/usr/local/phylogeny/phyml/bin/phyml-codon.sh JTT-ML91+-4-E-F input_files/20130704_120702/input.phy is translated to /usr/local/phylogeny/phyml/src/phyml -i input_files/20130704_120702/input.phy -d codon -b 0 --mechanistic_opt 11020 -o l --mechanistic_params "-9.0 -1.5 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0" --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: 1372907222 . 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) [ -6668.3708] [Branch lengths ] . ( 1 sec) [ -6668.0797] [Selective constraints on amino acids ][1.009856 * aa_fitness(a,b) + -1.596913 * (1-delta(a,b))] . ( 1 sec) [ -6642.3126] [GTR parameters ][rr_val: 0.088147 2.340645 1.137439 0.728588 0.940053 1.188633] . ( 2 sec) [ -6642.1835] [Branch lengths ] . ( 2 sec) [ -6635.6696] [Selective constraints on amino acids ][0.680359 * aa_fitness(a,b) + -1.596913 * (1-delta(a,b))] . ( 2 sec) [ -6635.0061] [GTR parameters ][rr_val: 0.050922 2.468683 1.137439 0.728588 0.940053 1.188633] . ( 3 sec) [ -6635.0013] [Branch lengths ] . ( 3 sec) [ -6634.9424] [Selective constraints on amino acids ][0.651315 * aa_fitness(a,b) + -1.591193 * (1-delta(a,b))] . ( 3 sec) [ -6634.9356] [GTR parameters ][rr_val: 0.047854 2.483250 1.137439 0.728588 0.940053 1.188633] . ( 4 sec) [ -6634.9356] [Branch lengths ] . ( 4 sec) [ -6634.9350] [Selective constraints on amino acids ][0.651315 * aa_fitness(a,b) + -1.587295 * (1-delta(a,b))] . ( 4 sec) [ -6634.9350] [GTR parameters ][rr_val: 0.047593 2.483250 1.137439 0.728588 0.940053 1.188633] . ( 5 sec) [ -6634.9340] [Selective constraints on amino acids ][0.654031 * aa_fitness(a,b) + -1.583595 * (1-delta(a,b))] . ( 5 sec) [ -6634.9340] [GTR parameters ][rr_val: 0.047593 2.483250 1.137439 0.728588 0.940053 1.188633] . Log likelihood of the current tree: -6634.933978. . 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