/usr/local/phylogeny/phyml/bin/phyml-mt-aa.sh JTT-ML91+-4-e-F input_files/20130703_190041/input.phy is translated to /usr/local/phylogeny/phyml/phyml-20100824-sm10/src/phyml -i input_files/20130703_190041/input.phy -d aa -b 0 --mechanistic_opt 11020 -o l --mechanistic_params "-9.0 -1.5 0.0 0.0001 1.0 1.0 1.0 1.0 1.0 0.25 0.25 0.25" --mechanistic "/usr/local/phylogeny/phyml/dat/Wmatrix-11_mtREV JTT-ML91+mod-0" -f e -c 1 --rate_var_over_sites --output_tree_trace . The scale_param_b for rate variation over sites has been specified; unreasonable values tend to be estimated for scale and w_0. .......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename: input.phy . Data type: aa . Alphabet size: 64 . Sequence format: interleaved . Number of data sets: 1 . Nb of bootstrapped data sets: 0 . Model name: /usr/local/phylogeny/phyml/dat/Wmatrix-11_mtREV JTT-ML91+mod-0 . Proportion of invariable sites: 0.000000 . Number of substitution categs: 1 . Amino acid equilibrium frequencies: empirical . Optimise tree topology: no . Evaluted tree: file "BioNJ" . Optimise branch lengths: yes . Optimise substitution model parameters: yes . Run ID: none . Random seed: 1372845641 . Subtree patterns aliasing: no . Version: 20100824-SM10 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 2282 patterns found (out of a total of 3618 sites). . 1338 sites without polymorphism (36.98%). . Computing pairwise distances... . Building BioNJ tree... . WARNING: this analysis requires at least 404 MB of memory space. . ( 20 sec) [ -145879.8580] [Branch lengths ] . ( 51 sec) [ -145285.4186] [Selective constraints on amino acids ][1.546198 * aa_fitness(a,b) + -1.683190 * (1-delta(a,b))] . ( 92 sec) [ -141865.3875] [GTR parameters ][rr_val: 0.259592 1.998254 1.000000 1.000000 1.000000 1.000000] . ( 115 sec) [ -140455.6410] [Branch lengths ] . ( 146 sec) [ -139960.7053] [Selective constraints on amino acids ][1.425397 * aa_fitness(a,b) + -1.820542 * (1-delta(a,b))] . ( 176 sec) [ -139767.3628] [GTR parameters ][rr_val: 0.375119 2.222130 1.000000 1.000000 1.000000 1.000000] . ( 198 sec) [ -139668.0607] [Branch lengths ] . ( 229 sec) [ -139358.8378] [Selective constraints on amino acids ][1.327810 * aa_fitness(a,b) + -1.922643 * (1-delta(a,b))] . ( 256 sec) [ -139306.3957] [GTR parameters ][rr_val: 0.442925 2.127713 1.000000 1.000000 1.000000 1.000000] . ( 279 sec) [ -139254.7296] [Branch lengths ] . ( 311 sec) [ -139071.1643] [Selective constraints on amino acids ][1.253627 * aa_fitness(a,b) + -2.000572 * (1-delta(a,b))] . ( 338 sec) [ -139048.1745] [GTR parameters ][rr_val: 0.490542 2.063338 1.000000 1.000000 1.000000 1.000000] . ( 361 sec) [ -139022.0150] [Branch lengths ] . ( 395 sec) [ -138913.8078] [Selective constraints on amino acids ][1.197133 * aa_fitness(a,b) + -2.059506 * (1-delta(a,b))] . ( 422 sec) [ -138904.0597] [GTR parameters ][rr_val: 0.522431 2.022088 1.000000 1.000000 1.000000 1.000000] . ( 444 sec) [ -138890.6472] [Branch lengths ] . ( 477 sec) [ -138826.4655] [Selective constraints on amino acids ][1.153546 * aa_fitness(a,b) + -2.103863 * (1-delta(a,b))] . ( 504 sec) [ -138822.4407] [GTR parameters ][rr_val: 0.543317 1.995315 1.000000 1.000000 1.000000 1.000000] . ( 526 sec) [ -138815.0733] [Branch lengths ] . ( 558 sec) [ -138776.8592] [Selective constraints on amino acids ][1.119517 * aa_fitness(a,b) + -2.136948 * (1-delta(a,b))] . ( 588 sec) [ -138775.2788] [GTR parameters ][rr_val: 0.556417 1.977579 1.000000 1.000000 1.000000 1.000000] . ( 610 sec) [ -138770.9333] [Branch lengths ] . ( 641 sec) [ -138749.0134] [Selective constraints on amino acids ][1.093883 * aa_fitness(a,b) + -2.159583 * (1-delta(a,b))] . ( 668 sec) [ -138748.4338] [GTR parameters ][rr_val: 0.564384 1.966080 1.000000 1.000000 1.000000 1.000000] . ( 690 sec) [ -138745.6132] [Branch lengths ] . ( 722 sec) [ -138732.4433] [Selective constraints on amino acids ][1.073604 * aa_fitness(a,b) + -2.175434 * (1-delta(a,b))] . ( 746 sec) [ -138732.2523] [GTR parameters ][rr_val: 0.568703 1.958433 1.000000 1.000000 1.000000 1.000000] . ( 768 sec) [ -138730.2804] [Branch lengths ] . ( 799 sec) [ -138722.3782] [Selective constraints on amino acids ][1.057474 * aa_fitness(a,b) + -2.185893 * (1-delta(a,b))] . ( 823 sec) [ -138722.3236] [GTR parameters ][rr_val: 0.570688 1.953481 1.000000 1.000000 1.000000 1.000000] . ( 845 sec) [ -138720.8110] [Branch lengths ] . ( 878 sec) [ -138716.0657] [Selective constraints on amino acids ][1.044565 * aa_fitness(a,b) + -2.192041 * (1-delta(a,b))] . ( 902 sec) [ -138716.0517] [GTR parameters ][rr_val: 0.571259 1.950341 1.000000 1.000000 1.000000 1.000000] . ( 924 sec) [ -138714.7778] [Branch lengths ] . ( 955 sec) [ -138711.9182] [Selective constraints on amino acids ][1.034184 * aa_fitness(a,b) + -2.194722 * (1-delta(a,b))] . ( 982 sec) [ -138711.9124] [GTR parameters ][rr_val: 0.570688 1.948390 1.000000 1.000000 1.000000 1.000000] . ( 1004 sec) [ -138710.8080] [Branch lengths ] . ( 1034 sec) [ -138709.0547] [Selective constraints on amino acids ][1.025799 * aa_fitness(a,b) + -2.194722 * (1-delta(a,b))] . ( 1060 sec) [ -138709.0489] [GTR parameters ][rr_val: 0.569995 1.946442 1.000000 1.000000 1.000000 1.000000] . ( 1082 sec) [ -138707.9691] [Branch lengths ] . ( 1112 sec) [ -138706.8100] [Selective constraints on amino acids ][1.018990 * aa_fitness(a,b) + -2.194722 * (1-delta(a,b))] . ( 1137 sec) [ -138706.7961] [GTR parameters ][rr_val: 0.571186 1.944495 1.000000 1.000000 1.000000 1.000000] . ( 1159 sec) [ -138705.8874] [Branch lengths ] . ( 1188 sec) [ -138705.1400] [Selective constraints on amino acids ][1.013529 * aa_fitness(a,b) + -2.194722 * (1-delta(a,b))] . ( 1216 sec) [ -138705.1013] [GTR parameters ][rr_val: 0.573339 1.942551 1.000000 1.000000 1.000000 1.000000] . ( 1238 sec) [ -138704.3954] [Branch lengths ] . ( 1268 sec) [ -138703.8037] [Selective constraints on amino acids ][1.009200 * aa_fitness(a,b) + -2.190509 * (1-delta(a,b))] . ( 1293 sec) [ -138703.7894] [GTR parameters ][rr_val: 0.571885 1.942551 1.000000 1.000000 1.000000 1.000000] . ( 1315 sec) [ -138703.0665] [Branch lengths ] . ( 1345 sec) [ -138702.5318] [Selective constraints on amino acids ][1.005641 * aa_fitness(a,b) + -2.186305 * (1-delta(a,b))] . ( 1372 sec) [ -138702.5318] [GTR parameters ][rr_val: 0.571885 1.942551 1.000000 1.000000 1.000000 1.000000] . ( 1394 sec) [ -138701.8250] [Branch lengths ] . ( 1426 sec) [ -138701.3188] [Selective constraints on amino acids ][1.002750 * aa_fitness(a,b) + -2.182109 * (1-delta(a,b))] . ( 1454 sec) [ -138701.3152] [GTR parameters ][rr_val: 0.572457 1.940608 1.000000 1.000000 1.000000 1.000000] . ( 1476 sec) [ -138700.6832] [Branch lengths ] . ( 1507 sec) [ -138700.1655] [Selective constraints on amino acids ][1.000421 * aa_fitness(a,b) + -2.177387 * (1-delta(a,b))] . ( 1533 sec) [ -138700.1645] [GTR parameters ][rr_val: 0.573029 1.940608 1.000000 1.000000 1.000000 1.000000] . ( 1555 sec) [ -138699.5813] [Branch lengths ] . ( 1586 sec) [ -138699.0185] [Selective constraints on amino acids ][0.998570 * aa_fitness(a,b) + -2.171924 * (1-delta(a,b))] . ( 1610 sec) [ -138699.0185] [GTR parameters ][rr_val: 0.573029 1.940608 1.000000 1.000000 1.000000 1.000000] . ( 1632 sec) [ -138698.4819] [Branch lengths ] . ( 1664 sec) [ -138697.8722] [Selective constraints on amino acids ][0.997074 * aa_fitness(a,b) + -2.165889 * (1-delta(a,b))] . ( 1691 sec) [ -138697.8722] [GTR parameters ][rr_val: 0.573029 1.940608 1.000000 1.000000 1.000000 1.000000] . ( 1713 sec) [ -138697.3232] [Branch lengths ] . ( 1743 sec) [ -138696.6635] [Selective constraints on amino acids ][0.995847 * aa_fitness(a,b) + -2.159368 * (1-delta(a,b))] . ( 1771 sec) [ -138696.6618] [GTR parameters ][rr_val: 0.572456 1.940608 1.000000 1.000000 1.000000 1.000000] . ( 1793 sec) [ -138696.1563] [Branch lengths ] . ( 1823 sec) [ -138695.4522] [Selective constraints on amino acids ][0.994846 * aa_fitness(a,b) + -2.152454 * (1-delta(a,b))] . ( 1850 sec) [ -138695.4505] [GTR parameters ][rr_val: 0.571884 1.940608 1.000000 1.000000 1.000000 1.000000] . ( 1872 sec) [ -138694.9326] [Branch lengths ] . ( 1902 sec) [ -138694.2244] [Selective constraints on amino acids ][0.993852 * aa_fitness(a,b) + -2.145427 * (1-delta(a,b))] . ( 1930 sec) [ -138694.2228] [GTR parameters ][rr_val: 0.571312 1.940608 1.000000 1.000000 1.000000 1.000000] . ( 1952 sec) [ -138693.6924] [Branch lengths ] . ( 1982 sec) [ -138692.9811] [Selective constraints on amino acids ][0.992858 * aa_fitness(a,b) + -2.138295 * (1-delta(a,b))] . ( 2011 sec) [ -138692.9796] [GTR parameters ][rr_val: 0.570740 1.940608 1.000000 1.000000 1.000000 1.000000] . ( 2033 sec) [ -138692.4355] [Branch lengths ] . ( 2062 sec) [ -138691.7218] [Selective constraints on amino acids ][0.991865 * aa_fitness(a,b) + -2.131061 * (1-delta(a,b))] . ( 2092 sec) [ -138691.7199] [GTR parameters ][rr_val: 0.570170 1.942601 1.000000 1.000000 1.000000 1.000000] . ( 2114 sec) [ -138691.1757] [Branch lengths ] . ( 2143 sec) [ -138690.1930] [Selective constraints on amino acids ][0.991865 * aa_fitness(a,b) + -2.122294 * (1-delta(a,b))] . ( 2171 sec) [ -138690.1913] [GTR parameters ][rr_val: 0.569599 1.942601 1.000000 1.000000 1.000000 1.000000] . ( 2193 sec) [ -138689.6179] [Branch lengths ] . ( 2222 sec) [ -138688.6196] [Selective constraints on amino acids ][0.991865 * aa_fitness(a,b) + -2.113404 * (1-delta(a,b))] . ( 2250 sec) [ -138688.6184] [GTR parameters ][rr_val: 0.569030 1.942601 1.000000 1.000000 1.000000 1.000000] . ( 2272 sec) [ -138688.0307] [Branch lengths ] . ( 2300 sec) [ -138687.0182] [Selective constraints on amino acids ][0.991865 * aa_fitness(a,b) + -2.104400 * (1-delta(a,b))] . ( 2329 sec) [ -138687.0176] [GTR parameters ][rr_val: 0.568461 1.942601 1.000000 1.000000 1.000000 1.000000] . ( 2351 sec) [ -138686.4146] [Branch lengths ] . ( 2379 sec) [ -138685.3880] [Selective constraints on amino acids ][0.991865 * aa_fitness(a,b) + -2.095283 * (1-delta(a,b))] . ( 2409 sec) [ -138685.3869] [GTR parameters ][rr_val: 0.567892 1.944877 1.000000 1.000000 1.000000 1.000000] . ( 2431 sec) [ -138684.7846] [Branch lengths ] . ( 2460 sec) [ -138683.7445] [Selective constraints on amino acids ][0.991865 * aa_fitness(a,b) + -2.086055 * (1-delta(a,b))] . ( 2488 sec) [ -138683.7441] [GTR parameters ][rr_val: 0.567325 1.944877 1.000000 1.000000 1.000000 1.000000] . ( 2510 sec) [ -138683.1103] [Branch lengths ] . ( 2539 sec) [ -138682.0546] [Selective constraints on amino acids ][0.991865 * aa_fitness(a,b) + -2.076706 * (1-delta(a,b))] . ( 2566 sec) [ -138682.0546] [GTR parameters ][rr_val: 0.567325 1.944877 1.000000 1.000000 1.000000 1.000000] . ( 2588 sec) [ -138681.3433] [Branch lengths ] . ( 2618 sec) [ -138680.5370] [Selective constraints on amino acids ][0.990873 * aa_fitness(a,b) + -2.068640 * (1-delta(a,b))] . ( 2646 sec) [ -138680.5355] [GTR parameters ][rr_val: 0.566757 1.944877 1.000000 1.000000 1.000000 1.000000] . ( 2668 sec) [ -138679.8720] [Branch lengths ] . ( 2697 sec) [ -138678.7899] [Selective constraints on amino acids ][0.990873 * aa_fitness(a,b) + -2.059075 * (1-delta(a,b))] . ( 2725 sec) [ -138678.7888] [GTR parameters ][rr_val: 0.566190 1.946821 1.000000 1.000000 1.000000 1.000000] . ( 2747 sec) [ -138678.1242] [Branch lengths ] . ( 2776 sec) [ -138677.0278] [Selective constraints on amino acids ][0.990873 * aa_fitness(a,b) + -2.049396 * (1-delta(a,b))] . ( 2804 sec) [ -138677.0264] [GTR parameters ][rr_val: 0.565624 1.946821 1.000000 1.000000 1.000000 1.000000] . ( 2826 sec) [ -138676.3314] [Branch lengths ] . ( 2855 sec) [ -138675.2197] [Selective constraints on amino acids ][0.990873 * aa_fitness(a,b) + -2.039600 * (1-delta(a,b))] . ( 2883 sec) [ -138675.2189] [GTR parameters ][rr_val: 0.565059 1.946821 1.000000 1.000000 1.000000 1.000000] . ( 2905 sec) [ -138674.5086] [Branch lengths ] . ( 2934 sec) [ -138673.3821] [Selective constraints on amino acids ][0.990873 * aa_fitness(a,b) + -2.029688 * (1-delta(a,b))] . ( 2962 sec) [ -138673.3818] [GTR parameters ][rr_val: 0.564494 1.946821 1.000000 1.000000 1.000000 1.000000] . ( 2984 sec) [ -138672.6549] [Branch lengths ] . ( 3013 sec) [ -138671.5153] [Selective constraints on amino acids ][0.990873 * aa_fitness(a,b) + -2.019670 * (1-delta(a,b))] . ( 3041 sec) [ -138671.5146] [GTR parameters ][rr_val: 0.564494 1.948935 1.000000 1.000000 1.000000 1.000000] . ( 3064 sec) [ -138670.7224] [Branch lengths ] . ( 3092 sec) [ -138669.5626] [Selective constraints on amino acids ][0.990873 * aa_fitness(a,b) + -2.009510 * (1-delta(a,b))] . ( 3118 sec) [ -138669.5606] [GTR parameters ][rr_val: 0.563928 1.948935 1.000000 1.000000 1.000000 1.000000] . ( 3140 sec) [ -138668.8006] [Branch lengths ] . ( 3168 sec) [ -138667.6319] [Selective constraints on amino acids ][0.990873 * aa_fitness(a,b) + -1.999265 * (1-delta(a,b))] . ( 3195 sec) [ -138667.6305] [GTR parameters ][rr_val: 0.563364 1.948935 1.000000 1.000000 1.000000 1.000000] . ( 3218 sec) [ -138666.8563] [Branch lengths ] . ( 3246 sec) [ -138665.6727] [Selective constraints on amino acids ][0.990873 * aa_fitness(a,b) + -1.988906 * (1-delta(a,b))] . ( 3274 sec) [ -138665.6718] [GTR parameters ][rr_val: 0.562801 1.948935 1.000000 1.000000 1.000000 1.000000] . ( 3297 sec) [ -138664.8808] [Branch lengths ] . ( 3325 sec) [ -138663.6829] [Selective constraints on amino acids ][0.990873 * aa_fitness(a,b) + -1.978437 * (1-delta(a,b))] . ( 3355 sec) [ -138663.6819] [GTR parameters ][rr_val: 0.562238 1.950956 1.000000 1.000000 1.000000 1.000000] . ( 3377 sec) [ -138662.8914] [Branch lengths ] . ( 3405 sec) [ -138661.6800] [Selective constraints on amino acids ][0.990873 * aa_fitness(a,b) + -1.967861 * (1-delta(a,b))] . ( 3434 sec) [ -138661.6792] [GTR parameters ][rr_val: 0.561676 1.950956 1.000000 1.000000 1.000000 1.000000] . ( 3456 sec) [ -138660.8559] [Branch lengths ] . ( 3484 sec) [ -138659.6292] [Selective constraints on amino acids ][0.990873 * aa_fitness(a,b) + -1.957169 * (1-delta(a,b))] . ( 3513 sec) [ -138659.6288] [GTR parameters ][rr_val: 0.561114 1.950956 1.000000 1.000000 1.000000 1.000000] . ( 3535 sec) [ -138658.7901] [Branch lengths ] . ( 3563 sec) [ -138657.5489] [Selective constraints on amino acids ][0.990873 * aa_fitness(a,b) + -1.946368 * (1-delta(a,b))] . ( 3590 sec) [ -138657.5489] [GTR parameters ][rr_val: 0.561114 1.950956 1.000000 1.000000 1.000000 1.000000] . ( 3613 sec) [ -138656.6228] [Branch lengths ] . ( 3642 sec) [ -138655.6509] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.936859 * (1-delta(a,b))] . ( 3671 sec) [ -138655.6492] [GTR parameters ][rr_val: 0.560553 1.950956 1.000000 1.000000 1.000000 1.000000] . ( 3693 sec) [ -138654.7804] [Branch lengths ] . ( 3722 sec) [ -138653.5139] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.925855 * (1-delta(a,b))] . ( 3752 sec) [ -138653.5116] [GTR parameters ][rr_val: 0.559992 1.953230 1.000000 1.000000 1.000000 1.000000] . ( 3774 sec) [ -138652.6447] [Branch lengths ] . ( 3802 sec) [ -138651.3655] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.914750 * (1-delta(a,b))] . ( 3831 sec) [ -138651.3638] [GTR parameters ][rr_val: 0.559432 1.953230 1.000000 1.000000 1.000000 1.000000] . ( 3853 sec) [ -138650.4633] [Branch lengths ] . ( 3881 sec) [ -138649.1682] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.903530 * (1-delta(a,b))] . ( 3910 sec) [ -138649.1669] [GTR parameters ][rr_val: 0.558873 1.953230 1.000000 1.000000 1.000000 1.000000] . ( 3932 sec) [ -138648.2497] [Branch lengths ] . ( 3961 sec) [ -138646.9415] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.892207 * (1-delta(a,b))] . ( 3989 sec) [ -138646.9407] [GTR parameters ][rr_val: 0.558314 1.953230 1.000000 1.000000 1.000000 1.000000] . ( 4011 sec) [ -138646.0090] [Branch lengths ] . ( 4040 sec) [ -138644.6870] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.880781 * (1-delta(a,b))] . ( 4070 sec) [ -138644.6860] [GTR parameters ][rr_val: 0.557756 1.955337 1.000000 1.000000 1.000000 1.000000] . ( 4092 sec) [ -138643.7560] [Branch lengths ] . ( 4120 sec) [ -138642.4222] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.869260 * (1-delta(a,b))] . ( 4149 sec) [ -138642.4215] [GTR parameters ][rr_val: 0.557198 1.955337 1.000000 1.000000 1.000000 1.000000] . ( 4171 sec) [ -138641.4594] [Branch lengths ] . ( 4199 sec) [ -138640.1108] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.857631 * (1-delta(a,b))] . ( 4228 sec) [ -138640.1105] [GTR parameters ][rr_val: 0.556641 1.955337 1.000000 1.000000 1.000000 1.000000] . ( 4250 sec) [ -138639.1323] [Branch lengths ] . ( 4278 sec) [ -138637.7703] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.845901 * (1-delta(a,b))] . ( 4305 sec) [ -138637.7703] [GTR parameters ][rr_val: 0.556641 1.955337 1.000000 1.000000 1.000000 1.000000] . ( 4328 sec) [ -138636.7038] [Branch lengths ] . ( 4356 sec) [ -138635.3222] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.834041 * (1-delta(a,b))] . ( 4384 sec) [ -138635.3211] [GTR parameters ][rr_val: 0.556084 1.955337 1.000000 1.000000 1.000000 1.000000] . ( 4407 sec) [ -138634.3129] [Branch lengths ] . ( 4435 sec) [ -138632.9271] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.822122 * (1-delta(a,b))] . ( 4465 sec) [ -138632.9255] [GTR parameters ][rr_val: 0.555528 1.957578 1.000000 1.000000 1.000000 1.000000] . ( 4487 sec) [ -138631.9256] [Branch lengths ] . ( 4516 sec) [ -138630.5283] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.810111 * (1-delta(a,b))] . ( 4544 sec) [ -138630.5272] [GTR parameters ][rr_val: 0.554973 1.957578 1.000000 1.000000 1.000000 1.000000] . ( 4566 sec) [ -138629.4926] [Branch lengths ] . ( 4595 sec) [ -138628.0813] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.797999 * (1-delta(a,b))] . ( 4622 sec) [ -138628.0807] [GTR parameters ][rr_val: 0.554418 1.957578 1.000000 1.000000 1.000000 1.000000] . ( 4644 sec) [ -138627.0332] [Branch lengths ] . ( 4672 sec) [ -138625.6097] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.785793 * (1-delta(a,b))] . ( 4701 sec) [ -138625.6096] [GTR parameters ][rr_val: 0.553863 1.957578 1.000000 1.000000 1.000000 1.000000] . ( 4723 sec) [ -138624.5478] [Branch lengths ] . ( 4752 sec) [ -138623.1131] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.773498 * (1-delta(a,b))] . ( 4779 sec) [ -138623.1130] [GTR parameters ][rr_val: 0.553863 1.959535 1.000000 1.000000 1.000000 1.000000] . ( 4801 sec) [ -138621.9809] [Branch lengths ] . ( 4829 sec) [ -138620.5295] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.761090 * (1-delta(a,b))] . ( 4858 sec) [ -138620.5278] [GTR parameters ][rr_val: 0.553309 1.959535 1.000000 1.000000 1.000000 1.000000] . ( 4880 sec) [ -138619.4398] [Branch lengths ] . ( 4908 sec) [ -138617.9833] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.748620 * (1-delta(a,b))] . ( 4937 sec) [ -138617.9822] [GTR parameters ][rr_val: 0.552756 1.959535 1.000000 1.000000 1.000000 1.000000] . ( 4959 sec) [ -138616.8843] [Branch lengths ] . ( 4988 sec) [ -138615.4169] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.736065 * (1-delta(a,b))] . ( 5016 sec) [ -138615.4163] [GTR parameters ][rr_val: 0.552203 1.959535 1.000000 1.000000 1.000000 1.000000] . ( 5038 sec) [ -138614.3056] [Branch lengths ] . ( 5067 sec) [ -138612.8287] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.723430 * (1-delta(a,b))] . ( 5095 sec) [ -138612.8285] [GTR parameters ][rr_val: 0.551651 1.959535 1.000000 1.000000 1.000000 1.000000] . ( 5118 sec) [ -138611.7076] [Branch lengths ] . ( 5146 sec) [ -138610.2210] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.710716 * (1-delta(a,b))] . ( 5173 sec) [ -138610.2210] [GTR parameters ][rr_val: 0.551651 1.959535 1.000000 1.000000 1.000000 1.000000] . ( 5196 sec) [ -138609.0096] [Branch lengths ] . ( 5224 sec) [ -138607.5081] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.697897 * (1-delta(a,b))] . ( 5253 sec) [ -138607.5069] [GTR parameters ][rr_val: 0.551099 1.961495 1.000000 1.000000 1.000000 1.000000] . ( 5276 sec) [ -138606.3817] [Branch lengths ] . ( 5304 sec) [ -138604.8810] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.685045 * (1-delta(a,b))] . ( 5333 sec) [ -138604.8800] [GTR parameters ][rr_val: 0.550548 1.961495 1.000000 1.000000 1.000000 1.000000] . ( 5355 sec) [ -138603.7270] [Branch lengths ] . ( 5383 sec) [ -138602.2161] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.672112 * (1-delta(a,b))] . ( 5410 sec) [ -138602.2156] [GTR parameters ][rr_val: 0.549998 1.961495 1.000000 1.000000 1.000000 1.000000] . ( 5433 sec) [ -138601.0539] [Branch lengths ] . ( 5461 sec) [ -138599.5348] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.659106 * (1-delta(a,b))] . ( 5488 sec) [ -138599.5348] [GTR parameters ][rr_val: 0.549998 1.961495 1.000000 1.000000 1.000000 1.000000] . ( 5511 sec) [ -138598.2837] [Branch lengths ] . ( 5539 sec) [ -138596.7506] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.646003 * (1-delta(a,b))] . ( 5567 sec) [ -138596.7495] [GTR parameters ][rr_val: 0.549448 1.961495 1.000000 1.000000 1.000000 1.000000] . ( 5590 sec) [ -138595.5690] [Branch lengths ] . ( 5618 sec) [ -138594.0363] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.632865 * (1-delta(a,b))] . ( 5647 sec) [ -138594.0358] [GTR parameters ][rr_val: 0.548898 1.961495 1.000000 1.000000 1.000000 1.000000] . ( 5670 sec) [ -138592.8476] [Branch lengths ] . ( 5698 sec) [ -138591.3088] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.619666 * (1-delta(a,b))] . ( 5726 sec) [ -138591.3086] [GTR parameters ][rr_val: 0.548898 1.963456 1.000000 1.000000 1.000000 1.000000] . ( 5748 sec) [ -138590.0542] [Branch lengths ] . ( 5777 sec) [ -138588.5037] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.606379 * (1-delta(a,b))] . ( 5803 sec) [ -138588.5019] [GTR parameters ][rr_val: 0.548349 1.963456 1.000000 1.000000 1.000000 1.000000] . ( 5825 sec) [ -138587.2983] [Branch lengths ] . ( 5854 sec) [ -138585.7481] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.593058 * (1-delta(a,b))] . ( 5882 sec) [ -138585.7470] [GTR parameters ][rr_val: 0.547801 1.963456 1.000000 1.000000 1.000000 1.000000] . ( 5904 sec) [ -138584.5393] [Branch lengths ] . ( 5933 sec) [ -138582.9832] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.579676 * (1-delta(a,b))] . ( 5960 sec) [ -138582.9827] [GTR parameters ][rr_val: 0.547253 1.963456 1.000000 1.000000 1.000000 1.000000] . ( 5983 sec) [ -138581.7676] [Branch lengths ] . ( 6011 sec) [ -138580.2075] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.566243 * (1-delta(a,b))] . ( 6037 sec) [ -138580.2075] [GTR parameters ][rr_val: 0.547253 1.963456 1.000000 1.000000 1.000000 1.000000] . ( 6059 sec) [ -138578.9085] [Branch lengths ] . ( 6088 sec) [ -138577.3386] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.552731 * (1-delta(a,b))] . ( 6115 sec) [ -138577.3378] [GTR parameters ][rr_val: 0.546706 1.963456 1.000000 1.000000 1.000000 1.000000] . ( 6137 sec) [ -138576.1110] [Branch lengths ] . ( 6166 sec) [ -138574.5455] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.539204 * (1-delta(a,b))] . ( 6194 sec) [ -138574.5453] [GTR parameters ][rr_val: 0.546159 1.963456 1.000000 1.000000 1.000000 1.000000] . ( 6217 sec) [ -138573.3170] [Branch lengths ] . ( 6245 sec) [ -138571.7475] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.525625 * (1-delta(a,b))] . ( 6272 sec) [ -138571.7475] [GTR parameters ][rr_val: 0.546159 1.963456 1.000000 1.000000 1.000000 1.000000] . ( 6295 sec) [ -138570.4344] [Branch lengths ] . ( 6323 sec) [ -138568.8557] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.511759 * (1-delta(a,b))] . ( 6349 sec) [ -138568.8538] [GTR parameters ][rr_val: 0.545613 1.963456 1.000000 1.000000 1.000000 1.000000] . ( 6371 sec) [ -138567.5746] [Branch lengths ] . ( 6399 sec) [ -138565.9992] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.497595 * (1-delta(a,b))] . ( 6428 sec) [ -138565.9957] [GTR parameters ][rr_val: 0.545028 1.965420 1.000000 1.000000 1.000000 1.000000] . ( 6451 sec) [ -138564.6839] [Branch lengths ] . ( 6479 sec) [ -138563.1072] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.483115 * (1-delta(a,b))] . ( 6508 sec) [ -138563.1019] [GTR parameters ][rr_val: 0.544234 1.965420 1.000000 1.000000 1.000000 1.000000] . ( 6530 sec) [ -138561.7447] [Branch lengths ] . ( 6559 sec) [ -138560.1671] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.468319 * (1-delta(a,b))] . ( 6586 sec) [ -138560.1614] [GTR parameters ][rr_val: 0.543411 1.965420 1.000000 1.000000 1.000000 1.000000] . ( 6609 sec) [ -138558.7502] [Branch lengths ] . ( 6638 sec) [ -138557.1719] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.453210 * (1-delta(a,b))] . ( 6668 sec) [ -138557.1661] [GTR parameters ][rr_val: 0.542579 1.965420 1.000000 1.000000 1.000000 1.000000] . ( 6691 sec) [ -138555.7013] [Branch lengths ] . ( 6719 sec) [ -138554.1228] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.437789 * (1-delta(a,b))] . ( 6749 sec) [ -138554.1170] [GTR parameters ][rr_val: 0.541745 1.965420 1.000000 1.000000 1.000000 1.000000] . ( 6772 sec) [ -138552.5956] [Branch lengths ] . ( 6800 sec) [ -138551.0173] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.425483 * (1-delta(a,b))] . ( 6826 sec) [ -138550.9898] [GTR parameters ][rr_val: 0.543743 1.965420 1.000000 1.000000 1.000000 1.000000] . ( 6849 sec) [ -138549.7034] [Branch lengths ] . ( 6876 sec) [ -138548.1458] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.413034 * (1-delta(a,b))] . ( 6905 sec) [ -138548.1386] [GTR parameters ][rr_val: 0.544690 1.963455 1.000000 1.000000 1.000000 1.000000] . ( 6928 sec) [ -138546.9445] [Branch lengths ] . ( 6956 sec) [ -138545.3945] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.400397 * (1-delta(a,b))] . ( 6980 sec) [ -138545.3938] [GTR parameters ][rr_val: 0.545235 1.963455 1.000000 1.000000 1.000000 1.000000] . ( 7003 sec) [ -138544.2394] [Branch lengths ] . ( 7026 sec) [ -138542.6928] [Selective constraints on amino acids ][0.989882 * aa_fitness(a,b) + -1.387562 * (1-delta(a,b))] . ( 7052 sec) [ -138542.6928] [GTR parameters ][rr_val: 0.545235 1.963455 1.000000 1.000000 1.000000 1.000000] . ( 7075 sec) [ -138541.5766] [Branch lengths ] . ( 7101 sec) [ -138539.6984] [Selective constraints on amino acids ][0.990872 * aa_fitness(a,b) + -1.373126 * (1-delta(a,b))] . ( 7128 sec) [ -138539.6983] [GTR parameters ][rr_val: 0.544690 1.963455 1.000000 1.000000 1.000000 1.000000] . ( 7151 sec) [ -138538.6257] [Branch lengths ] . ( 7178 sec) [ -138537.0866] [Selective constraints on amino acids ][0.990872 * aa_fitness(a,b) + -1.359916 * (1-delta(a,b))] . ( 7207 sec) [ -138537.0862] [GTR parameters ][rr_val: 0.544145 1.963455 1.000000 1.000000 1.000000 1.000000] . ( 7229 sec) [ -138535.9788] [Branch lengths ] . ( 7256 sec) [ -138534.4375] [Selective constraints on amino acids ][0.990872 * aa_fitness(a,b) + -1.346500 * (1-delta(a,b))] . ( 7285 sec) [ -138534.4369] [GTR parameters ][rr_val: 0.543601 1.963455 1.000000 1.000000 1.000000 1.000000] . ( 7307 sec) [ -138533.3001] [Branch lengths ] . ( 7334 sec) [ -138531.7576] [Selective constraints on amino acids ][0.990872 * aa_fitness(a,b) + -1.332885 * (1-delta(a,b))] . ( 7363 sec) [ -138531.7569] [GTR parameters ][rr_val: 0.543057 1.963455 1.000000 1.000000 1.000000 1.000000] . ( 7386 sec) [ -138530.5901] [Branch lengths ] . ( 7413 sec) [ -138529.0487] [Selective constraints on amino acids ][0.990872 * aa_fitness(a,b) + -1.319086 * (1-delta(a,b))] . ( 7442 sec) [ -138529.0480] [GTR parameters ][rr_val: 0.542514 1.963455 1.000000 1.000000 1.000000 1.000000] . ( 7466 sec) [ -138527.8547] [Branch lengths ] . ( 7492 sec) [ -138526.3147] [Selective constraints on amino acids ][0.990872 * aa_fitness(a,b) + -1.305109 * (1-delta(a,b))] . ( 7521 sec) [ -138526.3139] [GTR parameters ][rr_val: 0.541972 1.965418 1.000000 1.000000 1.000000 1.000000] . ( 7544 sec) [ -138525.1130] [Branch lengths ] . ( 7574 sec) [ -138523.2455] [Selective constraints on amino acids ][0.991863 * aa_fitness(a,b) + -1.289543 * (1-delta(a,b))] . ( 7603 sec) [ -138523.2447] [GTR parameters ][rr_val: 0.541430 1.965418 1.000000 1.000000 1.000000 1.000000] . ( 7627 sec) [ -138522.0019] [Branch lengths ] . ( 7658 sec) [ -138520.4681] [Selective constraints on amino acids ][0.991863 * aa_fitness(a,b) + -1.275238 * (1-delta(a,b))] . ( 7688 sec) [ -138520.4674] [GTR parameters ][rr_val: 0.540888 1.965418 1.000000 1.000000 1.000000 1.000000] . ( 7712 sec) [ -138519.1998] [Branch lengths ] . ( 7742 sec) [ -138517.6717] [Selective constraints on amino acids ][0.991863 * aa_fitness(a,b) + -1.260791 * (1-delta(a,b))] . ( 7772 sec) [ -138517.6713] [GTR parameters ][rr_val: 0.540347 1.965418 1.000000 1.000000 1.000000 1.000000] . ( 7797 sec) [ -138516.3848] [Branch lengths ] . ( 7828 sec) [ -138514.8615] [Selective constraints on amino acids ][0.991863 * aa_fitness(a,b) + -1.246206 * (1-delta(a,b))] . ( 7860 sec) [ -138514.8614] [GTR parameters ][rr_val: 0.539807 1.965418 1.000000 1.000000 1.000000 1.000000] . ( 7884 sec) [ -138513.5557] [Branch lengths ] . ( 7915 sec) [ -138511.7114] [Selective constraints on amino acids ][0.992855 * aa_fitness(a,b) + -1.230049 * (1-delta(a,b))] . ( 7943 sec) [ -138511.7114] [GTR parameters ][rr_val: 0.539807 1.965418 1.000000 1.000000 1.000000 1.000000] . ( 7984 sec) [ -138509.3406] [Selective constraints on amino acids ][1.001088 * aa_fitness(a,b) + -1.218158 * (1-delta(a,b))] . ( 8012 sec) [ -138509.3385] [GTR parameters ][rr_val: 0.540347 1.967668 1.000000 1.000000 1.000000 1.000000] . Log likelihood of the current tree: -138509.338548. . Printing the most likely tree in file 'input.phy_phyml_tree.txt'... . Printing the most likely tree in file 'input.phy_phyml_tree.txt'... . Time used 2h13m40s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo