
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: Erinaceus_europaeus       
Reading seq # 2: Ictidomys_tridecemlineatus       
Reading seq # 3: Marmota_flaviventris       
Reading seq # 4: Marmota_marmota       
Reading seq # 5: Marmota_monax       
Reading seq # 6: Urocitellus_parryii       
Reading seq # 7: Ursus_americanus       
Reading seq # 8: Ursus_arctos       
Reading seq # 9: Callorhinus_ursinus       
Reading seq #10: Heterocephalus_glaber       
Reading seq #11: Homo_sapiens       
Reading seq #12: Lemmus_lemmus       
Reading seq #13: Microtus_ochrogaster       
Reading seq #14: Mus_musculus       
Reading seq #15: Mustela_erminea       
Reading seq #16: Mustela_putorius_furo       
Reading seq #17: Myodes_glareolus       
Reading seq #18: Neovison_vison       
Reading seq #19: Ochotona_princeps       
Reading seq #20: Oryctolagus_cuniculus       
Reading seq #21: Phoca_vitulina       
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

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

   1   22.562857
   2   16.550541
   3   16.352952
   4   16.306544
   5   16.301909
   6   16.301084
   7   16.300974
   8   16.300966
  3537024 bytes for conP, adjusted

    0.018901    0.003969    0.029055    0.034051    0.143380    0.075855    0.066620    0.082498    0.112556    0.039633    0.078308    0.035376    0.064880    0.195107    0.194228    0.046823    0.049067    0.024516    0.037924    0.034249    0.055262    0.066195    0.060019    0.114382    0.098879    0.172599    0.153443    0.000197    0.142301    0.086390    0.027922    0.062301    0.063227    0.013874    0.027441    0.071626    0.018634    0.029698    0.036880    0.047267    0.025890    0.234326    0.000000    0.265401    0.175904    0.059413    0.040544    0.261309    2.077245    0.172262

ntime & nrate & np:    48     2    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   0.000004   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 999.000000 999.000000

np =    50
lnL0 = -7105.827746

Iterating by ming2
Initial: fx=  7105.827746
x=  0.01890  0.00397  0.02905  0.03405  0.14338  0.07585  0.06662  0.08250  0.11256  0.03963  0.07831  0.03538  0.06488  0.19511  0.19423  0.04682  0.04907  0.02452  0.03792  0.03425  0.05526  0.06620  0.06002  0.11438  0.09888  0.17260  0.15344  0.00020  0.14230  0.08639  0.02792  0.06230  0.06323  0.01387  0.02744  0.07163  0.01863  0.02970  0.03688  0.04727  0.02589  0.23433  0.00000  0.26540  0.17590  0.05941  0.04054  0.26131  2.07724  0.17226

  1 h-m-p  0.0000 0.0001 2160.1332 ++     6997.298923  m 0.0001    55 | 1/50
  2 h-m-p  0.0000 0.0000 1117.8716 ++     6978.047502  m 0.0000   108 | 2/50
  3 h-m-p  0.0000 0.0000 2022.3562 +CYYYYC  6969.035778  5 0.0000   168 | 2/50
  4 h-m-p  0.0000 0.0000 1575.7956 ++     6963.582811  m 0.0000   221 | 3/50
  5 h-m-p  0.0000 0.0004 257.5404 +YCCYC  6954.455652  4 0.0003   282 | 3/50
  6 h-m-p  0.0001 0.0003 413.8740 CYC    6952.428075  2 0.0001   338 | 3/50
  7 h-m-p  0.0001 0.0005 205.0019 YCCC   6950.450795  3 0.0002   396 | 3/50
  8 h-m-p  0.0003 0.0019 122.0466 CCC    6949.425883  2 0.0002   453 | 3/50
  9 h-m-p  0.0004 0.0019  59.0435 YYC    6948.953308  2 0.0003   508 | 3/50
 10 h-m-p  0.0004 0.0018  52.9769 CC     6948.576323  1 0.0004   563 | 3/50
 11 h-m-p  0.0004 0.0018  42.9594 CC     6948.255642  1 0.0004   618 | 3/50
 12 h-m-p  0.0002 0.0013  87.2435 CCC    6947.820400  2 0.0002   675 | 3/50
 13 h-m-p  0.0003 0.0039  62.0516 +YCCC  6946.333730  3 0.0010   734 | 3/50
 14 h-m-p  0.0003 0.0014 213.7183 YCCC   6943.666556  3 0.0005   792 | 3/50
 15 h-m-p  0.0004 0.0028 239.3721 YCCC   6937.682892  3 0.0009   850 | 3/50
 16 h-m-p  0.0003 0.0013 441.5191 YCCCC  6931.175770  4 0.0005   910 | 3/50
 17 h-m-p  0.0001 0.0005 592.1840 YC     6927.580690  1 0.0002   964 | 3/50
 18 h-m-p  0.0002 0.0009 263.0382 YCCC   6923.753193  3 0.0005  1022 | 3/50
 19 h-m-p  0.0002 0.0011 183.0671 YCCC   6921.010915  3 0.0005  1080 | 3/50
 20 h-m-p  0.0002 0.0010 103.1358 +YCCC  6919.176224  3 0.0005  1139 | 3/50
 21 h-m-p  0.0003 0.0017  64.0827 CCCC   6918.010970  3 0.0005  1198 | 3/50
 22 h-m-p  0.0004 0.0021  64.3108 CCCC   6916.480894  3 0.0006  1257 | 3/50
 23 h-m-p  0.0002 0.0010 100.7923 +YCCC  6914.033030  3 0.0006  1316 | 3/50
 24 h-m-p  0.0002 0.0009 137.6747 +YYCC  6910.363935  3 0.0007  1374 | 3/50
 25 h-m-p  0.0001 0.0007 289.3328 +YCYCC  6905.996064  4 0.0004  1434 | 3/50
 26 h-m-p  0.0001 0.0007 193.1143 YCCC   6903.717141  3 0.0003  1492 | 3/50
 27 h-m-p  0.0001 0.0007 119.8587 YCCC   6902.398278  3 0.0004  1550 | 3/50
 28 h-m-p  0.0001 0.0005  90.4277 +CC    6901.605080  1 0.0003  1606 | 3/50
 29 h-m-p  0.0002 0.0008  53.6368 ++     6900.474121  m 0.0008  1659 | 3/50
 30 h-m-p  0.0004 0.0022 107.9657 CCCC   6898.571140  3 0.0005  1718 | 3/50
 31 h-m-p  0.0001 0.0006  98.1901 +YCCC  6897.003491  3 0.0004  1777 | 3/50
 32 h-m-p  0.0001 0.0003 138.1824 ++     6894.370486  m 0.0003  1830 | 3/50
 33 h-m-p  0.0001 0.0005 148.7311 +YCCC  6892.480497  3 0.0003  1889 | 3/50
 34 h-m-p  0.0001 0.0003  97.6279 ++     6891.354760  m 0.0003  1942 | 3/50
 35 h-m-p  0.0003 0.0015 105.5877 CC     6890.260921  1 0.0003  1997 | 3/50
 36 h-m-p  0.0005 0.0024  56.2360 CCCC   6888.957779  3 0.0006  2056 | 3/50
 37 h-m-p  0.0003 0.0013  63.3261 YC     6887.426428  1 0.0006  2110 | 3/50
 38 h-m-p  0.0003 0.0015 109.7360 CCC    6885.375465  2 0.0005  2167 | 3/50
 39 h-m-p  0.0003 0.0016  65.6043 CCC    6884.538936  2 0.0004  2224 | 3/50
 40 h-m-p  0.0004 0.0046  59.4959 CCC    6883.555532  2 0.0006  2281 | 3/50
 41 h-m-p  0.0012 0.0102  32.1684 YC     6883.114453  1 0.0009  2335 | 3/50
 42 h-m-p  0.0013 0.0168  21.7153 YC     6882.967125  1 0.0007  2389 | 3/50
 43 h-m-p  0.0014 0.0108  10.3020 YC     6882.882440  1 0.0009  2443 | 3/50
 44 h-m-p  0.0005 0.0147  17.7804 YC     6882.667019  1 0.0010  2497 | 3/50
 45 h-m-p  0.0023 0.0114   7.8189 YCCC   6881.228433  3 0.0055  2555 | 3/50
 46 h-m-p  0.0010 0.0068  45.5366 CCC    6879.042456  2 0.0013  2612 | 3/50
 47 h-m-p  0.0006 0.0029  53.4201 YCCC   6876.223824  3 0.0014  2670 | 3/50
 48 h-m-p  0.0038 0.0241  20.2728 CYC    6874.391111  2 0.0034  2726 | 3/50
 49 h-m-p  0.0025 0.0127  21.8530 +CCC   6866.209570  2 0.0088  2784 | 3/50
 50 h-m-p  0.0021 0.0105  18.8218 YCC    6865.953742  2 0.0013  2840 | 3/50
 51 h-m-p  0.0069 0.1622   3.5554 CYC    6865.680145  2 0.0074  2896 | 3/50
 52 h-m-p  0.0115 0.1252   2.2975 +CCC   6856.653489  2 0.0576  2954 | 3/50
 53 h-m-p  0.1626 0.8131   0.3020 YCCC   6854.647503  3 0.3942  3012 | 3/50
 54 h-m-p  0.4163 2.0817   0.2111 CCC    6853.184473  2 0.5089  3116 | 3/50
 55 h-m-p  1.4891 7.8037   0.0721 YCC    6852.474335  2 0.9836  3219 | 3/50
 56 h-m-p  0.6616 3.3080   0.0291 CCC    6852.142830  2 0.9870  3323 | 3/50
 57 h-m-p  1.2807 7.4208   0.0224 YC     6851.921598  1 0.7798  3424 | 3/50
 58 h-m-p  0.8038 8.0000   0.0218 CCC    6851.536192  2 1.2561  3528 | 3/50
 59 h-m-p  1.6000 8.0000   0.0146 CCC    6851.018095  2 1.9757  3632 | 3/50
 60 h-m-p  1.3325 8.0000   0.0216 CC     6850.701393  1 1.6962  3734 | 3/50
 61 h-m-p  1.6000 8.0000   0.0130 CCC    6850.476084  2 1.8920  3838 | 3/50
 62 h-m-p  1.6000 8.0000   0.0068 CC     6850.361917  1 2.1303  3940 | 3/50
 63 h-m-p  1.6000 8.0000   0.0065 YC     6850.251613  1 2.7260  4041 | 3/50
 64 h-m-p  1.6000 8.0000   0.0052 CC     6850.079742  1 2.1188  4143 | 3/50
 65 h-m-p  1.4273 8.0000   0.0077 CC     6849.944225  1 1.8183  4245 | 3/50
 66 h-m-p  1.6000 8.0000   0.0079 CC     6849.863161  1 2.4930  4347 | 3/50
 67 h-m-p  1.6000 8.0000   0.0083 CC     6849.756024  1 2.4530  4449 | 3/50
 68 h-m-p  1.6000 8.0000   0.0056 CC     6849.690723  1 1.3525  4551 | 3/50
 69 h-m-p  1.6000 8.0000   0.0039 YC     6849.675201  1 1.2044  4652 | 3/50
 70 h-m-p  1.6000 8.0000   0.0019 C      6849.671285  0 1.4583  4752 | 3/50
 71 h-m-p  1.6000 8.0000   0.0013 +YC    6849.664483  1 4.9231  4854 | 3/50
 72 h-m-p  1.6000 8.0000   0.0011 ++     6849.614010  m 8.0000  4954 | 3/50
 73 h-m-p  1.3857 6.9286   0.0030 CCCC   6849.544304  3 1.8379  5060 | 3/50
 74 h-m-p  0.8861 8.0000   0.0062 YC     6849.506152  1 1.8226  5161 | 3/50
 75 h-m-p  1.6000 8.0000   0.0015 C      6849.501458  0 1.6788  5261 | 3/50
 76 h-m-p  1.6000 8.0000   0.0011 YC     6849.500866  1 1.1644  5362 | 3/50
 77 h-m-p  1.6000 8.0000   0.0003 C      6849.500813  0 1.3531  5462 | 3/50
 78 h-m-p  1.6000 8.0000   0.0001 C      6849.500807  0 1.4225  5562 | 3/50
 79 h-m-p  1.6000 8.0000   0.0000 Y      6849.500806  0 1.1947  5662 | 3/50
 80 h-m-p  1.6000 8.0000   0.0000 Y      6849.500806  0 0.9589  5762 | 3/50
 81 h-m-p  1.6000 8.0000   0.0000 Y      6849.500806  0 1.1694  5862 | 3/50
 82 h-m-p  1.6000 8.0000   0.0000 -----Y  6849.500806  0 0.0004  5967
Out..
lnL  = -6849.500806
5968 lfun, 5968 eigenQcodon, 286464 P(t)

Time used:  4:04
