
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

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   35.250182
   2   34.232420
   3   33.996761
   4   33.986862
   5   33.985101
   6   33.984866
   7   33.984864
  4222176 bytes for conP, adjusted

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

    0.023749    0.074521    0.093026    0.071693    0.137841    0.085477    0.062625    0.050371    0.103045    0.083028    0.075495    0.093217    0.032541    0.113133    0.119294    0.030623    0.079876    0.047289    0.071122    0.081473    0.060213    0.059018    0.018392    0.062342    0.070646    0.115952    0.079655    0.024945    0.036131    0.023132    0.113020    0.093491    0.113586    0.100655    0.011736    0.097429    0.080129    0.099500    0.037617    0.067856    0.063877    0.053298    0.046743    0.040515    0.107519    0.010691    0.011567    0.051865    0.046335    0.080919    0.178128    0.000000    0.149876    0.135589    0.041084    0.056519    0.146454    2.415525    0.168371

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 = -9032.119519

Iterating by ming2
Initial: fx=  9032.119519
x=  0.02375  0.07452  0.09303  0.07169  0.13784  0.08548  0.06262  0.05037  0.10305  0.08303  0.07550  0.09322  0.03254  0.11313  0.11929  0.03062  0.07988  0.04729  0.07112  0.08147  0.06021  0.05902  0.01839  0.06234  0.07065  0.11595  0.07966  0.02495  0.03613  0.02313  0.11302  0.09349  0.11359  0.10066  0.01174  0.09743  0.08013  0.09950  0.03762  0.06786  0.06388  0.05330  0.04674  0.04052  0.10752  0.01069  0.01157  0.05187  0.04634  0.08092  0.17813  0.00000  0.14988  0.13559  0.04108  0.05652  0.14645  2.41553  0.16837

  1 h-m-p  0.0000 0.0000 3323.5972 ++     8881.261025  m 0.0000    64 | 1/59
  2 h-m-p  0.0000 0.0001 1853.5557 ++     8670.426654  m 0.0001   126 | 0/59
  3 h-m-p  0.0000 0.0000 2609569.5610 ++     8658.369308  m 0.0000   188 | 1/59
  4 h-m-p  0.0000 0.0000 944.5270 ++     8658.366472  m 0.0000   250 | 2/59
  5 h-m-p  0.0000 0.0000 1297.8706 +YCYYCC  8645.818756  5 0.0000   321 | 2/59
  6 h-m-p  0.0000 0.0000 2263.7818 ++     8641.072650  m 0.0000   383 | 3/59
  7 h-m-p  0.0000 0.0000 712.1729 +CCYC  8637.615008  3 0.0000   451 | 2/59
  8 h-m-p  0.0000 0.0000 751.5485 ++     8636.616709  m 0.0000   513 | 2/59
  9 h-m-p  0.0000 0.0000 329.2659 ++     8634.447938  m 0.0000   575 | 3/59
 10 h-m-p  0.0001 0.0004 182.2498 YCC    8632.979992  2 0.0001   640 | 3/59
 11 h-m-p  0.0001 0.0004  92.5450 CCCC   8632.520204  3 0.0001   708 | 3/59
 12 h-m-p  0.0001 0.0003 107.9866 YCCC   8631.892750  3 0.0001   775 | 3/59
 13 h-m-p  0.0001 0.0005 138.1112 CCC    8631.294517  2 0.0001   841 | 3/59
 14 h-m-p  0.0002 0.0024  81.8528 +YYC   8628.782311  2 0.0007   906 | 3/59
 15 h-m-p  0.0002 0.0012 168.8388 YCCC   8623.806419  3 0.0005   973 | 3/59
 16 h-m-p  0.0002 0.0009 370.9804 +YCCCC  8611.391889  4 0.0005  1043 | 3/59
 17 h-m-p  0.0002 0.0008 613.3006 YCCC   8595.690415  3 0.0004  1110 | 3/59
 18 h-m-p  0.0001 0.0004 708.4728 +YCCCC  8584.819676  4 0.0002  1180 | 3/59
 19 h-m-p  0.0001 0.0005 419.3738 YCCCC  8576.756453  4 0.0003  1249 | 3/59
 20 h-m-p  0.0002 0.0008 175.8609 YCCC   8571.682980  3 0.0004  1316 | 3/59
 21 h-m-p  0.0002 0.0012 158.5856 YC     8566.810363  1 0.0004  1379 | 3/59
 22 h-m-p  0.0002 0.0011 173.4198 YCCC   8559.268809  3 0.0005  1446 | 3/59
 23 h-m-p  0.0004 0.0022 181.8509 YCCC   8547.340516  3 0.0008  1513 | 3/59
 24 h-m-p  0.0001 0.0006 291.0527 +CYC   8535.568418  2 0.0005  1579 | 3/59
 25 h-m-p  0.0002 0.0010 393.8410 YCCCC  8522.445145  4 0.0005  1648 | 3/59
 26 h-m-p  0.0002 0.0009 430.4155 CCC    8515.276254  2 0.0003  1714 | 3/59
 27 h-m-p  0.0001 0.0007 261.2575 YCCC   8511.411606  3 0.0003  1781 | 3/59
 28 h-m-p  0.0002 0.0012 166.3295 CCCC   8508.666332  3 0.0004  1849 | 3/59
 29 h-m-p  0.0004 0.0019 108.6545 CC     8507.126758  1 0.0004  1913 | 3/59
 30 h-m-p  0.0002 0.0011  72.5688 YCCC   8505.549433  3 0.0005  1980 | 3/59
 31 h-m-p  0.0003 0.0014  91.1261 CCCC   8503.866673  3 0.0004  2048 | 3/59
 32 h-m-p  0.0004 0.0022  76.4600 CCC    8502.486444  2 0.0004  2114 | 3/59
 33 h-m-p  0.0003 0.0013  78.3621 YCCC   8499.644934  3 0.0006  2181 | 3/59
 34 h-m-p  0.0001 0.0005 130.6326 +CC    8497.292742  1 0.0003  2246 | 3/59
 35 h-m-p  0.0005 0.0023  78.9138 YCC    8496.366793  2 0.0004  2311 | 3/59
 36 h-m-p  0.0001 0.0006  77.1931 +YC    8495.847451  1 0.0003  2375 | 3/59
 37 h-m-p  0.0006 0.0029  38.6736 YCC    8495.642776  2 0.0003  2440 | 3/59
 38 h-m-p  0.0006 0.0083  20.8529 CC     8495.484654  1 0.0006  2504 | 3/59
 39 h-m-p  0.0008 0.0039  15.2341 C      8495.313236  0 0.0008  2566 | 3/59
 40 h-m-p  0.0006 0.0088  19.3925 CCC    8494.893450  2 0.0009  2632 | 3/59
 41 h-m-p  0.0003 0.0013  17.3365 ++     8493.106889  m 0.0013  2694 | 4/59
 42 h-m-p  0.0003 0.0019  84.2363 +YCC   8488.405824  2 0.0007  2760 | 4/59
 43 h-m-p  0.0003 0.0016 100.8421 YCCC   8484.117709  3 0.0006  2827 | 4/59
 44 h-m-p  0.0006 0.0032  68.5475 CCC    8482.420846  2 0.0006  2893 | 4/59
 45 h-m-p  0.0011 0.0067  38.5354 YC     8481.935170  1 0.0007  2956 | 4/59
 46 h-m-p  0.0023 0.0114  12.0432 CC     8481.869338  1 0.0007  3020 | 4/59
 47 h-m-p  0.0016 0.0230   5.7599 CC     8481.792046  1 0.0017  3084 | 3/59
 48 h-m-p  0.0009 0.0457  10.7908 CCC    8481.621467  2 0.0013  3150 | 3/59
 49 h-m-p  0.0002 0.0008  26.0675 +C     8481.283147  0 0.0006  3213 | 3/59
 50 h-m-p  0.0005 0.0043  31.6906 +YCC   8479.716062  2 0.0016  3279 | 3/59
 51 h-m-p  0.0002 0.0011  56.4372 ++     8476.764983  m 0.0011  3341 | 4/59
 52 h-m-p  0.0006 0.0032  54.1949 YCY    8473.567578  2 0.0012  3406 | 4/59
 53 h-m-p  0.0008 0.0042  45.7075 CCCC   8471.366159  3 0.0012  3474 | 4/59
 54 h-m-p  0.0005 0.0026  41.6177 CCCC   8470.662156  3 0.0006  3542 | 4/59
 55 h-m-p  0.0015 0.0172  16.7676 YC     8470.521235  1 0.0010  3605 | 3/59
 56 h-m-p  0.0013 0.0202  12.6262 YC     8470.471810  1 0.0006  3668 | 3/59
 57 h-m-p  0.0001 0.0003  15.7858 ++     8470.435570  m 0.0003  3730 | 4/59
 58 h-m-p  0.0003 0.0241  12.0309 YC     8470.391843  1 0.0008  3793 | 4/59
 59 h-m-p  0.0032 0.0728   2.8565 +YC    8469.977930  1 0.0082  3857 | 3/59
 60 h-m-p  0.0019 0.0355  12.1681 CYC    8469.277959  2 0.0021  3922 | 3/59
 61 h-m-p  0.0002 0.0010  45.0645 +YC    8468.174566  1 0.0009  3986 | 3/59
 62 h-m-p  0.0027 0.0230  14.9293 CC     8468.069312  1 0.0008  4050 | 3/59
 63 h-m-p  0.0038 0.0669   3.2630 CC     8467.997698  1 0.0035  4114 | 3/59
 64 h-m-p  0.0044 0.1712   2.6195 +CCC   8466.774526  2 0.0202  4181 | 3/59
 65 h-m-p  0.0002 0.0010  21.9850 ++     8465.341088  m 0.0010  4243 | 4/59
 66 h-m-p  0.0003 0.0069  61.4559 +YCC   8463.527064  2 0.0010  4309 | 4/59
 67 h-m-p  0.0309 0.2227   1.9370 -YC    8463.505478  1 0.0037  4373 | 4/59
 68 h-m-p  0.0234 1.0178   0.3024 ++YC   8460.358389  1 0.2609  4438 | 4/59
 69 h-m-p  0.4669 2.3343   0.0705 CCCC   8459.095759  3 0.5999  4561 | 4/59
 70 h-m-p  1.1982 7.5537   0.0353 CCC    8458.374317  2 0.9871  4682 | 4/59
 71 h-m-p  1.2139 6.7636   0.0287 CYC    8457.794341  2 1.1499  4802 | 3/59
 72 h-m-p  0.0011 0.0084  29.5554 CCC    8457.733354  2 0.0003  4923 | 3/59
 73 h-m-p  0.4084 4.0190   0.0181 +YCC   8457.330892  2 1.1769  4989 | 3/59
 74 h-m-p  1.1690 7.0201   0.0183 CYC    8456.944613  2 1.2876  5110 | 3/59
 75 h-m-p  1.3074 8.0000   0.0180 CC     8456.627919  1 1.3968  5230 | 3/59
 76 h-m-p  1.6000 8.0000   0.0147 CC     8456.452995  1 1.3134  5350 | 3/59
 77 h-m-p  1.4228 8.0000   0.0136 CC     8456.327817  1 1.2636  5470 | 3/59
 78 h-m-p  1.6000 8.0000   0.0079 CC     8456.215601  1 1.7295  5590 | 3/59
 79 h-m-p  1.6000 8.0000   0.0078 CC     8456.057521  1 2.0769  5710 | 3/59
 80 h-m-p  1.6000 8.0000   0.0076 YC     8455.693236  1 3.2948  5829 | 3/59
 81 h-m-p  1.6000 8.0000   0.0086 YC     8455.149615  1 2.5765  5948 | 3/59
 82 h-m-p  1.4102 7.2451   0.0157 CC     8454.745438  1 1.6916  6068 | 3/59
 83 h-m-p  0.8714 4.3572   0.0110 +YC    8454.413157  1 2.3772  6188 | 3/59
 84 h-m-p  0.3548 1.7739   0.0081 ++     8454.106498  m 1.7739  6306 | 4/59
 85 h-m-p  1.3327 8.0000   0.0098 YCC    8454.006396  2 0.8537  6427 | 4/59
 86 h-m-p  0.4483 7.2322   0.0186 CC     8453.907451  1 0.7072  6546 | 4/59
 87 h-m-p  1.6000 8.0000   0.0057 CC     8453.857521  1 1.7167  6665 | 4/59
 88 h-m-p  1.6000 8.0000   0.0043 CC     8453.849298  1 1.3520  6784 | 4/59
 89 h-m-p  1.6000 8.0000   0.0017 C      8453.845420  0 1.8601  6901 | 4/59
 90 h-m-p  1.6000 8.0000   0.0013 C      8453.844229  0 1.5266  7018 | 4/59
 91 h-m-p  1.6000 8.0000   0.0009 C      8453.843863  0 1.3891  7135 | 3/59
 92 h-m-p  0.0227 8.0000   0.0569 --Y    8453.843863  0 0.0003  7254 | 3/59
 93 h-m-p  0.0373 2.6918   0.0004 +++C   8453.843622  0 2.1059  7375 | 3/59
 94 h-m-p  0.0555 0.2776   0.0002 ++     8453.843561  m 0.2776  7493 | 4/59
 95 h-m-p  0.0609 8.0000   0.0010 ++YC   8453.842255  1 1.7019  7614 | 4/59
 96 h-m-p  1.6000 8.0000   0.0002 ++     8453.834817  m 8.0000  7731 | 3/59
 97 h-m-p  0.0001 0.0081  13.8083 +C     8453.818933  0 0.0005  7849 | 3/59
 98 h-m-p  1.5496 8.0000   0.0048 CC     8453.782593  1 1.7463  7913 | 3/59
 99 h-m-p  1.5174 8.0000   0.0056 CC     8453.756745  1 2.2736  8033 | 3/59
100 h-m-p  1.6000 8.0000   0.0019 YC     8453.754250  1 1.0407  8152 | 3/59
101 h-m-p  1.6000 8.0000   0.0003 C      8453.754148  0 1.2879  8270 | 3/59
102 h-m-p  1.6000 8.0000   0.0001 Y      8453.754141  0 1.1555  8388 | 3/59
103 h-m-p  1.6000 8.0000   0.0000 C      8453.754140  0 1.5115  8506 | 3/59
104 h-m-p  1.6000 8.0000   0.0000 Y      8453.754140  0 1.2464  8624 | 3/59
105 h-m-p  1.6000 8.0000   0.0000 Y      8453.754140  0 1.2107  8742 | 3/59
106 h-m-p  1.6000 8.0000   0.0000 C      8453.754140  0 1.6000  8860 | 3/59
107 h-m-p  1.6000 8.0000   0.0000 Y      8453.754140  0 2.8613  8978 | 3/59
108 h-m-p  1.6000 8.0000   0.0000 C      8453.754140  0 0.4000  9096 | 3/59
109 h-m-p  0.6432 8.0000   0.0000 C      8453.754140  0 0.6432  9214 | 3/59
110 h-m-p  1.6000 8.0000   0.0000 C      8453.754140  0 1.6000  9332 | 3/59
111 h-m-p  1.6000 8.0000   0.0000 C      8453.754140  0 1.6000  9450 | 3/59
112 h-m-p  1.6000 8.0000   0.0000 C      8453.754140  0 1.6000  9568 | 3/59
113 h-m-p  1.6000 8.0000   0.0000 Y      8453.754140  0 0.4000  9686
Out..
lnL  = -8453.754140
9687 lfun, 9687 eigenQcodon, 552159 P(t)

Time used:  9:28
