/usr/local/phylogeny/phyml/phyml-20100824-sm10/src/phyml -i input_files/20130703_161723/input.phy -d codon -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_with_EI-11_JTT JTT-ML91+mod-0" -f e -c 1 --rate_var_over_sites --output_tree_trace . Sum=1.000003 . Scaling frequencies... . 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: codon . 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_with_EI-11_JTT JTT-ML91+mod-0 . Proportion of invariable sites: 0.000000 . Number of substitution categs: 1 . Codon 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: 1372835843 . Subtree patterns aliasing: no . Version: 20100824-SM10 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 318 patterns found (out of a total of 1112 sites). . 832 sites without polymorphism (74.82%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 7 Mo of memory space. . ( 0 sec) [ -6663.4173] [Branch lengths ] . ( 0 sec) [ -6659.2132] [Selective constraints on amino acids ][0.742027 * aa_fitness(a,b) + -1.495086 * (1-delta(a,b))] . ( 1 sec) [ -6624.0654] [GTR parameters ][rr_val: 0.077509 1.998086 1.000000 1.000000 1.000000 1.000000] . ( 1 sec) [ -6623.9463] [Branch lengths ] . ( 1 sec) [ -6623.7826] [Selective constraints on amino acids ][0.694770 * aa_fitness(a,b) + -1.483409 * (1-delta(a,b))] . ( 2 sec) [ -6622.4577] [GTR parameters ][rr_val: 0.065565 2.381423 1.000000 1.000000 1.000000 1.000000] . ( 2 sec) [ -6622.4563] [Branch lengths ] . ( 2 sec) [ -6622.4214] [Selective constraints on amino acids ][0.674388 * aa_fitness(a,b) + -1.470254 * (1-delta(a,b))] . ( 3 sec) [ -6622.4023] [GTR parameters ][rr_val: 0.059839 2.398510 1.000000 1.000000 1.000000 1.000000] . ( 3 sec) [ -6622.4023] [Branch lengths ] . ( 3 sec) [ -6622.3983] [Selective constraints on amino acids ][0.677224 * aa_fitness(a,b) + -1.459910 * (1-delta(a,b))] . ( 4 sec) [ -6622.3982] [GTR parameters ][rr_val: 0.059456 2.402690 1.000000 1.000000 1.000000 1.000000] . ( 4 sec) [ -6622.3982] [Branch lengths ] . ( 4 sec) [ -6622.3944] [Selective constraints on amino acids ][0.682504 * aa_fitness(a,b) + -1.452557 * (1-delta(a,b))] . ( 4 sec) [ -6622.3944] [GTR parameters ][rr_val: 0.059456 2.400287 1.000000 1.000000 1.000000 1.000000] . ( 5 sec) [ -6622.3944] [Branch lengths ] . ( 5 sec) [ -6622.3922] [Selective constraints on amino acids ][0.686694 * aa_fitness(a,b) + -1.447410 * (1-delta(a,b))] . ( 5 sec) [ -6622.3922] [GTR parameters ][rr_val: 0.059526 2.400287 1.000000 1.000000 1.000000 1.000000] . ( 6 sec) [ -6622.3922] [Branch lengths ] . ( 6 sec) [ -6622.3911] [Selective constraints on amino acids ][0.689599 * aa_fitness(a,b) + -1.443807 * (1-delta(a,b))] . ( 6 sec) [ -6622.3911] [GTR parameters ][rr_val: 0.059585 2.400287 1.000000 1.000000 1.000000 1.000000] . ( 7 sec) [ -6622.3911] [Branch lengths ] . ( 7 sec) [ -6622.3906] [Selective constraints on amino acids ][0.691641 * aa_fitness(a,b) + -1.440866 * (1-delta(a,b))] . ( 7 sec) [ -6622.3906] [GTR parameters ][rr_val: 0.059585 2.400287 1.000000 1.000000 1.000000 1.000000] . ( 8 sec) [ -6622.3903] [Selective constraints on amino acids ][0.693276 * aa_fitness(a,b) + -1.437926 * (1-delta(a,b))] . ( 8 sec) [ -6622.3903] [GTR parameters ][rr_val: 0.059526 2.400287 1.000000 1.000000 1.000000 1.000000] . Log likelihood of the current tree: -6622.390328. . 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 0h0m8s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo