/usr/local/phylogeny/phyml/bin/phyml-mt-aa.sh is translated to /usr/local/phylogeny/phyml/phyml-20100824-sm10/src/phyml -i input_files/20130703_180051/input.phy -d aa -b 0 --mechanistic_opt 11020 -o l --mechanistic_params "-9.0 -1.5 0.0 0.0 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: 1372842051 . 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) [ -145889.8290] [Branch lengths ] . ( 52 sec) [ -145293.8433] [Selective constraints on amino acids ][1.546420 * aa_fitness(a,b) + -1.683269 * (1-delta(a,b))] . ( 103 sec) [ -144252.7124] [GTR parameters ][rr_val: 0.000000 1.670056 0.881396 1.000000 1.000000 1.000000] . ( 125 sec) [ -142555.4709] [Branch lengths ] . ( 157 sec) [ -142207.1035] [Selective constraints on amino acids ][1.457170 * aa_fitness(a,b) + -1.806464 * (1-delta(a,b))] . ( 212 sec) [ -142121.8458] [GTR parameters ][rr_val: 0.000000 1.931809 0.856051 1.000000 1.000000 1.000000] . ( 234 sec) [ -142077.8019] [Branch lengths ] . ( 266 sec) [ -141842.6615] [Selective constraints on amino acids ][1.377423 * aa_fitness(a,b) + -1.896441 * (1-delta(a,b))] . ( 302 sec) [ -141837.0525] [GTR parameters ][rr_val: 0.000000 2.007847 0.867079 1.000000 1.000000 1.000000] . ( 324 sec) [ -141836.4127] [Branch lengths ] . ( 358 sec) [ -141682.6294] [Selective constraints on amino acids ][1.312210 * aa_fitness(a,b) + -1.966617 * (1-delta(a,b))] . ( 392 sec) [ -141680.4826] [GTR parameters ][rr_val: 0.000000 2.022045 0.886498 1.000000 1.000000 1.000000] . ( 414 sec) [ -141679.0149] [Branch lengths ] . ( 446 sec) [ -141576.1091] [Selective constraints on amino acids ][1.258627 * aa_fitness(a,b) + -2.022687 * (1-delta(a,b))] . ( 483 sec) [ -141574.0451] [GTR parameters ][rr_val: 0.000000 2.019313 0.905313 1.000000 1.000000 1.000000] . ( 505 sec) [ -141571.9628] [Branch lengths ] . ( 538 sec) [ -141502.4639] [Selective constraints on amino acids ][1.214242 * aa_fitness(a,b) + -2.067916 * (1-delta(a,b))] . ( 574 sec) [ -141500.8513] [GTR parameters ][rr_val: 0.000000 2.014175 0.921683 1.000000 1.000000 1.000000] . ( 596 sec) [ -141498.8542] [Branch lengths ] . ( 629 sec) [ -141452.0364] [Selective constraints on amino acids ][1.177378 * aa_fitness(a,b) + -2.104193 * (1-delta(a,b))] . ( 665 sec) [ -141450.9081] [GTR parameters ][rr_val: 0.000000 2.010262 0.935362 1.000000 1.000000 1.000000] . ( 687 sec) [ -141449.1294] [Branch lengths ] . ( 718 sec) [ -141418.7888] [Selective constraints on amino acids ][1.147884 * aa_fitness(a,b) + -2.131359 * (1-delta(a,b))] . ( 760 sec) [ -141418.0692] [GTR parameters ][rr_val: 0.000000 2.008047 0.946310 1.000000 1.000000 1.000000] . ( 783 sec) [ -141416.4752] [Branch lengths ] . ( 815 sec) [ -141396.0799] [Selective constraints on amino acids ][1.123307 * aa_fitness(a,b) + -2.152374 * (1-delta(a,b))] . ( 844 sec) [ -141395.5899] [GTR parameters ][rr_val: 0.000000 2.007149 0.956472 1.000000 1.000000 1.000000] . ( 866 sec) [ -141394.0657] [Branch lengths ] . ( 899 sec) [ -141380.2988] [Selective constraints on amino acids ][1.102707 * aa_fitness(a,b) + -2.168292 * (1-delta(a,b))] . ( 941 sec) [ -141380.0381] [GTR parameters ][rr_val: 0.000000 2.007092 0.963431 1.000000 1.000000 1.000000] . ( 963 sec) [ -141378.6527] [Branch lengths ] . ( 994 sec) [ -141369.5624] [Selective constraints on amino acids ][1.085556 * aa_fitness(a,b) + -2.179752 * (1-delta(a,b))] . ( 1036 sec) [ -141369.3544] [GTR parameters ][rr_val: 0.000000 2.008252 0.969652 1.000000 1.000000 1.000000] . ( 1057 sec) [ -141368.0169] [Branch lengths ] . ( 1092 sec) [ -141361.9984] [Selective constraints on amino acids ][1.071212 * aa_fitness(a,b) + -2.187493 * (1-delta(a,b))] . ( 1133 sec) [ -141361.8517] [GTR parameters ][rr_val: 0.000000 2.009228 0.974789 1.000000 1.000000 1.000000] . ( 1156 sec) [ -141360.5198] [Branch lengths ] . ( 1190 sec) [ -141356.5351] [Selective constraints on amino acids ][1.059197 * aa_fitness(a,b) + -2.192079 * (1-delta(a,b))] . ( 1230 sec) [ -141356.4277] [GTR parameters ][rr_val: 0.000000 2.010478 0.979120 1.000000 1.000000 1.000000] . ( 1253 sec) [ -141355.1019] [Branch lengths ] . ( 1288 sec) [ -141352.4548] [Selective constraints on amino acids ][1.049120 * aa_fitness(a,b) + -2.196350 * (1-delta(a,b))] . ( 1329 sec) [ -141352.3372] [GTR parameters ][rr_val: 0.000000 2.007666 0.983245 1.000000 1.000000 1.000000] . ( 1351 sec) [ -141351.3798] [Branch lengths ] . ( 1382 sec) [ -141349.5861] [Selective constraints on amino acids ][1.040723 * aa_fitness(a,b) + -2.196350 * (1-delta(a,b))] . ( 1416 sec) [ -141349.5351] [GTR parameters ][rr_val: 0.000000 2.010686 0.985726 1.000000 1.000000 1.000000]