/usr/local/phylogeny/phyml/phyml-20100824-sm10/src/phyml -i input_files/20130703_153522/input.phy -d codon -b 0 --mechanistic_opt 01020 -o l --mechanistic_params "0.0 -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 EI-11" -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 EI-11 . 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: 1372833322 . 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. . ( 1 sec) [ -6717.4607] [Branch lengths ] . ( 1 sec) [ -6672.6140] [Selective constraints on amino acids ][0.000000 * aa_fitness(a,b) + -2.588733 * (1-delta(a,b))] . ( 1 sec) [ -6635.7364] [GTR parameters ][rr_val: 0.059291 1.998469 1.000000 1.000000 1.000000 1.000000] . ( 2 sec) [ -6635.6412] [Branch lengths ] . ( 2 sec) [ -6635.3644] [Selective constraints on amino acids ][0.000000 * aa_fitness(a,b) + -2.494604 * (1-delta(a,b))] . ( 2 sec) [ -6633.3870] [GTR parameters ][rr_val: 0.050449 2.481118 1.000000 1.000000 1.000000 1.000000] . ( 3 sec) [ -6633.3851] [Branch lengths ] . ( 3 sec) [ -6633.2898] [Selective constraints on amino acids ][0.000000 * aa_fitness(a,b) + -2.438161 * (1-delta(a,b))] . ( 3 sec) [ -6633.2619] [GTR parameters ][rr_val: 0.045247 2.506959 1.000000 1.000000 1.000000 1.000000] . ( 4 sec) [ -6633.2619] [Branch lengths ] . ( 4 sec) [ -6633.2599] [Selective constraints on amino acids ][0.000000 * aa_fitness(a,b) + -2.430055 * (1-delta(a,b))] . ( 4 sec) [ -6633.2596] [GTR parameters ][rr_val: 0.044772 2.512677 1.000000 1.000000 1.000000 1.000000] . ( 4 sec) [ -6633.2596] [Branch lengths ] . ( 5 sec) [ -6633.2596] [Selective constraints on amino acids ][0.000000 * aa_fitness(a,b) + -2.430055 * (1-delta(a,b))] . ( 5 sec) [ -6633.2596] [GTR parameters ][rr_val: 0.044772 2.510164 1.000000 1.000000 1.000000 1.000000] . ( 5 sec) [ -6633.2596] [Selective constraints on amino acids ][0.000000 * aa_fitness(a,b) + -2.430055 * (1-delta(a,b))] . ( 5 sec) [ -6633.2596] [GTR parameters ][rr_val: 0.044772 2.510164 1.000000 1.000000 1.000000 1.000000] . Log likelihood of the current tree: -6633.259606. . 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 0h0m5s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo