/usr/local/phylogeny/phyml/bin/phyml-codon.sh JTT-ML91+-11-e-F input_files/20130704_103321/input.phy is translated to /usr/local/phylogeny/phyml/bin/phyml -i input_files/20130704_103321/input.phy -d codon -b 0 --mechanistic_opt 11063 -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: 1372901602 . 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) [ -6663.4173] [Branch lengths ] . ( 1 sec) [ -6659.2132] [Selective constraints on amino acids ][0.742027 * aa_fitness(a,b) + -1.495086 * (1-delta(a,b))] . ( 3 sec) [ -6621.6879] [GTR parameters ][rr_val: 0.077509 2.278421 0.964970 0.938863 1.284829 0.934072] . ( 4 sec) [ -6613.5811] [Nucleotide equlibrium freqs.][ACGT: 0.305240 0.256203 0.236512 0.202045] . ( 4 sec) [ -6613.4589] [Branch lengths ] . ( 4 sec) [ -6613.1067] [Selective constraints on amino acids ][0.674006 * aa_fitness(a,b) + -1.465612 * (1-delta(a,b))] . ( 6 sec) [ -6612.4508] [GTR parameters ][rr_val: 0.056531 2.536403 0.971416 0.953876 1.241501 0.962038] . ( 6 sec) [ -6612.4104] [Nucleotide equlibrium freqs.][ACGT: 0.309943 0.253073 0.235316 0.201667] . ( 7 sec) [ -6612.4092] [Branch lengths ] . ( 7 sec) [ -6612.3868] [Selective constraints on amino acids ][0.668219 * aa_fitness(a,b) + -1.440241 * (1-delta(a,b))] . ( 8 sec) [ -6612.3685] [GTR parameters ][rr_val: 0.052214 2.568021 0.970469 0.952756 1.240263 0.964107] . ( 9 sec) [ -6612.3677] [Nucleotide equlibrium freqs.][ACGT: 0.310620 0.252693 0.234962 0.201725] . ( 9 sec) [ -6612.3677] [Branch lengths ] . ( 10 sec) [ -6612.3491] [Selective constraints on amino acids ][0.678078 * aa_fitness(a,b) + -1.420946 * (1-delta(a,b))] . ( 11 sec) [ -6612.3488] [GTR parameters ][rr_val: 0.051708 2.573235 0.969869 0.952054 1.241298 0.964973] . ( 11 sec) [ -6612.3487] [Nucleotide equlibrium freqs.][ACGT: 0.310776 0.252692 0.234806 0.201726] . ( 12 sec) [ -6612.3487] [Branch lengths ] . ( 12 sec) [ -6612.3352] [Selective constraints on amino acids ][0.688187 * aa_fitness(a,b) + -1.406886 * (1-delta(a,b))] . ( 13 sec) [ -6612.3351] [GTR parameters ][rr_val: 0.051708 2.571923 0.969740 0.951977 1.240100 0.966284] . ( 13 sec) [ -6612.3351] [Nucleotide equlibrium freqs.][ACGT: 0.310783 0.252771 0.234728 0.201718] . ( 13 sec) [ -6612.3351] [Branch lengths ] . ( 14 sec) [ -6612.3273] [Selective constraints on amino acids ][0.696112 * aa_fitness(a,b) + -1.396812 * (1-delta(a,b))] . ( 15 sec) [ -6612.3273] [GTR parameters ][rr_val: 0.051784 2.571135 0.969487 0.951572 1.239980 0.966983] . ( 15 sec) [ -6612.3273] [Nucleotide equlibrium freqs.][ACGT: 0.310800 0.252825 0.234669 0.201706] . ( 15 sec) [ -6612.3273] [Branch lengths ] . ( 16 sec) [ -6612.3233] [Selective constraints on amino acids ][0.701815 * aa_fitness(a,b) + -1.389580 * (1-delta(a,b))] . ( 17 sec) [ -6612.3233] [GTR parameters ][rr_val: 0.051836 2.570644 0.969255 0.951496 1.240003 0.967359] . ( 17 sec) [ -6612.3233] [Nucleotide equlibrium freqs.][ACGT: 0.310815 0.252863 0.234623 0.201699] . ( 17 sec) [ -6612.3233] [Branch lengths ] . ( 18 sec) [ -6612.3212] [Selective constraints on amino acids ][0.705891 * aa_fitness(a,b) + -1.384382 * (1-delta(a,b))] . ( 19 sec) [ -6612.3212] [GTR parameters ][rr_val: 0.051888 2.570165 0.969059 0.951314 1.239971 0.967770] . ( 19 sec) [ -6612.3212] [Nucleotide equlibrium freqs.][ACGT: 0.310826 0.252890 0.234590 0.201694] . ( 19 sec) [ -6612.3212] [Branch lengths ] . ( 19 sec) [ -6612.3201] [Selective constraints on amino acids ][0.708837 * aa_fitness(a,b) + -1.380641 * (1-delta(a,b))] . ( 20 sec) [ -6612.3201] [GTR parameters ][rr_val: 0.051888 2.570163 0.969010 0.951302 1.239963 0.967765] . ( 20 sec) [ -6612.3200] [Nucleotide equlibrium freqs.][ACGT: 0.310839 0.252906 0.234565 0.201690] . ( 21 sec) [ -6612.3200] [Branch lengths ] . ( 21 sec) [ -6612.3195] [Selective constraints on amino acids ][0.710931 * aa_fitness(a,b) + -1.377729 * (1-delta(a,b))] . ( 22 sec) [ -6612.3195] [GTR parameters ][rr_val: 0.051888 2.569709 0.968832 0.951085 1.239898 0.968186] . ( 22 sec) [ -6612.3195] [Nucleotide equlibrium freqs.][ACGT: 0.310843 0.252920 0.234547 0.201689] . ( 23 sec) [ -6612.3192] [Selective constraints on amino acids ][0.712564 * aa_fitness(a,b) + -1.374818 * (1-delta(a,b))] . ( 23 sec) [ -6612.3192] [GTR parameters ][rr_val: 0.051888 2.569708 0.968777 0.951074 1.239891 0.968179] . ( 24 sec) [ -6612.3192] [Nucleotide equlibrium freqs.][ACGT: 0.310853 0.252930 0.234525 0.201692] . Log likelihood of the current tree: -6612.319156. . 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 0h0m24s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo