
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 = 28  	ls = 918
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: Callorhinus_ursinus       
Reading seq #12: Heterocephalus_glaber       
Reading seq #13: Homo_sapiens       
Reading seq #14: Lemmus_lemmus       
Reading seq #15: Microtus_ochrogaster       
Reading seq #16: Mus_musculus       
Reading seq #17: Mustela_erminea       
Reading seq #18: Mustela_putorius_furo       
Reading seq #19: Myodes_glareolus       
Reading seq #20: Neovison_vison       
Reading seq #21: Ochotona_princeps       
Reading seq #22: Oryctolagus_cuniculus       
Reading seq #23: Phoca_vitulina       
Reading seq #24: Pteropus_vampyrus       
Reading seq #25: Rattus_norvegicus       
Reading seq #26: Sorex_araneus       
Reading seq #27: Talpa_europaea       
Reading seq #28: 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

     3024 bytes for distance
   293776 bytes for conP
        0 bytes for fhK
  5000000 bytes for space

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

   1   24.903546
   2   22.699355
   3   22.634525
   4   22.623014
   5   22.621478
   6   22.621273
   7   22.621268
  3819088 bytes for conP, adjusted

    0.047713    0.056918    0.030920    0.065018    0.160164    0.086537    0.088921    0.089204    0.088063    0.076174    0.068024    0.029167    0.046505    0.154643    0.156484    0.053468    0.041801    0.022423    0.056290    0.049912    0.050254    0.065204    0.021760    0.085770    0.126156    0.156252    0.182533    0.020477    0.068172    0.006550    0.170532    0.047944    0.089737    0.050852    0.049343    0.132586    0.120351    0.109913    0.065235    0.028164    0.025042    0.025917    0.036445    0.053871    0.027223    0.067890    0.178746    0.000000    0.218558    0.122884    0.054574    0.031759    0.247431    2.114678    0.167682

ntime & nrate & np:    53     2    55

Bounds (np=55):
   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 999.000000 999.000000

np =    55
lnL0 = -8535.627216

Iterating by ming2
Initial: fx=  8535.627216
x=  0.04771  0.05692  0.03092  0.06502  0.16016  0.08654  0.08892  0.08920  0.08806  0.07617  0.06802  0.02917  0.04650  0.15464  0.15648  0.05347  0.04180  0.02242  0.05629  0.04991  0.05025  0.06520  0.02176  0.08577  0.12616  0.15625  0.18253  0.02048  0.06817  0.00655  0.17053  0.04794  0.08974  0.05085  0.04934  0.13259  0.12035  0.10991  0.06523  0.02816  0.02504  0.02592  0.03644  0.05387  0.02722  0.06789  0.17875  0.00000  0.21856  0.12288  0.05457  0.03176  0.24743  2.11468  0.16768

  1 h-m-p  0.0000 0.0001 2162.0981 ++     8393.602764  m 0.0001    60 | 1/55
  2 h-m-p  0.0000 0.0001 1076.9664 ++     8335.169740  m 0.0001   118 | 1/55
  3 h-m-p  0.0000 0.0000 5139.3251 ++     8324.609090  m 0.0000   176 | 2/55
  4 h-m-p  0.0000 0.0000 6096.1314 +YYYCYCCC  8298.376370  7 0.0000   245 | 2/55
  5 h-m-p  0.0000 0.0000 4462.7638 ++     8291.552868  m 0.0000   303 | 2/55
  6 h-m-p  0.0000 0.0000 1577.4644 
h-m-p:      1.23750816e-21      6.18754081e-21      1.57746440e+03  8291.552868
..  | 2/55
  7 h-m-p  0.0000 0.0001 836.9967 +CCCC  8283.111358  3 0.0000   423 | 2/55
  8 h-m-p  0.0000 0.0001 521.3290 +YYCYYCCC  8271.659826  7 0.0001   492 | 2/55
  9 h-m-p  0.0000 0.0000 7742.5967 ++     8261.556865  m 0.0000   550 | 2/55
 10 h-m-p  0.0000 0.0000 5136.1390 +YYCYCCC  8248.207083  6 0.0000   618 | 2/55
 11 h-m-p  0.0000 0.0000 10280.4290 +CYC   8232.826657  2 0.0000   680 | 2/55
 12 h-m-p  0.0000 0.0001 3352.5067 YYCCC  8221.236938  4 0.0000   744 | 2/55
 13 h-m-p  0.0000 0.0001 393.0370 +CYC   8215.763877  2 0.0001   806 | 2/55
 14 h-m-p  0.0000 0.0002 211.3499 ++     8212.880091  m 0.0002   864 | 2/55
 15 h-m-p  0.0001 0.0006 215.9155 CCC    8211.263925  2 0.0002   926 | 2/55
 16 h-m-p  0.0001 0.0007 191.9841 CC     8209.900758  1 0.0002   986 | 2/55
 17 h-m-p  0.0001 0.0003 145.9213 YCCC   8209.322512  3 0.0001  1049 | 2/55
 18 h-m-p  0.0001 0.0007  85.9861 YCC    8208.854292  2 0.0003  1110 | 2/55
 19 h-m-p  0.0003 0.0015  86.8074 YCC    8208.561267  2 0.0002  1171 | 2/55
 20 h-m-p  0.0002 0.0024  86.8479 C      8208.315109  0 0.0002  1229 | 2/55
 21 h-m-p  0.0002 0.0008 101.1619 CCC    8208.090120  2 0.0002  1291 | 2/55
 22 h-m-p  0.0002 0.0010  61.3516 CC     8207.951106  1 0.0002  1351 | 2/55
 23 h-m-p  0.0002 0.0025  71.6445 CC     8207.802628  1 0.0002  1411 | 2/55
 24 h-m-p  0.0004 0.0076  40.5851 CC     8207.675511  1 0.0004  1471 | 2/55
 25 h-m-p  0.0003 0.0031  63.1999 CC     8207.581550  1 0.0002  1531 | 2/55
 26 h-m-p  0.0003 0.0040  55.1872 CC     8207.504726  1 0.0002  1591 | 2/55
 27 h-m-p  0.0002 0.0046  69.7395 YC     8207.370567  1 0.0004  1650 | 2/55
 28 h-m-p  0.0002 0.0010  82.3923 CY     8207.284527  1 0.0002  1710 | 2/55
 29 h-m-p  0.0004 0.0123  42.9622 CC     8207.182625  1 0.0005  1770 | 2/55
 30 h-m-p  0.0005 0.0023  49.5992 CC     8207.143877  1 0.0002  1830 | 2/55
 31 h-m-p  0.0002 0.0041  54.6761 CC     8207.090619  1 0.0003  1890 | 2/55
 32 h-m-p  0.0006 0.0159  22.1438 CC     8207.053643  1 0.0005  1950 | 2/55
 33 h-m-p  0.0008 0.0052  14.7214 YC     8207.037679  1 0.0004  2009 | 2/55
 34 h-m-p  0.0005 0.0250  12.4072 CC     8207.017549  1 0.0007  2069 | 2/55
 35 h-m-p  0.0012 0.0239   7.3859 CC     8207.011393  1 0.0004  2129 | 2/55
 36 h-m-p  0.0005 0.0441   7.0976 CC     8207.007063  1 0.0004  2189 | 2/55
 37 h-m-p  0.0005 0.0466   5.2504 C      8207.002806  0 0.0005  2247 | 2/55
 38 h-m-p  0.0006 0.0566   4.1679 C      8206.998441  0 0.0006  2305 | 2/55
 39 h-m-p  0.0015 0.0715   1.8205 YC     8206.985517  1 0.0027  2364 | 2/55
 40 h-m-p  0.0012 0.0216   4.1497 CC     8206.950954  1 0.0018  2424 | 2/55
 41 h-m-p  0.0008 0.0157   9.7091 YC     8206.828758  1 0.0018  2483 | 2/55
 42 h-m-p  0.0012 0.0123  14.5117 CCC    8206.690306  2 0.0009  2545 | 2/55
 43 h-m-p  0.0005 0.0099  26.5764 +YC    8206.209227  1 0.0013  2605 | 2/55
 44 h-m-p  0.0008 0.0039  24.9362 YC     8205.649005  1 0.0013  2664 | 2/55
 45 h-m-p  0.0012 0.0071  28.2024 YCC    8205.249778  2 0.0009  2725 | 2/55
 46 h-m-p  0.0008 0.0065  30.8066 CC     8204.864469  1 0.0010  2785 | 2/55
 47 h-m-p  0.0012 0.0075  26.3367 YC     8204.745033  1 0.0005  2844 | 2/55
 48 h-m-p  0.0007 0.0180  19.6819 YC     8204.687919  1 0.0005  2903 | 2/55
 49 h-m-p  0.0017 0.0450   5.7953 YC     8204.673944  1 0.0010  2962 | 2/55
 50 h-m-p  0.0019 0.1353   2.9256 YC     8204.669866  1 0.0011  3021 | 2/55
 51 h-m-p  0.0032 0.4629   0.9683 YC     8204.667777  1 0.0022  3080 | 2/55
 52 h-m-p  0.0024 0.4229   0.8723 CC     8204.662461  1 0.0034  3193 | 2/55
 53 h-m-p  0.0021 0.2565   1.4262 +YC    8204.620843  1 0.0061  3306 | 2/55
 54 h-m-p  0.0040 0.0922   2.1752 +YC    8204.209458  1 0.0103  3366 | 2/55
 55 h-m-p  0.0015 0.0172  15.4468 CC     8203.975210  1 0.0012  3426 | 2/55
 56 h-m-p  0.0046 0.0618   4.0527 C      8203.964500  0 0.0013  3484 | 2/55
 57 h-m-p  0.0017 0.0621   2.9649 YC     8203.961119  1 0.0010  3543 | 2/55
 58 h-m-p  0.0033 0.3165   0.8695 YC     8203.960014  1 0.0018  3602 | 2/55
 59 h-m-p  0.0030 0.3792   0.5146 YC     8203.955853  1 0.0063  3714 | 2/55
 60 h-m-p  0.0041 0.3437   0.7934 +YC    8203.916620  1 0.0120  3827 | 2/55
 61 h-m-p  0.0062 0.0502   1.5338 YCC    8203.654491  2 0.0105  3941 | 2/55
 62 h-m-p  1.6000 8.0000   0.0099 CCC    8203.536140  2 1.8546  4003 | 2/55
 63 h-m-p  1.6000 8.0000   0.0046 YC     8203.482338  1 2.5464  4115 | 2/55
 64 h-m-p  1.6000 8.0000   0.0038 CC     8203.442950  1 2.4323  4228 | 2/55
 65 h-m-p  1.6000 8.0000   0.0025 YC     8203.437863  1 0.9700  4340 | 2/55
 66 h-m-p  1.6000 8.0000   0.0007 YC     8203.437588  1 0.9990  4452 | 2/55
 67 h-m-p  1.6000 8.0000   0.0001 Y      8203.437547  0 3.1505  4563 | 2/55
 68 h-m-p  1.6000 8.0000   0.0001 Y      8203.437502  0 2.5857  4674 | 2/55
 69 h-m-p  1.6000 8.0000   0.0001 C      8203.437497  0 1.8294  4785 | 2/55
 70 h-m-p  1.6000 8.0000   0.0000 Y      8203.437490  0 3.9623  4896 | 2/55
 71 h-m-p  1.6000 8.0000   0.0000 Y      8203.437490  0 1.1976  5007 | 2/55
 72 h-m-p  1.6000 8.0000   0.0000 Y      8203.437490  0 1.0853  5118 | 2/55
 73 h-m-p  1.1542 8.0000   0.0000 +Y     8203.437490  0 3.0763  5230 | 2/55
 74 h-m-p  1.6000 8.0000   0.0000 -C     8203.437490  0 0.1250  5342 | 2/55
 75 h-m-p  0.0160 8.0000   0.0000 -Y     8203.437490  0 0.0010  5454
Out..
lnL  = -8203.437490
5455 lfun, 5455 eigenQcodon, 289115 P(t)

Time used:  3:25
