/usr/local/phylogeny/phyml/bin/phyml-codon.sh JTT-ML91+-4-E-F input_files/20130704_103522/input.phy is translated to /usr/local/phylogeny/phyml/bin/phyml -i input_files/20130704_103522/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: 1372901722 . 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) [ -6681.2580] [Branch lengths ] . ( 0 sec) [ -6678.6712] [Selective constraints on amino acids ][1.168880 * aa_fitness(a,b) + -1.650910 * (1-delta(a,b))] . ( 1 sec) [ -6649.2557] [GTR parameters ][rr_val: 0.026297 2.507914 1.137439 0.728588 0.940053 1.188633] . ( 1 sec) [ -6647.6696] [Branch lengths ] . ( 1 sec) [ -6639.8575] [Selective constraints on amino acids ][0.787490 * aa_fitness(a,b) + -1.686613 * (1-delta(a,b))] . ( 2 sec) [ -6639.2358] [GTR parameters ][rr_val: 0.007644 2.739832 1.137439 0.728588 0.940053 1.188633] . ( 2 sec) [ -6639.0097] [Branch lengths ] . ( 2 sec) [ -6638.7657] [Selective constraints on amino acids ][0.725935 * aa_fitness(a,b) + -1.703271 * (1-delta(a,b))] . ( 3 sec) [ -6638.7608] [GTR parameters ][rr_val: 0.006153 2.743685 1.137439 0.728588 0.940053 1.188633] . ( 3 sec) [ -6638.7534] [Branch lengths ] . ( 3 sec) [ -6638.7379] [Selective constraints on amino acids ][0.712055 * aa_fitness(a,b) + -1.714169 * (1-delta(a,b))] . ( 4 sec) [ -6638.7377] [GTR parameters ][rr_val: 0.005843 2.740941 1.137439 0.728588 0.940053 1.188633] . ( 4 sec) [ -6638.7376] [Branch lengths ] . ( 4 sec) [ -6638.7332] [Selective constraints on amino acids ][0.705412 * aa_fitness(a,b) + -1.721650 * (1-delta(a,b))] . ( 5 sec) [ -6638.7332] [GTR parameters ][rr_val: 0.005753 2.740941 1.137439 0.728588 0.940053 1.188633] . ( 5 sec) [ -6638.7332] [Branch lengths ] . ( 5 sec) [ -6638.7312] [Selective constraints on amino acids ][0.701021 * aa_fitness(a,b) + -1.726949 * (1-delta(a,b))] . ( 6 sec) [ -6638.7312] [GTR parameters ][rr_val: 0.005703 2.744708 1.137439 0.728588 0.940053 1.188633] . ( 6 sec) [ -6638.7312] [Branch lengths ] . ( 6 sec) [ -6638.7301] [Selective constraints on amino acids ][0.697803 * aa_fitness(a,b) + -1.730722 * (1-delta(a,b))] . ( 7 sec) [ -6638.7301] [GTR parameters ][rr_val: 0.005663 2.744708 1.137439 0.728588 0.940053 1.188633] . ( 7 sec) [ -6638.7301] [Branch lengths ] . ( 7 sec) [ -6638.7297] [Selective constraints on amino acids ][0.695600 * aa_fitness(a,b) + -1.733956 * (1-delta(a,b))] . ( 8 sec) [ -6638.7297] [GTR parameters ][rr_val: 0.005652 2.744708 1.137439 0.728588 0.940053 1.188633] . ( 8 sec) [ -6638.7294] [Selective constraints on amino acids ][0.693760 * aa_fitness(a,b) + -1.733956 * (1-delta(a,b))] . ( 8 sec) [ -6638.7294] [GTR parameters ][rr_val: 0.005581 2.744708 1.137439 0.728588 0.940053 1.188633] . Log likelihood of the current tree: -6638.729415. . 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