
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

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   18.655031
   2   17.034120
   3   16.678710
   4   16.670410
   5   16.668933
   6   16.668583
   7   16.668500
   8   16.668495
  4126528 bytes for conP, adjusted

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

    0.006510    0.024074    0.061189    0.057696    0.137816    0.096390    0.072540    0.073613    0.112417    0.039926    0.052099    0.079131    0.076384    0.170318    0.179629    0.034161    0.024558    0.019089    0.047847    0.068988    0.069166    0.063144    0.051188    0.094386    0.081939    0.159918    0.170298    0.066138    0.055916    0.047939    0.179631    0.067866    0.086094    0.103854    0.065281    0.127354    0.102028    0.090592    0.075636    0.053175    0.046722    0.026028    0.072201    0.019969    0.065582    0.024830    0.055405    0.074958    0.023152    0.045706    0.235544    0.000000    0.262311    0.166635    0.033918    0.032871    0.241291    1.925433    0.917036

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 = -9227.638807

Iterating by ming2
Initial: fx=  9227.638807
x=  0.00651  0.02407  0.06119  0.05770  0.13782  0.09639  0.07254  0.07361  0.11242  0.03993  0.05210  0.07913  0.07638  0.17032  0.17963  0.03416  0.02456  0.01909  0.04785  0.06899  0.06917  0.06314  0.05119  0.09439  0.08194  0.15992  0.17030  0.06614  0.05592  0.04794  0.17963  0.06787  0.08609  0.10385  0.06528  0.12735  0.10203  0.09059  0.07564  0.05318  0.04672  0.02603  0.07220  0.01997  0.06558  0.02483  0.05540  0.07496  0.02315  0.04571  0.23554  0.00000  0.26231  0.16663  0.03392  0.03287  0.24129  1.92543  0.91704

  1 h-m-p  0.0000 0.0001 1653.1039 ++     9096.642796  m 0.0001    64 | 1/59
  2 h-m-p  0.0000 0.0000 2430.4649 ++     9087.392207  m 0.0000   126 | 2/59
  3 h-m-p  0.0000 0.0000 6742.4743 ++     9071.770363  m 0.0000   188 | 3/59
  4 h-m-p  0.0000 0.0000 5719.1733 ++     9006.348926  m 0.0000   250 | 4/59
  5 h-m-p  0.0000 0.0000 35377.1762 ++     8942.294186  m 0.0000   312 | 4/59
  6 h-m-p  0.0000 0.0000 19288.3461 
h-m-p:      3.07399619e-19      1.53699810e-18      1.92883461e+04  8942.294186
..  | 4/59
  7 h-m-p  0.0000 0.0001 220435.9384 ---YYCCYC  8936.567257  5 0.0000   444 | 4/59
  8 h-m-p  0.0000 0.0001 1064.1100 ++     8857.725398  m 0.0001   506 | 3/59
  9 h-m-p  0.0000 0.0000 76297.9917 
h-m-p:      5.73981544e-22      2.86990772e-21      7.62979917e+04  8857.725398
..  | 3/59
 10 h-m-p  0.0000 0.0001 392278.1763 ---YYCYCCC  8845.479892  6 0.0000   640 | 3/59
 11 h-m-p  0.0000 0.0000 965.9781 ++     8841.446246  m 0.0000   702 | 4/59
 12 h-m-p  0.0000 0.0000 10527.1323 ++     8721.242744  m 0.0000   764 | 4/59
 13 h-m-p  0.0000 0.0000 70771.1194 ++     8537.294187  m 0.0000   826 | 4/59
 14 h-m-p  0.0000 0.0000 23269.3731 ++     8447.925840  m 0.0000   888 | 4/59
 15 h-m-p  0.0000 0.0000 66408.9443 CCYC   8446.104441  3 0.0000   955 | 4/59
 16 h-m-p  0.0000 0.0001 663.1671 +YYCCC  8440.903595  4 0.0000  1024 | 4/59
 17 h-m-p  0.0001 0.0003 450.9647 +YCY   8432.503169  2 0.0002  1090 | 4/59
 18 h-m-p  0.0000 0.0001 459.0384 +YCYCCC  8428.032092  5 0.0001  1161 | 4/59
 19 h-m-p  0.0000 0.0000 967.4525 +YCYC  8425.452439  3 0.0000  1228 | 4/59
 20 h-m-p  0.0000 0.0002 650.3663 +YCCCC  8419.093852  4 0.0001  1298 | 4/59
 21 h-m-p  0.0001 0.0003 449.8953 YCCCC  8415.063318  4 0.0001  1367 | 4/59
 22 h-m-p  0.0001 0.0005 275.3946 CCC    8413.305937  2 0.0001  1433 | 4/59
 23 h-m-p  0.0001 0.0005 277.9558 CCC    8411.507201  2 0.0001  1499 | 4/59
 24 h-m-p  0.0001 0.0005 213.7434 CCC    8410.380487  2 0.0001  1565 | 4/59
 25 h-m-p  0.0002 0.0008 151.3252 CCCC   8409.193103  3 0.0002  1633 | 4/59
 26 h-m-p  0.0001 0.0003 232.3739 YCCC   8408.098785  3 0.0001  1700 | 4/59
 27 h-m-p  0.0001 0.0007 199.5979 CCCC   8406.914199  3 0.0002  1768 | 4/59
 28 h-m-p  0.0001 0.0006 148.7043 CCCC   8406.338106  3 0.0001  1836 | 4/59
 29 h-m-p  0.0001 0.0005 186.8979 CCCC   8405.717530  3 0.0001  1904 | 4/59
 30 h-m-p  0.0003 0.0013  77.7311 CCC    8405.314274  2 0.0003  1970 | 3/59
 31 h-m-p  0.0002 0.0016 146.8766 YCC    8404.665671  2 0.0003  2035 | 3/59
 32 h-m-p  0.0003 0.0015 127.9088 YCCC   8403.297603  3 0.0007  2102 | 3/59
 33 h-m-p  0.0001 0.0007 147.6985 CCC    8402.840437  2 0.0002  2168 | 3/59
 34 h-m-p  0.0002 0.0008  81.4509 YCCC   8402.437129  3 0.0004  2235 | 3/59
 35 h-m-p  0.0001 0.0005 101.7195 ++     8401.811240  m 0.0005  2297 | 3/59
 36 h-m-p  0.0007 0.0035  64.6495 CYC    8401.300089  2 0.0007  2362 | 3/59
 37 h-m-p  0.0006 0.0028  65.5552 YCC    8401.070591  2 0.0003  2427 | 3/59
 38 h-m-p  0.0003 0.0029  68.6499 CYC    8400.831778  2 0.0003  2492 | 3/59
 39 h-m-p  0.0004 0.0025  59.4612 CYC    8400.606900  2 0.0003  2557 | 3/59
 40 h-m-p  0.0003 0.0014  48.2586 CCC    8400.351575  2 0.0005  2623 | 3/59
 41 h-m-p  0.0003 0.0015  66.2154 CC     8400.107769  1 0.0003  2687 | 3/59
 42 h-m-p  0.0002 0.0008  49.1433 YC     8399.910490  1 0.0003  2750 | 3/59
 43 h-m-p  0.0004 0.0019  19.9204 YC     8399.649687  1 0.0010  2813 | 3/59
 44 h-m-p  0.0010 0.0074  19.5809 CCC    8399.182830  2 0.0015  2879 | 3/59
 45 h-m-p  0.0006 0.0031  52.9015 C      8398.720472  0 0.0006  2941 | 3/59
 46 h-m-p  0.0006 0.0029  36.5606 YCCC   8398.150376  3 0.0010  3008 | 3/59
 47 h-m-p  0.0002 0.0012  57.8332 +YC    8397.604201  1 0.0008  3072 | 3/59
 48 h-m-p  0.0002 0.0012  23.2678 YC     8397.489853  1 0.0006  3135 | 3/59
 49 h-m-p  0.0004 0.0019  14.4450 YC     8397.442833  1 0.0006  3198 | 3/59
 50 h-m-p  0.0005 0.0025  11.0427 CC     8397.413418  1 0.0007  3262 | 3/59
 51 h-m-p  0.0004 0.0019   7.2776 YC     8397.392147  1 0.0008  3325 | 3/59
 52 h-m-p  0.0009 0.0469   6.7580 YC     8397.351269  1 0.0016  3388 | 3/59
 53 h-m-p  0.0016 0.0554   6.7246 YC     8397.243131  1 0.0031  3451 | 3/59
 54 h-m-p  0.0024 0.0289   8.6081 CY     8397.079707  1 0.0025  3515 | 3/59
 55 h-m-p  0.0018 0.0205  11.9144 CC     8396.767111  1 0.0024  3579 | 3/59
 56 h-m-p  0.0023 0.0238  11.9877 CC     8396.325870  1 0.0026  3643 | 3/59
 57 h-m-p  0.0011 0.0306  27.6065 CYC    8395.910024  2 0.0013  3708 | 3/59
 58 h-m-p  0.0021 0.0105  13.6202 YC     8395.833316  1 0.0009  3771 | 3/59
 59 h-m-p  0.0022 0.0108   4.6900 YC     8395.818187  1 0.0013  3834 | 3/59
 60 h-m-p  0.0032 0.0158   1.5287 YC     8395.812170  1 0.0023  3897 | 3/59
 61 h-m-p  0.0014 0.0069   2.3161 +YC    8395.793068  1 0.0035  3961 | 3/59
 62 h-m-p  0.0005 0.0024   3.9623 ++     8395.759112  m 0.0024  4023 | 4/59
 63 h-m-p  0.0045 0.1561   2.0157 +YC    8395.409133  1 0.0133  4087 | 4/59
 64 h-m-p  0.0010 0.0156  25.8848 YC     8394.530350  1 0.0020  4150 | 4/59
 65 h-m-p  0.0030 0.0213  17.9239 CC     8394.411755  1 0.0008  4214 | 3/59
 66 h-m-p  0.0021 0.0777   6.7115 YC     8394.404482  1 0.0003  4277 | 3/59
 67 h-m-p  0.0006 0.0034   3.9352 CC     8394.398032  1 0.0009  4341 | 3/59
 68 h-m-p  0.0044 0.8894   0.8054 YC     8394.383093  1 0.0087  4404 | 3/59
 69 h-m-p  0.0067 0.2193   1.0552 YC     8394.259016  1 0.0155  4523 | 3/59
 70 h-m-p  0.0034 0.0190   4.8487 YC     8393.652363  1 0.0064  4586 | 3/59
 71 h-m-p  0.0031 0.0209  10.0250 YC     8393.493469  1 0.0023  4649 | 3/59
 72 h-m-p  0.7475 3.7377   0.0142 +CCC   8392.258012  2 2.6685  4716 | 3/59
 73 h-m-p  0.3537 1.7683   0.0353 ++     8391.548674  m 1.7683  4834 | 4/59
 74 h-m-p  1.6000 8.0000   0.0111 CC     8390.970273  1 2.3710  4954 | 4/59
 75 h-m-p  0.5967 2.9833   0.0198 YCC    8390.881916  2 0.4109  5074 | 3/59
 76 h-m-p  0.0003 0.0025  26.2786 +CC    8390.715709  1 0.0012  5194 | 3/59
 77 h-m-p  0.3273 1.6363   0.0207 +CC    8390.528464  1 1.2288  5259 | 3/59
 78 h-m-p  1.3910 6.9551   0.0045 CC     8390.467640  1 1.9321  5379 | 3/59
 79 h-m-p  0.7378 3.6890   0.0024 +YC    8390.423972  1 3.1885  5499 | 3/59
 80 h-m-p  1.6000 8.0000   0.0026 +YC    8390.366729  1 4.2991  5619 | 3/59
 81 h-m-p  1.6000 8.0000   0.0023 ++     
error: end of tree file.8390.135681  m 8.0000  5737 | 3/59
 82 h-m-p  0.6799 3.3994   0.0119 ++     8389.656653  m 3.3994  5855 | 4/59
 83 h-m-p  1.6000 8.0000   0.0099 YCC    8389.588279  2 0.6198  5976 | 4/59
 84 h-m-p  0.1035 1.9562   0.0594 YC     8389.400974  1 0.2290  6094 | 4/59
 85 h-m-p  1.6000 8.0000   0.0033 YCCC   8389.143940  3 3.3228  6216 | 4/59
 86 h-m-p  1.6000 8.0000   0.0047 CC     8389.057049  1 2.0858  6335 | 4/59
 87 h-m-p  1.6000 8.0000   0.0022 CC     8389.042416  1 1.7556  6454 | 3/59
 88 h-m-p  0.0072 1.5520   0.5435 -Y     8389.042382  0 0.0002  6572 | 3/59
 89 h-m-p  0.1990 8.0000   0.0006 ++YC   8389.039620  1 2.5372  6693 | 3/59
 90 h-m-p  1.6000 8.0000   0.0003 ++     8389.031449  m 8.0000  6811 | 3/59
 91 h-m-p  1.6000 8.0000   0.0010 YC     8389.019995  1 3.4111  6930 | 3/59
 92 h-m-p  1.6000 8.0000   0.0009 CC     8389.014654  1 1.9850  7050 | 3/59
 93 h-m-p  1.6000 8.0000   0.0007 Y      8389.014450  0 1.1788  7168 | 3/59
 94 h-m-p  1.6000 8.0000   0.0001 C      8389.014445  0 1.3775  7286 | 3/59
 95 h-m-p  1.6000 8.0000   0.0000 Y      8389.014444  0 1.1965  7404 | 3/59
 96 h-m-p  1.6000 8.0000   0.0000 Y      8389.014444  0 0.2448  7522 | 3/59
 97 h-m-p  0.2842 8.0000   0.0000 Y      8389.014444  0 0.0711  7640 | 3/59
 98 h-m-p  0.0748 8.0000   0.0000 ---------C  8389.014444  0 0.0000  7767
Out..
lnL  = -8389.014444
7768 lfun, 7768 eigenQcodon, 442776 P(t)
