
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 = 939
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,    309 patterns at    313 /    313 sites (100.0%),  0:00

Collecting fpatt[] & pose[],    309 patterns at    313 /    313 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
   301584 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)), Erinaceus_europaeus #1)));

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   25.283342
   2   22.323207
   3   21.483248
   4   21.472362
   5   21.469779
   6   21.469435
   7   21.469373
   8   21.469359
  4222176 bytes for conP, adjusted

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

    0.051326    0.055520    0.062849    0.026803    0.130251    0.066635    0.087559    0.083584    0.077769    0.030460    0.057728    0.041495    0.029814    0.179933    0.175855    0.045332    0.032882    0.022348    0.052285    0.067611    0.059382    0.070630    0.048553    0.117495    0.125075    0.146909    0.135674    0.042222    0.097214    0.053253    0.149869    0.070676    0.089741    0.094597    0.015785    0.129810    0.143339    0.094008    0.083292    0.026109    0.021374    0.067607    0.031617    0.051488    0.105062    0.062390    0.023759    0.081841    0.018306    0.080811    0.197652    0.000000    0.246687    0.148025    0.010271    0.022104    0.209936    0.159373    0.178762    0.145684

ntime & nrate & np:    57     3    60

Bounds (np=60):
   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   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 999.000000

np =    60
lnL0 = -9868.706889

Iterating by ming2
Initial: fx=  9868.706889
x=  0.05133  0.05552  0.06285  0.02680  0.13025  0.06664  0.08756  0.08358  0.07777  0.03046  0.05773  0.04150  0.02981  0.17993  0.17586  0.04533  0.03288  0.02235  0.05228  0.06761  0.05938  0.07063  0.04855  0.11750  0.12507  0.14691  0.13567  0.04222  0.09721  0.05325  0.14987  0.07068  0.08974  0.09460  0.01578  0.12981  0.14334  0.09401  0.08329  0.02611  0.02137  0.06761  0.03162  0.05149  0.10506  0.06239  0.02376  0.08184  0.01831  0.08081  0.19765  0.00000  0.24669  0.14803  0.01027  0.02210  0.20994  0.15937  0.17876  0.14568

  1 h-m-p  0.0000 0.0001 4974.5600 ++     9070.272511  m 0.0001    65 | 1/60
  2 h-m-p  0.0000 0.0001 1215.3549 ++     8960.115564  m 0.0001   128 | 1/60
  3 h-m-p  0.0000 0.0000 25056.8262 ++     8935.094554  m 0.0000   191 | 2/60
  4 h-m-p  0.0000 0.0000 507263.3573 +YCYYYYCCCC  8874.274556  9 0.0000   268 | 2/60
  5 h-m-p  0.0000 0.0000 3808.0629 ++     8835.465965  m 0.0000   331 | 3/60
  6 h-m-p  0.0000 0.0000 2601.1924 ++     8810.202776  m 0.0000   394 | 3/60
  7 h-m-p -0.0000 -0.0000 600.0891 
h-m-p:     -3.80570063e-21     -1.90285032e-20      6.00089122e+02  8810.202776
..  | 3/60
  8 h-m-p  0.0000 0.0001 1209.6409 ++     8766.615207  m 0.0001   517 | 2/60
  9 h-m-p  0.0000 0.0000 80500.5409 ++     8750.449156  m 0.0000   580 | 2/60
 10 h-m-p  0.0000 0.0000 9099.2961 ++     8749.126759  m 0.0000   643 | 2/60
 11 h-m-p  0.0000 0.0000 1881.1970 ++     8736.559661  m 0.0000   706 | 2/60
 12 h-m-p  0.0000 0.0000 1559.8161 +CCYYYYCCCC  8718.183505  9 0.0000   784 | 2/60
 13 h-m-p  0.0000 0.0000 9457.6050 ++     8634.317326  m 0.0000   847 | 2/60
 14 h-m-p  0.0000 0.0000 10778.6876 +YCCCC  8618.837252  4 0.0000   918 | 2/60
 15 h-m-p  0.0000 0.0000 4145.5893 +CYYCC  8600.774855  4 0.0000   988 | 2/60
 16 h-m-p  0.0000 0.0000 978.7262 +CYYCC  8595.661017  4 0.0000  1058 | 2/60
 17 h-m-p  0.0000 0.0000 9015.4195 +CYCCC  8549.309016  4 0.0000  1129 | 2/60
 18 h-m-p  0.0000 0.0001 1611.2290 ++     8515.980266  m 0.0001  1192 | 2/60
 19 h-m-p -0.0000 -0.0000 5368.0289 
h-m-p:     -3.89860497e-22     -1.94930248e-21      5.36802895e+03  8515.980266
..  | 2/60
 20 h-m-p  0.0000 0.0001 23939.5392 -YYCYYC  8508.787498  5 0.0000  1323 | 2/60
 21 h-m-p  0.0000 0.0000 1318.4136 ++     8504.467055  m 0.0000  1386 | 3/60
 22 h-m-p  0.0000 0.0000 638.7675 +YYCYYYC  8495.684826  6 0.0000  1457 | 3/60
 23 h-m-p  0.0000 0.0001 631.6740 YCCCC  8491.337195  4 0.0000  1527 | 3/60
 24 h-m-p  0.0000 0.0001 341.8243 +YCYC  8489.607749  3 0.0000  1595 | 3/60
 25 h-m-p  0.0000 0.0001 546.5138 CCCC   8488.571543  3 0.0000  1664 | 3/60
 26 h-m-p  0.0000 0.0004 277.8126 +YYC   8486.164737  2 0.0001  1730 | 3/60
 27 h-m-p  0.0000 0.0001 492.3385 +YCYC  8483.444677  3 0.0001  1798 | 3/60
 28 h-m-p  0.0000 0.0002 764.5006 +YCC   8479.398548  2 0.0001  1865 | 3/60
 29 h-m-p  0.0001 0.0005 713.0893 +YCCC  8471.916711  3 0.0003  1934 | 3/60
 30 h-m-p  0.0001 0.0004 394.4186 +YCCC  8467.582012  3 0.0002  2003 | 3/60
 31 h-m-p  0.0000 0.0002 501.9015 +YCCC  8465.117756  3 0.0001  2072 | 3/60
 32 h-m-p  0.0001 0.0008 412.6844 +YCC   8459.491100  2 0.0004  2139 | 3/60
 33 h-m-p  0.0000 0.0002 271.4793 +YCCC  8458.271125  3 0.0001  2208 | 3/60
 34 h-m-p  0.0001 0.0007 189.7034 CYC    8457.544984  2 0.0001  2274 | 3/60
 35 h-m-p  0.0003 0.0017  84.8205 CCC    8457.080047  2 0.0003  2341 | 3/60
 36 h-m-p  0.0003 0.0016  68.8161 YYC    8456.784095  2 0.0003  2406 | 3/60
 37 h-m-p  0.0004 0.0018  53.7204 YC     8456.665024  1 0.0002  2470 | 3/60
 38 h-m-p  0.0002 0.0055  48.5035 CY     8456.572341  1 0.0002  2535 | 3/60
 39 h-m-p  0.0002 0.0036  54.0932 CC     8456.484823  1 0.0002  2600 | 3/60
 40 h-m-p  0.0006 0.0061  20.1895 YC     8456.447326  1 0.0003  2664 | 3/60
 41 h-m-p  0.0002 0.0105  29.2791 CC     8456.406627  1 0.0003  2729 | 3/60
 42 h-m-p  0.0003 0.0060  32.9460 C      8456.369471  0 0.0003  2792 | 3/60
 43 h-m-p  0.0003 0.0107  26.9898 YC     8456.354439  1 0.0002  2856 | 3/60
 44 h-m-p  0.0002 0.0083  19.7704 CC     8456.339292  1 0.0003  2921 | 3/60
 45 h-m-p  0.0005 0.0329  10.1988 YC     8456.329929  1 0.0004  2985 | 3/60
 46 h-m-p  0.0003 0.0138  11.0321 CC     8456.318372  1 0.0005  3050 | 3/60
 47 h-m-p  0.0009 0.0260   6.1366 YC     8456.313965  1 0.0004  3114 | 3/60
 48 h-m-p  0.0005 0.0141   4.7470 CC     8456.310357  1 0.0004  3179 | 3/60
 49 h-m-p  0.0002 0.0531   9.3001 CC     8456.304676  1 0.0003  3244 | 3/60
 50 h-m-p  0.0008 0.0415   3.7530 CC     8456.296453  1 0.0010  3309 | 3/60
 51 h-m-p  0.0003 0.0144  11.4374 CC     8456.285465  1 0.0004  3374 | 3/60
 52 h-m-p  0.0009 0.0390   4.7303 CC     8456.259608  1 0.0014  3439 | 3/60
 53 h-m-p  0.0005 0.0378  12.5890 YC     8456.199376  1 0.0010  3503 | 3/60
 54 h-m-p  0.0012 0.0305  10.3836 CC     8456.094676  1 0.0014  3568 | 3/60
 55 h-m-p  0.0007 0.0079  22.1225 CCC    8455.941713  2 0.0007  3635 | 3/60
 56 h-m-p  0.0004 0.0057  45.2902 CC     8455.763424  1 0.0004  3700 | 3/60
 57 h-m-p  0.0009 0.0092  19.3474 YC     8455.232981  1 0.0019  3764 | 3/60
 58 h-m-p  0.0004 0.0022  63.8657 C      8454.862661  0 0.0004  3827 | 3/60
 59 h-m-p  0.0009 0.0044  31.2663 CC     8454.544154  1 0.0009  3892 | 3/60
 60 h-m-p  0.0012 0.0075  22.5152 YC     8454.418746  1 0.0007  3956 | 3/60
 61 h-m-p  0.0006 0.0072  25.2140 YC     8454.358438  1 0.0004  4020 | 3/60
 62 h-m-p  0.0013 0.0545   7.4045 C      8454.327315  0 0.0014  4083 | 3/60
 63 h-m-p  0.0016 0.0526   6.3164 YC     8454.314407  1 0.0010  4147 | 3/60
 64 h-m-p  0.0016 0.0561   4.0150 YC     8454.309448  1 0.0009  4211 | 3/60
 65 h-m-p  0.0030 0.4427   1.2131 YC     8454.307466  1 0.0016  4275 | 3/60
 66 h-m-p  0.0017 0.2611   1.1742 CC     8454.303700  1 0.0023  4340 | 3/60
 67 h-m-p  0.0023 0.2798   1.1560 YC     8454.284937  1 0.0051  4404 | 3/60
 68 h-m-p  0.0022 0.1164   2.7185 +YC    8454.162991  1 0.0062  4469 | 3/60
 69 h-m-p  0.0015 0.0322  11.3344 CC     8454.040500  1 0.0014  4534 | 3/60
 70 h-m-p  0.0020 0.0561   8.0739 YC     8453.988428  1 0.0015  4598 | 3/60
 71 h-m-p  0.0019 0.1019   6.2338 YC     8453.973443  1 0.0010  4662 | 3/60
 72 h-m-p  0.0139 0.7615   0.4478 YC     8453.972736  1 0.0024  4726 | 3/60
 73 h-m-p  0.0017 0.4304   0.6283 C      8453.971421  0 0.0022  4846 | 3/60
 74 h-m-p  0.0023 0.8076   0.6070 +C     8453.958251  0 0.0093  4967 | 3/60
 75 h-m-p  0.0018 0.0641   3.0775 YC     8453.913209  1 0.0035  5088 | 3/60
 76 h-m-p  0.0016 0.0324   6.7020 YC     8453.822550  1 0.0026  5152 | 3/60
 77 h-m-p  0.0020 0.0339   8.4651 CC     8453.798289  1 0.0008  5217 | 3/60
 78 h-m-p  0.0018 0.1269   3.7541 YC     8453.788057  1 0.0014  5281 | 3/60
 79 h-m-p  0.0142 0.3100   0.3676 Y      8453.787762  0 0.0024  5344 | 3/60
 80 h-m-p  0.0896 8.0000   0.0098 ++C    8453.693046  0 1.4330  5466 | 3/60
 81 h-m-p  1.6000 8.0000   0.0067 C      8453.673312  0 1.6988  5586 | 3/60
 82 h-m-p  1.6000 8.0000   0.0010 C      8453.671286  0 1.3975  5706 | 3/60
 83 h-m-p  1.6000 8.0000   0.0006 C      8453.670960  0 1.4643  5826 | 3/60
 84 h-m-p  1.6000 8.0000   0.0002 Y      8453.670943  0 1.2202  5946 | 3/60
 85 h-m-p  1.6000 8.0000   0.0000 C      8453.670942  0 1.5856  6066 | 3/60
 86 h-m-p  1.6000 8.0000   0.0000 Y      8453.670942  0 1.0541  6186 | 3/60
 87 h-m-p  1.6000 8.0000   0.0000 ------Y  8453.670942  0 0.0001  6312
Out..
lnL  = -8453.670942
6313 lfun, 12626 eigenQcodon, 359841 P(t)

Time used:  4:57
