/usr/local/phylogeny/phyml/phyml-20100824-sm10/src/phyml -i input_files/20130703_153949/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 LG-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 LG-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: 1372833589 . 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) [ -6695.1663] [Branch lengths ] . ( 1 sec) [ -6667.3155] [Selective constraints on amino acids ][0.500459 * aa_fitness(a,b) + -1.588632 * (1-delta(a,b))] . ( 1 sec) [ -6627.8834] [GTR parameters ][rr_val: 0.073087 1.998765 1.000000 1.000000 1.000000 1.000000] . ( 2 sec) [ -6627.7451] [Branch lengths ] . ( 2 sec) [ -6627.0700] [Selective constraints on amino acids ][0.433129 * aa_fitness(a,b) + -1.588632 * (1-delta(a,b))] . ( 2 sec) [ -6624.5533] [GTR parameters ][rr_val: 0.060850 2.548208 1.000000 1.000000 1.000000 1.000000] . ( 3 sec) [ -6624.5515] [Branch lengths ] . ( 3 sec) [ -6624.4588] [Selective constraints on amino acids ][0.412069 * aa_fitness(a,b) + -1.559889 * (1-delta(a,b))] . ( 3 sec) [ -6624.4153] [GTR parameters ][rr_val: 0.053329 2.578588 1.000000 1.000000 1.000000 1.000000] . ( 4 sec) [ -6624.4153] [Branch lengths ] . ( 4 sec) [ -6624.3933] [Selective constraints on amino acids ][0.418373 * aa_fitness(a,b) + -1.536844 * (1-delta(a,b))] . ( 4 sec) [ -6624.3927] [GTR parameters ][rr_val: 0.052715 2.585475 1.000000 1.000000 1.000000 1.000000] . ( 5 sec) [ -6624.3927] [Branch lengths ] . ( 5 sec) [ -6624.3731] [Selective constraints on amino acids ][0.426769 * aa_fitness(a,b) + -1.520046 * (1-delta(a,b))] . ( 5 sec) [ -6624.3731] [GTR parameters ][rr_val: 0.052770 2.590738 1.000000 1.000000 1.000000 1.000000] . ( 6 sec) [ -6624.3731] [Branch lengths ] . ( 6 sec) [ -6624.3619] [Selective constraints on amino acids ][0.433172 * aa_fitness(a,b) + -1.507546 * (1-delta(a,b))] . ( 6 sec) [ -6624.3619] [GTR parameters ][rr_val: 0.052823 2.590738 1.000000 1.000000 1.000000 1.000000] . ( 7 sec) [ -6624.3619] [Branch lengths ] . ( 7 sec) [ -6624.3557] [Selective constraints on amino acids ][0.438042 * aa_fitness(a,b) + -1.498433 * (1-delta(a,b))] . ( 7 sec) [ -6624.3557] [GTR parameters ][rr_val: 0.052890 2.590738 1.000000 1.000000 1.000000 1.000000] . ( 8 sec) [ -6624.3557] [Branch lengths ] . ( 8 sec) [ -6624.3523] [Selective constraints on amino acids ][0.441614 * aa_fitness(a,b) + -1.491796 * (1-delta(a,b))] . ( 8 sec) [ -6624.3523] [GTR parameters ][rr_val: 0.052947 2.594985 1.000000 1.000000 1.000000 1.000000] . ( 9 sec) [ -6624.3523] [Branch lengths ] . ( 9 sec) [ -6624.3505] [Selective constraints on amino acids ][0.444127 * aa_fitness(a,b) + -1.486769 * (1-delta(a,b))] . ( 9 sec) [ -6624.3505] [GTR parameters ][rr_val: 0.052947 2.594985 1.000000 1.000000 1.000000 1.000000] . ( 10 sec) [ -6624.3505] [Branch lengths ] . ( 10 sec) [ -6624.3495] [Selective constraints on amino acids ][0.446082 * aa_fitness(a,b) + -1.483106 * (1-delta(a,b))] . ( 10 sec) [ -6624.3495] [GTR parameters ][rr_val: 0.053000 2.594985 1.000000 1.000000 1.000000 1.000000] . ( 11 sec) [ -6624.3495] [Branch lengths ] . ( 11 sec) [ -6624.3489] [Selective constraints on amino acids ][0.447536 * aa_fitness(a,b) + -1.480435 * (1-delta(a,b))] . ( 11 sec) [ -6624.3489] [GTR parameters ][rr_val: 0.053000 2.594985 1.000000 1.000000 1.000000 1.000000] . ( 12 sec) [ -6624.3487] [Selective constraints on amino acids ][0.448576 * aa_fitness(a,b) + -1.477765 * (1-delta(a,b))] . ( 12 sec) [ -6624.3487] [GTR parameters ][rr_val: 0.053000 2.594985 1.000000 1.000000 1.000000 1.000000] . Log likelihood of the current tree: -6624.348650. . 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 0h0m12s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo