
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 = 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: 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,    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  26  27  28  29  30

     3480 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), ((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   63.854051
   2   59.463439
   3   58.481121
   4   58.308637
   5   58.267806
   6   58.258122
   7   58.256398
   8   58.256368
  4126528 bytes for conP, adjusted

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

    0.009782    0.035410    0.053557    0.050143    0.112163    0.052651    0.065897    0.092954    0.061463    0.052981    0.094019    0.054597    0.030369    0.097128    0.135259    0.052633    0.087083    0.015013    0.085835    0.084687    0.088496    0.051883    0.019225    0.110228    0.055842    0.100293    0.087960    0.012851    0.030216    0.022452    0.107461    0.103838    0.078647    0.089470    0.054475    0.097728    0.084249    0.045456    0.085739    0.054175    0.076860    0.057720    0.013812    0.013338    0.065655    0.072881    0.042479    0.069577    0.077803    0.090177    0.096003    0.000000    0.178154    0.065310    0.079950    0.079594    0.122123    1.152286    0.810921

ntime & nrate & np:    57     2    59

Bounds (np=59):
   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
  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

np =    59
lnL0 = -9672.299090

Iterating by ming2
Initial: fx=  9672.299090
x=  0.00978  0.03541  0.05356  0.05014  0.11216  0.05265  0.06590  0.09295  0.06146  0.05298  0.09402  0.05460  0.03037  0.09713  0.13526  0.05263  0.08708  0.01501  0.08583  0.08469  0.08850  0.05188  0.01923  0.11023  0.05584  0.10029  0.08796  0.01285  0.03022  0.02245  0.10746  0.10384  0.07865  0.08947  0.05448  0.09773  0.08425  0.04546  0.08574  0.05417  0.07686  0.05772  0.01381  0.01334  0.06566  0.07288  0.04248  0.06958  0.07780  0.09018  0.09600  0.00000  0.17815  0.06531  0.07995  0.07959  0.12212  1.15229  0.81092

  1 h-m-p  0.0000 0.0001 4759.5501 ++     9407.018827  m 0.0001    64 | 1/59
  2 h-m-p  0.0000 0.0001 1837.2613 ++     9162.043881  m 0.0001   126 | 1/59
  3 h-m-p  0.0000 0.0000 21424.0344 ++     9019.778735  m 0.0000   188 | 2/59
  4 h-m-p  0.0000 0.0000 1595.1316 ++     8985.065105  m 0.0000   250 | 3/59
  5 h-m-p  0.0000 0.0000 3175.0448 ++     8896.796629  m 0.0000   312 | 2/59
  6 h-m-p  0.0000 0.0000 82626.8049 
h-m-p:      2.08076329e-22      1.04038164e-21      8.26268049e+04  8896.796629
..  | 2/59
  7 h-m-p  0.0000 0.0001 373781.9182 ---YYCYCCC  8884.775920  6 0.0000   446 | 2/59
  8 h-m-p  0.0000 0.0000 994.7518 ++     8877.478318  m 0.0000   508 | 3/59
  9 h-m-p  0.0000 0.0000 4799.6542 ++     8787.043197  m 0.0000   570 | 2/59
 10 h-m-p  0.0000 0.0000 49518.3585 
h-m-p:      4.87811146e-22      2.43905573e-21      4.95183585e+04  8787.043197
..  | 2/59
 11 h-m-p  0.0000 0.0001 220773.8684 ---YYCCYC  8781.326009  5 0.0000   702 | 2/59
 12 h-m-p  0.0000 0.0000 994.9858 ++     8781.210014  m 0.0000   764 | 3/59
 13 h-m-p  0.0000 0.0001 4091.6184 ++     8598.959857  m 0.0001   826 | 3/59
 14 h-m-p  0.0000 0.0001 2988.4092 YYCC   8590.918400  3 0.0000   892 | 3/59
 15 h-m-p  0.0001 0.0016 330.3958 +CCCC  8562.727119  3 0.0007   961 | 3/59
 16 h-m-p  0.0001 0.0004 426.0369 +YYCCC  8552.334956  4 0.0002  1030 | 3/59
 17 h-m-p  0.0002 0.0010 212.1668 YC     8546.108939  1 0.0005  1093 | 3/59
 18 h-m-p  0.0001 0.0006 291.6635 YCCC   8542.668836  3 0.0002  1160 | 3/59
 19 h-m-p  0.0001 0.0006 351.4954 YCCC   8538.838972  3 0.0002  1227 | 3/59
 20 h-m-p  0.0001 0.0007 208.0484 CCCC   8537.027580  3 0.0002  1295 | 3/59
 21 h-m-p  0.0003 0.0030 182.8085 YCCC   8534.852021  3 0.0004  1362 | 3/59
 22 h-m-p  0.0006 0.0028 114.2958 YCC    8533.727764  2 0.0004  1427 | 3/59
 23 h-m-p  0.0004 0.0033 113.0352 CC     8532.932412  1 0.0004  1491 | 3/59
 24 h-m-p  0.0004 0.0021  74.6150 YYC    8532.527059  2 0.0003  1555 | 3/59
 25 h-m-p  0.0004 0.0062  59.0893 CCC    8532.279990  2 0.0003  1621 | 3/59
 26 h-m-p  0.0003 0.0026  59.5246 CYC    8532.090689  2 0.0003  1686 | 3/59
 27 h-m-p  0.0004 0.0048  38.3510 YC     8531.978058  1 0.0003  1749 | 3/59
 28 h-m-p  0.0005 0.0156  25.0083 CC     8531.864735  1 0.0005  1813 | 3/59
 29 h-m-p  0.0005 0.0053  25.2216 CC     8531.766033  1 0.0004  1877 | 3/59
 30 h-m-p  0.0005 0.0099  21.9667 CC     8531.628256  1 0.0006  1941 | 3/59
 31 h-m-p  0.0004 0.0082  29.9627 YC     8531.344062  1 0.0007  2004 | 3/59
 32 h-m-p  0.0009 0.0063  25.5188 CCC    8530.828573  2 0.0010  2070 | 3/59
 33 h-m-p  0.0006 0.0038  44.3323 CC     8529.668631  1 0.0009  2134 | 3/59
 34 h-m-p  0.0004 0.0018  61.6164 YCCC   8527.713928  3 0.0007  2201 | 3/59
 35 h-m-p  0.0002 0.0010  83.0061 +YYYCYCCC  8521.394585  7 0.0009  2274 | 3/59
 36 h-m-p  0.0000 0.0002  81.9263 +YYCCC  8520.562936  4 0.0001  2343 | 3/59
 37 h-m-p  0.0005 0.0059  20.0971 +YCYCC  8514.236598  4 0.0040  2412 | 3/59
 38 h-m-p  0.0003 0.0013 209.7685 YCCC   8501.230895  3 0.0006  2479 | 3/59
 39 h-m-p  0.0001 0.0005 199.3431 YCYCCC  8496.045246  5 0.0003  2549 | 3/59
 40 h-m-p  0.0001 0.0005  89.1350 YCCC   8495.297263  3 0.0002  2616 | 3/59
 41 h-m-p  0.0002 0.0011  60.6522 YCCC   8494.602949  3 0.0005  2683 | 3/59
 42 h-m-p  0.0002 0.0013 145.9226 YC     8493.512949  1 0.0004  2746 | 3/59
 43 h-m-p  0.0009 0.0043  54.9418 YC     8493.159977  1 0.0004  2809 | 3/59
 44 h-m-p  0.0005 0.0037  42.9417 YC     8492.947523  1 0.0004  2872 | 3/59
 45 h-m-p  0.0008 0.0074  24.6449 YC     8492.860398  1 0.0004  2935 | 3/59
 46 h-m-p  0.0007 0.0125  14.9558 CC     8492.761141  1 0.0009  2999 | 3/59
 47 h-m-p  0.0008 0.0096  16.4769 YC     8492.694978  1 0.0005  3062 | 3/59
 48 h-m-p  0.0005 0.0083  14.4256 YC     8492.543310  1 0.0009  3125 | 3/59
 49 h-m-p  0.0005 0.0084  24.3595 YC     8492.055180  1 0.0011  3188 | 3/59
 50 h-m-p  0.0011 0.0074  25.0098 CCC    8491.081684  2 0.0012  3254 | 3/59
 51 h-m-p  0.0004 0.0020  52.4426 +YYCCC  8487.483200  4 0.0012  3323 | 3/59
 52 h-m-p  0.0001 0.0004  91.4070 +YYCYC  8485.057568  4 0.0003  3391 | 3/59
 53 h-m-p  0.0001 0.0007  76.1293 YCCCC  8483.807688  4 0.0003  3460 | 3/59
 54 h-m-p  0.0008 0.0039  24.4180 YCC    8483.601061  2 0.0006  3525 | 3/59
 55 h-m-p  0.0013 0.0155  11.0288 YC     8483.506086  1 0.0008  3588 | 3/59
 56 h-m-p  0.0006 0.0065  16.5434 YCC    8483.280823  2 0.0010  3653 | 3/59
 57 h-m-p  0.0010 0.0131  16.7372 YC     8482.597157  1 0.0017  3716 | 3/59
 58 h-m-p  0.0009 0.0123  31.2133 YCCC   8480.415692  3 0.0018  3783 | 3/59
 59 h-m-p  0.0005 0.0027  61.9897 YCCC   8475.887033  3 0.0012  3850 | 3/59
 60 h-m-p  0.0005 0.0025  58.1660 YCCC   8473.055287  3 0.0011  3917 | 3/59
 61 h-m-p  0.0009 0.0044  33.7280 CYC    8472.602850  2 0.0008  3982 | 3/59
 62 h-m-p  0.0023 0.0155  12.3935 CC     8472.535969  1 0.0009  4046 | 3/59
 63 h-m-p  0.0018 0.0292   5.7463 CC     8472.493830  1 0.0016  4110 | 3/59
 64 h-m-p  0.0040 0.1272   2.2969 YC     8472.290913  1 0.0082  4173 | 3/59
 65 h-m-p  0.0027 0.0346   6.9607 YC     8471.426641  1 0.0044  4236 | 3/59
 66 h-m-p  0.0013 0.0093  24.3017 CC     8470.388901  1 0.0015  4300 | 3/59
 67 h-m-p  0.0031 0.0158  12.1601 CC     8470.315134  1 0.0009  4364 | 3/59
 68 h-m-p  0.0016 0.0309   6.9964 YC     8470.290405  1 0.0011  4427 | 3/59
 69 h-m-p  0.0033 0.1071   2.2801 YC     8470.279183  1 0.0018  4490 | 3/59
 70 h-m-p  0.0060 0.6083   0.6802 +YC    8469.787312  1 0.0476  4554 | 3/59
 71 h-m-p  0.0022 0.0253  14.7704 YCC    8468.578338  2 0.0037  4675 | 3/59
 72 h-m-p  0.5404 2.7018   0.0576 CC     8468.105561  1 0.7372  4739 | 3/59
 73 h-m-p  0.8799 5.4101   0.0482 CCC    8467.789029  2 0.9249  4861 | 3/59
 74 h-m-p  0.7854 3.9271   0.0351 YC     8467.660242  1 0.5101  4980 | 3/59
 75 h-m-p  1.4398 7.1989   0.0068 YCC    8467.557874  2 1.1727  5101 | 3/59
 76 h-m-p  0.8393 8.0000   0.0095 YC     8467.476888  1 1.4320  5220 | 3/59
 77 h-m-p  0.7570 8.0000   0.0180 CC     8467.375526  1 1.0954  5340 | 3/59
 78 h-m-p  1.6000 8.0000   0.0110 CC     8467.242366  1 1.5121  5460 | 3/59
 79 h-m-p  1.6000 8.0000   0.0062 CYC    8467.103515  2 1.7614  5581 | 3/59
 80 h-m-p  1.4071 8.0000   0.0077 CCC    8466.971775  2 1.7851  5703 | 3/59
 81 h-m-p  1.6000 8.0000   0.0073 YC     8466.907635  1 1.0419  5822 | 3/59
 82 h-m-p  1.0185 8.0000   0.0075 YC     8466.886808  1 0.7537  5941 | 3/59
 83 h-m-p  1.6000 8.0000   0.0028 YC     8466.878658  1 1.0033  6060 | 3/59
 84 h-m-p  1.6000 8.0000   0.0012 C      8466.876523  0 1.3719  6178 | 3/59
 85 h-m-p  1.6000 8.0000   0.0009 Y      8466.876212  0 1.2089  6296 | 3/59
 86 h-m-p  1.6000 8.0000   0.0003 C      8466.876147  0 1.3466  6414 | 3/59
 87 h-m-p  1.6000 8.0000   0.0001 C      8466.876124  0 1.4012  6532 | 3/59
 88 h-m-p  1.3863 8.0000   0.0001 C      8466.876119  0 1.1848  6650 | 3/59
 89 h-m-p  1.6000 8.0000   0.0000 Y      8466.876118  0 0.9524  6768 | 3/59
 90 h-m-p  1.6000 8.0000   0.0000 Y      8466.876118  0 0.9877  6886 | 3/59
 91 h-m-p  1.6000 8.0000   0.0000 C      8466.876118  0 1.3814  7004 | 3/59
 92 h-m-p  1.6000 8.0000   0.0000 C      8466.876118  0 1.3589  7122 | 3/59
 93 h-m-p  1.2849 8.0000   0.0000 ---Y   8466.876118  0 0.0050  7243
Out..
lnL  = -8466.876118
7244 lfun, 14488 eigenQcodon, 412908 P(t)

Time used:  7:27
