
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

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), (Phoca_vitulina, Callorhinus_ursinus))), ((Sorex_araneus, (Talpa_europaea, Talpa_occidentalis)), Erinaceus_europaeus #1)));

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   30.352524
   2   24.142701
   3   24.019792
   4   23.998010
   5   23.995105
   6   23.994588
   7   23.994424
   8   23.994419
  3819088 bytes for conP, adjusted

    0.011038    0.054137    0.058296    0.031889    0.157844    0.093028    0.046726    0.078623    0.095358    0.065872    0.064124    0.068194    0.031052    0.172223    0.147300    0.068978    0.027623    0.072113    0.046171    0.049628    0.018141    0.073459    0.068704    0.080040    0.092755    0.111046    0.169447    0.053538    0.076842    0.028537    0.149684    0.045462    0.100479    0.078841    0.041436    0.093235    0.141763    0.072131    0.067420    0.047110    0.040160    0.020245    0.023452    0.088292    0.054664    0.059367    0.167437    0.000000    0.240709    0.154986    0.025940    0.012757    0.234948    0.155696    0.151117    0.144541

ntime & nrate & np:    53     3    56

Bounds (np=56):
   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   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 999.000000

np =    56
lnL0 = -9589.599532

Iterating by ming2
Initial: fx=  9589.599532
x=  0.01104  0.05414  0.05830  0.03189  0.15784  0.09303  0.04673  0.07862  0.09536  0.06587  0.06412  0.06819  0.03105  0.17222  0.14730  0.06898  0.02762  0.07211  0.04617  0.04963  0.01814  0.07346  0.06870  0.08004  0.09275  0.11105  0.16945  0.05354  0.07684  0.02854  0.14968  0.04546  0.10048  0.07884  0.04144  0.09324  0.14176  0.07213  0.06742  0.04711  0.04016  0.02024  0.02345  0.08829  0.05466  0.05937  0.16744  0.00000  0.24071  0.15499  0.02594  0.01276  0.23495  0.15570  0.15112  0.14454

  1 h-m-p  0.0000 0.0001 4997.0150 ++     8732.012897  m 0.0001    61 | 0/56
  2 h-m-p  0.0000 0.0001 1644.9648 ++     8673.963975  m 0.0001   120 | 1/56
  3 h-m-p  0.0000 0.0000 1340.1724 ++     8624.005103  m 0.0000   179 | 2/56
  4 h-m-p  0.0000 0.0000 3886.8528 ++     8606.225446  m 0.0000   238 | 3/56
  5 h-m-p  0.0000 0.0003 809.4602 ++     8562.237186  m 0.0003   297 | 3/56
  6 h-m-p  0.0000 0.0000 49298.9329 CCC    8560.133802  2 0.0000   360 | 3/56
  7 h-m-p  0.0000 0.0001 860.2360 +YCCC  8548.795299  3 0.0001   425 | 3/56
  8 h-m-p  0.0001 0.0003 199.6078 +YCC   8543.306657  2 0.0003   488 | 3/56
  9 h-m-p  0.0001 0.0006 205.0099 YCCC   8539.717132  3 0.0003   552 | 3/56
 10 h-m-p  0.0001 0.0004 207.2780 +YCCC  8537.110650  3 0.0003   617 | 3/56
 11 h-m-p  0.0000 0.0002 105.5550 ++     8536.119313  m 0.0002   676 | 4/56
 12 h-m-p  0.0006 0.0053  35.1915 YC     8534.961595  1 0.0011   736 | 4/56
 13 h-m-p  0.0001 0.0007 150.6959 YCCC   8533.610028  3 0.0003   800 | 4/56
 14 h-m-p  0.0003 0.0014 108.1239 CCCC   8531.955715  3 0.0005   865 | 4/56
 15 h-m-p  0.0005 0.0025  60.1953 CCCCC  8529.935329  4 0.0007   932 | 4/56
 16 h-m-p  0.0003 0.0013  64.2922 +CC    8524.889199  1 0.0011   994 | 3/56
 17 h-m-p  0.0001 0.0004 131.9475 +CCC   8522.580962  2 0.0003  1058 | 3/56
 18 h-m-p  0.0001 0.0005 262.4951 +YYCCC  8511.413250  4 0.0003  1124 | 3/56
 19 h-m-p  0.0000 0.0002 236.2003 ++     8501.860646  m 0.0002  1183 | 3/56
 20 h-m-p  0.0000 0.0000 390.8154 
h-m-p:      6.57324907e-22      3.28662454e-21      3.90815373e+02  8501.860646
..  | 3/56
 21 h-m-p  0.0000 0.0002 1330.6777 ++YCYYCC  8454.867901  5 0.0002  1307 | 3/56
 22 h-m-p  0.0000 0.0001 735.8839 +CYYCYCCC  8430.777782  7 0.0001  1378 | 2/56
 23 h-m-p  0.0000 0.0000 17714.9876 +YCYCCC  8408.037269  5 0.0000  1446 | 2/56
 24 h-m-p  0.0000 0.0000 2658.3550 ++     8404.500472  m 0.0000  1505 | 3/56
 25 h-m-p  0.0000 0.0000 3349.1853 ++     8383.406434  m 0.0000  1564 | 3/56
 26 h-m-p  0.0000 0.0000 3149.5190 +YYYYYC  8361.704047  5 0.0000  1629 | 3/56
 27 h-m-p  0.0000 0.0000 1384.7306 +YYYYCC  8351.838183  5 0.0000  1695 | 3/56
 28 h-m-p  0.0000 0.0001 2594.6809 +YYYYCC  8324.893301  5 0.0001  1761 | 3/56
 29 h-m-p  0.0000 0.0001 722.4833 +YCCC  8318.908722  3 0.0001  1826 | 3/56
 30 h-m-p  0.0000 0.0002 411.9418 +YCCC  8314.767173  3 0.0001  1891 | 3/56
 31 h-m-p  0.0000 0.0002 835.5131 +YCCC  8306.999415  3 0.0001  1956 | 3/56
 32 h-m-p  0.0001 0.0005 214.9503 CCC    8305.137030  2 0.0002  2019 | 3/56
 33 h-m-p  0.0001 0.0003 217.5534 CCCC   8304.173611  3 0.0001  2084 | 3/56
 34 h-m-p  0.0001 0.0012 186.5711 CC     8303.111001  1 0.0002  2145 | 3/56
 35 h-m-p  0.0001 0.0005  93.9063 CCCC   8302.791518  3 0.0001  2210 | 3/56
 36 h-m-p  0.0002 0.0028  73.2398 YC     8302.363730  1 0.0003  2270 | 3/56
 37 h-m-p  0.0004 0.0023  49.7593 YC     8302.204184  1 0.0002  2330 | 3/56
 38 h-m-p  0.0003 0.0058  36.5475 CC     8302.069894  1 0.0003  2391 | 3/56
 39 h-m-p  0.0003 0.0018  42.9457 CYC    8301.948511  2 0.0002  2453 | 3/56
 40 h-m-p  0.0004 0.0027  26.3633 CCC    8301.809000  2 0.0004  2516 | 3/56
 41 h-m-p  0.0003 0.0067  35.5512 YC     8301.407464  1 0.0007  2576 | 3/56
 42 h-m-p  0.0003 0.0013  40.8659 YCCC   8300.820094  3 0.0006  2640 | 3/56
 43 h-m-p  0.0002 0.0015 113.7254 YC     8299.446107  1 0.0005  2700 | 3/56
 44 h-m-p  0.0005 0.0032  94.9894 CC     8296.757791  1 0.0009  2761 | 3/56
 45 h-m-p  0.0007 0.0034 110.0522 CCC    8291.802798  2 0.0011  2824 | 3/56
 46 h-m-p  0.0005 0.0027 134.7109 CCCC   8285.996708  3 0.0008  2889 | 3/56
 47 h-m-p  0.0003 0.0014 133.8038 YCCC   8281.215498  3 0.0006  2953 | 3/56
 48 h-m-p  0.0004 0.0018  87.5883 YCCC   8276.339993  3 0.0008  3017 | 2/56
 49 h-m-p  0.0001 0.0005 133.3603 +YYYCC  8273.334735  4 0.0004  3082 | 2/56
 50 h-m-p  0.0001 0.0006 176.2585 +YYCC  8269.291075  3 0.0004  3146 | 2/56
 51 h-m-p  0.0001 0.0004 248.3237 CCC    8268.413295  2 0.0001  3209 | 2/56
 52 h-m-p  0.0002 0.0016  90.1510 YC     8266.600428  1 0.0006  3269 | 2/56
 53 h-m-p  0.0003 0.0016  78.0903 +YCCC  8264.430137  3 0.0009  3334 | 2/56
 54 h-m-p  0.0001 0.0006 113.8903 ++     8261.955488  m 0.0006  3393 | 3/56
 55 h-m-p  0.0009 0.0077  80.2266 YCC    8257.234248  2 0.0015  3455 | 3/56
 56 h-m-p  0.0005 0.0024 139.7133 CCCC   8253.283096  3 0.0006  3520 | 3/56
 57 h-m-p  0.0003 0.0017 115.1647 CCCC   8250.340287  3 0.0005  3585 | 3/56
 58 h-m-p  0.0005 0.0024  78.9845 CCC    8247.325448  2 0.0008  3648 | 3/56
 59 h-m-p  0.0005 0.0040 111.5907 CYC    8244.389228  2 0.0006  3710 | 3/56
 60 h-m-p  0.0004 0.0019  80.6949 CCC    8242.977317  2 0.0005  3773 | 2/56
 61 h-m-p  0.0006 0.0045  72.9507 YCCC   8242.631975  3 0.0002  3837 | 2/56
 62 h-m-p  0.0005 0.0031  35.0581 CC     8242.234069  1 0.0007  3898 | 2/56
 63 h-m-p  0.0013 0.0063  19.3502 C      8241.943231  0 0.0013  3957 | 2/56
 64 h-m-p  0.0027 0.0238   9.0746 CC     8241.238469  1 0.0040  4018 | 2/56
 65 h-m-p  0.0010 0.0052  18.2739 +YC    8238.311177  1 0.0045  4079 | 2/56
 66 h-m-p  0.0000 0.0002  59.1392 ++     8237.244123  m 0.0002  4138 | 3/56
 67 h-m-p  0.0003 0.0063  46.0538 +CCCC  8235.026159  3 0.0014  4204 | 3/56
 68 h-m-p  0.0008 0.0042  62.7417 CCC    8233.255688  2 0.0011  4267 | 2/56
 69 h-m-p  0.0015 0.0084  48.5857 YCCC   8232.742507  3 0.0007  4331 | 2/56
 70 h-m-p  0.0001 0.0006  60.6914 +CC    8232.367187  1 0.0004  4393 | 2/56
 71 h-m-p  0.0003 0.0014  22.6858 +YC    8232.083995  1 0.0013  4454 | 2/56
 72 h-m-p  0.0000 0.0001  19.4690 ++     8232.054738  m 0.0001  4513 | 3/56
 73 h-m-p  0.0002 0.0431   8.8995 ++YC   8231.826956  1 0.0023  4575 | 3/56
 74 h-m-p  0.0017 0.0425  11.9644 +YC    8230.715416  1 0.0042  4636 | 3/56
 75 h-m-p  0.0016 0.0080  21.9505 +YYCCC  8225.173928  4 0.0049  4702 | 2/56
 76 h-m-p  0.0001 0.0003 202.2522 +YCYC  8223.613471  3 0.0002  4766 | 2/56
 77 h-m-p  0.0002 0.0010  53.1165 YCYC   8222.738363  3 0.0005  4829 | 2/56
 78 h-m-p  0.0020 0.0224  12.9266 CCC    8222.478275  2 0.0023  4892 | 2/56
 79 h-m-p  0.0011 0.0057   6.6404 +YC    8222.212288  1 0.0036  4953 | 2/56
 80 h-m-p  0.0032 0.0158   4.9604 ++     8218.310407  m 0.0158  5012 | 2/56
 81 h-m-p -0.0000 -0.0000  38.7021 
h-m-p:     -1.07432742e-20     -5.37163712e-20      3.87020518e+01  8218.310407
..  | 2/56
 82 h-m-p  0.0000 0.0001 1102.2062 YYCCC  8213.852195  4 0.0000  5133 | 2/56
 83 h-m-p  0.0000 0.0002 237.4220 YCCC   8211.679948  3 0.0001  5197 | 2/56
 84 h-m-p  0.0001 0.0003 212.8739 CCC    8211.093048  2 0.0000  5260 | 2/56
 85 h-m-p  0.0000 0.0003 214.3719 YCCC   8209.884984  3 0.0001  5324 | 2/56
 86 h-m-p  0.0001 0.0007 260.2591 YC     8208.289098  1 0.0002  5384 | 2/56
 87 h-m-p  0.0000 0.0002 168.7967 YCYCC  8207.853287  4 0.0001  5449 | 2/56
 88 h-m-p  0.0001 0.0003 159.8748 +YC    8207.035151  1 0.0002  5510 | 2/56
 89 h-m-p  0.0002 0.0014 123.1857 CC     8206.455136  1 0.0002  5571 | 2/56
 90 h-m-p  0.0002 0.0008 143.3133 C      8206.064169  0 0.0001  5630 | 2/56
 91 h-m-p  0.0002 0.0008 141.3324 CC     8205.647424  1 0.0002  5691 | 2/56
 92 h-m-p  0.0001 0.0007 136.7499 CCCC   8205.337867  3 0.0002  5756 | 2/56
 93 h-m-p  0.0001 0.0022 151.5178 CCC    8205.116133  2 0.0001  5819 | 2/56
 94 h-m-p  0.0002 0.0012  68.5857 CCC    8204.917303  2 0.0003  5882 | 2/56
 95 h-m-p  0.0002 0.0010  87.4647 CC     8204.695484  1 0.0003  5943 | 2/56
 96 h-m-p  0.0002 0.0009  80.4470 YC     8204.458425  1 0.0003  6003 | 2/56
 97 h-m-p  0.0002 0.0013 151.3636 CCC    8204.217947  2 0.0002  6066 | 2/56
 98 h-m-p  0.0002 0.0010 171.1473 CC     8204.009996  1 0.0002  6127 | 2/56
 99 h-m-p  0.0002 0.0022 120.5776 CC     8203.805696  1 0.0002  6188 | 2/56
100 h-m-p  0.0002 0.0012  55.7421 C      8203.721282  0 0.0002  6247 | 2/56
101 h-m-p  0.0004 0.0119  31.7913 YC     8203.673468  1 0.0003  6307 | 2/56
102 h-m-p  0.0002 0.0022  44.9328 CC     8203.621071  1 0.0002  6368 | 2/56
103 h-m-p  0.0002 0.0008  45.4188 CC     8203.579523  1 0.0002  6429 | 2/56
104 h-m-p  0.0003 0.0046  39.4611 CC     8203.521356  1 0.0004  6490 | 2/56
105 h-m-p  0.0008 0.0066  19.1533 YC     8203.492715  1 0.0005  6550 | 2/56
106 h-m-p  0.0005 0.0064  18.8947 YC     8203.478305  1 0.0003  6610 | 2/56
107 h-m-p  0.0005 0.0232  10.7915 YC     8203.472195  1 0.0003  6670 | 2/56
108 h-m-p  0.0004 0.0123   7.8916 YC     8203.469091  1 0.0002  6730 | 2/56
109 h-m-p  0.0004 0.0406   5.0053 YC     8203.467416  1 0.0003  6790 | 2/56
110 h-m-p  0.0005 0.0366   2.6870 YC     8203.466589  1 0.0004  6850 | 2/56
111 h-m-p  0.0004 0.0455   2.4021 C      8203.465812  0 0.0005  6909 | 2/56
112 h-m-p  0.0010 0.3568   1.3149 YC     8203.465464  1 0.0006  6969 | 2/56
113 h-m-p  0.0008 0.1973   1.0544 Y      8203.465241  0 0.0006  7028 | 2/56
114 h-m-p  0.0007 0.3044   0.9513 C      8203.465038  0 0.0007  7087 | 2/56
115 h-m-p  0.0009 0.4689   0.7212 C      8203.464821  0 0.0009  7200 | 2/56
116 h-m-p  0.0012 0.5472   0.5549 C      8203.464467  0 0.0015  7313 | 2/56
117 h-m-p  0.0008 0.1404   1.0345 C      8203.464032  0 0.0007  7426 | 2/56
118 h-m-p  0.0009 0.4018   0.8754 +CC    8203.459920  1 0.0048  7488 | 2/56
119 h-m-p  0.0012 0.0142   3.5027 YC     8203.456568  1 0.0008  7602 | 2/56
120 h-m-p  0.0009 0.0527   3.1476 C      8203.451626  0 0.0010  7661 | 2/56
121 h-m-p  0.0009 0.0383   3.4668 CC     8203.444012  1 0.0011  7722 | 2/56
122 h-m-p  0.0008 0.0079   4.8926 C      8203.435104  0 0.0008  7781 | 2/56
123 h-m-p  0.0013 0.0947   3.1203 CC     8203.421922  1 0.0021  7842 | 2/56
124 h-m-p  0.0015 0.0379   4.2077 YC     8203.414741  1 0.0011  7902 | 2/56
125 h-m-p  0.0018 0.1064   2.5863 YC     8203.411849  1 0.0012  7962 | 2/56
126 h-m-p  0.0030 0.3068   1.0445 YC     8203.411190  1 0.0015  8022 | 2/56
127 h-m-p  0.0078 1.4764   0.1955 -Y     8203.411166  0 0.0009  8082 | 2/56
128 h-m-p  0.0064 3.1924   0.0626 Y      8203.411121  0 0.0042  8195 | 2/56
129 h-m-p  0.0058 2.9135   0.1220 C      8203.410698  0 0.0074  8308 | 2/56
130 h-m-p  0.0029 0.3536   0.3121 +YC    8203.406879  1 0.0083  8423 | 2/56
131 h-m-p  0.0020 0.0491   1.2881 CC     8203.399327  1 0.0023  8538 | 2/56
132 h-m-p  0.0014 0.0487   2.1049 CC     8203.395563  1 0.0012  8599 | 2/56
133 h-m-p  0.0021 0.2249   1.1800 C      8203.395070  0 0.0008  8658 | 2/56
134 h-m-p  0.0058 1.5113   0.1543 C      8203.395048  0 0.0015  8717 | 2/56
135 h-m-p  0.0380 8.0000   0.0060 +C     8203.394419  0 0.1750  8831 | 2/56
136 h-m-p  0.0013 0.1781   0.8057 +YC    8203.391028  1 0.0042  8946 | 2/56
137 h-m-p  0.0112 1.4211   0.3053 Y      8203.390928  0 0.0021  9059 | 2/56
138 h-m-p  1.6000 8.0000   0.0003 Y      8203.390753  0 1.0726  9172 | 2/56
139 h-m-p  1.6000 8.0000   0.0002 Y      8203.390749  0 1.0431  9285 | 2/56
140 h-m-p  1.6000 8.0000   0.0000 Y      8203.390749  0 1.0965  9398 | 2/56
141 h-m-p  1.6000 8.0000   0.0000 --C    8203.390749  0 0.0250  9513 | 2/56
142 h-m-p  0.0160 8.0000   0.0000 --C    8203.390749  0 0.0003  9628
Out..
lnL  = -8203.390749
9629 lfun, 19258 eigenQcodon, 510337 P(t)

Time used:  5:15
