0.0181  16.1884 YC     7896.372400  1 0.0018  5535 | 3/58
 86 h-m-p  0.0282 0.3418   1.0547 -YC    7896.371718  1 0.0011  5598 | 3/58
 87 h-m-p  0.0657 8.0000   0.0182 ++C    7896.312674  0 1.0134  5661 | 3/58
 88 h-m-p  1.6000 8.0000   0.0020 CC     7896.283884  1 2.2605  5779 | 3/58
 89 h-m-p  1.5596 8.0000   0.0029 CC     7896.278398  1 1.3433  5897 | 3/58
 90 h-m-p  1.6000 8.0000   0.0005 CC     7896.276590  1 2.2352  6015 | 3/58
 91 h-m-p  1.6000 8.0000   0.0006 C      7896.276152  0 1.4430  6131 | 3/58
 92 h-m-p  1.6000 8.0000   0.0003 C      7896.276121  0 1.5709  6247 | 3/58
 93 h-m-p  1.6000 8.0000   0.0001 Y      7896.276119  0 1.2573  6363 | 3/58
 94 h-m-p  1.6000 8.0000   0.0000 Y      7896.276119  0 1.0584  6479 | 3/58
 95 h-m-p  1.6000 8.0000   0.0000 C      7896.276119  0 2.2804  6595 | 3/58
 96 h-m-p  1.6000 8.0000   0.0000 C      7896.276119  0 0.4000  6711 | 3/58
 97 h-m-p  0.2937 8.0000   0.0000 Y      7896.276119  0 0.1576  6827 | 3/58
 98 h-m-p  0.1036 8.0000   0.0000 ---Y   7896.276119  0 0.0007  6946
Out..
lnL  = -7896.276119
6947 lfun, 13894 eigenQcodon, 382085 P(t)

Time used:  3:54
