
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

2 branch types are in tree. Stop if wrong.
Tree is 
((((((Mus_musculus, Rattus_norvegicus), ((Myodes_glareolus, Microtus_ochrogaster), Lemmus_lemmus)), Heterocephalus_glaber), (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
((((((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   22.601675
   2   19.934704
   3   19.177932
   4   19.174829
   5   19.174596
   6   19.174554
   7   19.174553
  3389648 bytes for conP, adjusted

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

    0.000000    0.057046    0.085653    0.137688    0.084638    0.085882    0.066637    0.088103    0.015573    0.085238    0.037239    0.058458    0.167733    0.116921    0.110366    0.111740    0.164287    0.046403    0.065986    0.006236    0.135201    0.086853    0.121232    0.054122    0.069492    0.136855    0.136215    0.076017    0.113522    0.049400    0.029085    0.032375    0.030275    0.067640    0.105855    0.053029    0.059107    0.069963    0.035670    0.068093    0.193258    0.018028    0.248555    0.135989    0.020712    0.033687    0.241434    0.130442    0.124651    0.172286

ntime & nrate & np:    47     3    50

Bounds (np=50):
   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 999.000000 999.000000 999.000000

np =    50
lnL0 = -9195.453154

Iterating by ming2
Initial: fx=  9195.453154
x=  0.00000  0.05705  0.08565  0.13769  0.08464  0.08588  0.06664  0.08810  0.01557  0.08524  0.03724  0.05846  0.16773  0.11692  0.11037  0.11174  0.16429  0.04640  0.06599  0.00624  0.13520  0.08685  0.12123  0.05412  0.06949  0.13686  0.13622  0.07602  0.11352  0.04940  0.02909  0.03237  0.03028  0.06764  0.10585  0.05303  0.05911  0.06996  0.03567  0.06809  0.19326  0.01803  0.24855  0.13599  0.02071  0.03369  0.24143  0.13044  0.12465  0.17229

  1 h-m-p  0.0000 0.0001 4703.2375 ++     8157.462591  m 0.0001    55 | 0/50
  2 h-m-p  0.0000 0.0000 44063.5513 ++     8093.372066  m 0.0000   108 | 0/50
  3 h-m-p  0.0000 0.0000 67434.2968 ++     8087.335942  m 0.0000   161 | 1/50
  4 h-m-p  0.0000 0.0000 2989.9506 ++     8081.730157  m 0.0000   214 | 1/50
  5 h-m-p  0.0000 0.0000 757.4085 ++     8080.606057  m 0.0000   267 | 2/50
  6 h-m-p  0.0000 0.0000 1643.7979 ++     8071.186619  m 0.0000   320 | 2/50
  7 h-m-p -0.0000 -0.0000 1897.5213 
h-m-p:     -0.00000000e+00     -0.00000000e+00      1.89752126e+03  8071.186619
..  | 2/50
  8 h-m-p  0.0000 0.0002 3295.2219 CYYCCC  8064.882628  5 0.0000   431 | 2/50
  9 h-m-p  0.0000 0.0002 671.8421 ++     8015.870157  m 0.0002   484 | 2/50
 10 h-m-p  0.0000 0.0000 4147.9196 +CCCC  7989.131674  3 0.0000   544 | 2/50
 11 h-m-p  0.0000 0.0001 2137.5053 ++     7961.206918  m 0.0001   597 | 2/50
 12 h-m-p  0.0000 0.0001 1737.4123 +CYCCC  7929.620360  4 0.0001   658 | 2/50
 13 h-m-p  0.0000 0.0001 929.6503 +CYYCYCCC  7917.046318  7 0.0001   723 | 2/50
 14 h-m-p  0.0000 0.0000 15121.9132 +YYYCCC  7898.490821  5 0.0000   784 | 2/50
 15 h-m-p  0.0000 0.0001 1973.9041 +YCCC  7884.177743  3 0.0001   843 | 2/50
 16 h-m-p  0.0000 0.0001 678.4068 +YYYYCC  7874.512992  5 0.0001   903 | 2/50
 17 h-m-p  0.0002 0.0009 235.3617 +CYCC  7861.907587  3 0.0007   962 | 2/50
 18 h-m-p  0.0000 0.0001 1311.7246 YCCC   7859.078594  3 0.0000  1020 | 2/50
 19 h-m-p  0.0001 0.0004 430.0063 YC     7855.329970  1 0.0001  1074 | 2/50
 20 h-m-p  0.0002 0.0010 306.2731 YCCCC  7848.902391  4 0.0004  1134 | 2/50
 21 h-m-p  0.0001 0.0006 551.4086 CYCCC  7847.225946  4 0.0001  1194 | 2/50
 22 h-m-p  0.0003 0.0034 148.9525 YCCC   7844.310071  3 0.0006  1252 | 2/50
 23 h-m-p  0.0006 0.0032  84.4884 CC     7843.020596  1 0.0006  1307 | 2/50
 24 h-m-p  0.0002 0.0010  66.8573 YCC    7842.782114  2 0.0002  1363 | 2/50
 25 h-m-p  0.0002 0.0025  76.7392 YC     7842.356530  1 0.0004  1417 | 2/50
 26 h-m-p  0.0007 0.0103  40.3930 C      7842.019824  0 0.0007  1470 | 2/50
 27 h-m-p  0.0011 0.0070  27.5988 YCC    7841.833221  2 0.0007  1526 | 2/50
 28 h-m-p  0.0008 0.0093  22.3481 CC     7841.628209  1 0.0009  1581 | 2/50
 29 h-m-p  0.0011 0.0126  19.3171 CYC    7841.381958  2 0.0010  1637 | 2/50
 30 h-m-p  0.0010 0.0092  20.8237 CCC    7840.798648  2 0.0015  1694 | 2/50
 31 h-m-p  0.0007 0.0060  47.1937 YCCC   7839.315643  3 0.0012  1752 | 2/50
 32 h-m-p  0.0008 0.0041  61.9192 CCCC   7837.092290  3 0.0011  1811 | 2/50
 33 h-m-p  0.0007 0.0034  51.2718 YCCCC  7833.639836  4 0.0014  1871 | 2/50
 34 h-m-p  0.0002 0.0012  77.3465 +YYCC  7830.346175  3 0.0009  1929 | 2/50
 35 h-m-p  0.0001 0.0006  68.6127 +CYC   7829.339934  2 0.0005  1986 | 2/50
 36 h-m-p  0.0002 0.0011  29.0665 YC     7829.177668  1 0.0004  2040 | 2/50
 37 h-m-p  0.0003 0.0013  17.9957 YC     7829.124165  1 0.0004  2094 | 2/50
 38 h-m-p  0.0016 0.0441   4.5859 CC     7829.074698  1 0.0022  2149 | 2/50
 39 h-m-p  0.0011 0.0291   9.3000 CC     7828.977473  1 0.0017  2204 | 2/50
 40 h-m-p  0.0010 0.0195  15.2811 CC     7828.829702  1 0.0012  2259 | 2/50
 41 h-m-p  0.0011 0.0148  16.8380 CC     7828.504723  1 0.0017  2314 | 2/50
 42 h-m-p  0.0010 0.0080  28.3681 CCC    7827.860489  2 0.0015  2371 | 2/50
 43 h-m-p  0.0019 0.0143  22.2067 YCC    7827.347573  2 0.0012  2427 | 2/50
 44 h-m-p  0.0015 0.0416  17.9829 +YCC   7825.455655  2 0.0045  2484 | 2/50
 45 h-m-p  0.0007 0.0035  58.7554 CCC    7824.478803  2 0.0009  2541 | 2/50
 46 h-m-p  0.0024 0.0144  20.8845 CC     7824.327940  1 0.0008  2596 | 2/50
 47 h-m-p  0.0025 0.0216   6.7433 CC     7824.307368  1 0.0009  2651 | 2/50
 48 h-m-p  0.0024 0.1573   2.4063 C      7824.290184  0 0.0024  2704 | 2/50
 49 h-m-p  0.0018 0.1097   3.1884 YC     7824.233368  1 0.0035  2758 | 2/50
 50 h-m-p  0.0027 0.0840   4.1556 +YC    7823.870012  1 0.0068  2813 | 2/50
 51 h-m-p  0.0018 0.0110  15.6134 YCCC   7822.706269  3 0.0032  2871 | 2/50
 52 h-m-p  0.0011 0.0054  44.4139 CCC    7821.487008  2 0.0012  2928 | 1/50
 53 h-m-p  0.0023 0.0129  23.3144 CY     7821.353451  1 0.0006  2983 | 1/50
 54 h-m-p  0.0001 0.0006  17.8484 +YC    7821.306859  1 0.0004  3038 | 1/50
 55 h-m-p  0.0029 0.1437   2.5519 CC     7821.302163  1 0.0011  3093 | 1/50
 56 h-m-p  0.0017 0.0546   1.7076 C      7821.297500  0 0.0018  3146 | 1/50
 57 h-m-p  0.0015 0.0988   2.0628 YC     7821.282515  1 0.0033  3200 | 1/50
 58 h-m-p  0.0070 0.4030   0.9620 +YC    7821.115234  1 0.0186  3255 | 1/50
 59 h-m-p  0.0013 0.0565  13.9208 +CC    7820.076998  1 0.0052  3360 | 1/50
 60 h-m-p  0.0063 0.0313   4.7306 -YC    7820.069352  1 0.0007  3415 | 1/50
 61 h-m-p  0.0562 8.0000   0.0560 ++YCC  7819.437987  2 1.4313  3473 | 1/50
 62 h-m-p  1.4434 7.2172   0.0346 YYC    7819.114172  2 1.2221  3577 | 1/50
 63 h-m-p  1.6000 8.0000   0.0119 CCC    7818.711752  2 1.9907  3683 | 1/50
 64 h-m-p  1.2014 6.6135   0.0197 CCC    7818.364059  2 1.8287  3789 | 1/50
 65 h-m-p  1.1551 8.0000   0.0313 CCC    7818.210377  2 1.3293  3895 | 1/50
 66 h-m-p  1.6000 8.0000   0.0091 CC     7818.099885  1 2.0901  3999 | 1/50
 67 h-m-p  1.6000 8.0000   0.0048 CC     7817.980968  1 2.4673  4103 | 1/50
 68 h-m-p  1.6000 8.0000   0.0068 YCC    7817.763981  2 2.7148  4208 | 1/50
 69 h-m-p  1.6000 8.0000   0.0069 CC     7817.581620  1 1.7552  4312 | 1/50
 70 h-m-p  1.6000 8.0000   0.0057 CCC    7817.492096  2 1.8549  4418 | 1/50
 71 h-m-p  1.6000 8.0000   0.0042 CC     7817.418910  1 2.4119  4522 | 1/50
 72 h-m-p  1.6000 8.0000   0.0027 CC     7817.374087  1 2.0673  4626 | 1/50
 73 h-m-p  1.6000 8.0000   0.0033 CC     7817.360505  1 1.8369  4730 | 1/50
 74 h-m-p  1.6000 8.0000   0.0010 C      7817.358140  0 1.5788  4832 | 1/50
 75 h-m-p  1.6000 8.0000   0.0006 C      7817.357793  0 1.5022  4934 | 1/50
 76 h-m-p  1.6000 8.0000   0.0001 C      7817.357748  0 1.3466  5036 | 1/50
 77 h-m-p  1.6000 8.0000   0.0001 Y      7817.357744  0 1.2144  5138 | 1/50
 78 h-m-p  1.6000 8.0000   0.0000 Y      7817.357743  0 1.0044  5240 | 1/50
 79 h-m-p  1.6000 8.0000   0.0000 C      7817.357743  0 1.4487  5342 | 1/50
 80 h-m-p  1.6000 8.0000   0.0000 ---C   7817.357743  0 0.0063  5447
Out..
lnL  = -7817.357743
5448 lfun, 10896 eigenQcodon, 256056 P(t)

Time used:  2:38
