/usr/local/phylogeny/phyml/phyml-20100824-sm10/src/phyml -i input_files/20130703_161321/input.phy -d aa -b 0 --mechanistic_opt 11023 -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 . 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: aa . 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 . Amino acid 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: 1372835601 . Subtree patterns aliasing: no . Version: 20100824-SM10 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 78 patterns found (out of a total of 1112 sites). . 1049 sites without polymorphism (94.33%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 2 Mo of memory space. . ( 1 sec) [ -3749.3706] [Branch lengths ] . ( 1 sec) [ -3748.8304] [Selective constraints on amino acids ][0.931852 * aa_fitness(a,b) + -1.593850 * (1-delta(a,b))] . ( 1 sec) [ -3742.0228] [GTR parameters ][rr_val: 0.137717 1.648727 1.000000 1.000000 1.000000 1.000000] . ( 3 sec) [ -3736.9762] [Nucleotide equlibrium freqs.][ACGT: 0.384405 0.215022 0.259256 0.141316] . ( 3 sec) [ -3735.9526] [Branch lengths ] . ( 3 sec) [ -3735.6133] [Selective constraints on amino acids ][0.873231 * aa_fitness(a,b) + -1.659519 * (1-delta(a,b))] . ( 4 sec) [ -3735.5456] [GTR parameters ][rr_val: 0.125447 1.521873 1.000000 1.000000 1.000000 1.000000] . ( 4 sec) [ -3735.5381] [Nucleotide equlibrium freqs.][ACGT: 0.384704 0.210257 0.263516 0.141523] . ( 5 sec) [ -3735.5197] [Branch lengths ] . ( 5 sec) [ -3735.3642] [Selective constraints on amino acids ][0.834900 * aa_fitness(a,b) + -1.705719 * (1-delta(a,b))] . ( 5 sec) [ -3735.3637] [GTR parameters ][rr_val: 0.123444 1.529930 1.000000 1.000000 1.000000 1.000000] . ( 6 sec) [ -3735.3598] [Nucleotide equlibrium freqs.][ACGT: 0.384578 0.206814 0.265831 0.142777] . ( 6 sec) [ -3735.3593] [Branch lengths ] . ( 6 sec) [ -3735.2803] [Selective constraints on amino acids ][0.807704 * aa_fitness(a,b) + -1.738471 * (1-delta(a,b))] . ( 7 sec) [ -3735.2800] [GTR parameters ][rr_val: 0.121546 1.535290 1.000000 1.000000 1.000000 1.000000] . ( 7 sec) [ -3735.2782] [Nucleotide equlibrium freqs.][ACGT: 0.384267 0.204591 0.267495 0.143647] . ( 8 sec) [ -3735.2780] [Branch lengths ] . ( 8 sec) [ -3735.2378] [Selective constraints on amino acids ][0.788315 * aa_fitness(a,b) + -1.761605 * (1-delta(a,b))] . ( 8 sec) [ -3735.2376] [GTR parameters ][rr_val: 0.120080 1.539220 1.000000 1.000000 1.000000 1.000000] . ( 9 sec) [ -3735.2367] [Nucleotide equlibrium freqs.][ACGT: 0.383875 0.203028 0.268799 0.144298] . ( 9 sec) [ -3735.2367] [Branch lengths ] . ( 9 sec) [ -3735.2160] [Selective constraints on amino acids ][0.774356 * aa_fitness(a,b) + -1.777960 * (1-delta(a,b))] . ( 9 sec) [ -3735.2159] [GTR parameters ][rr_val: 0.119009 1.542118 1.000000 1.000000 1.000000 1.000000] . ( 10 sec) [ -3735.2155] [Nucleotide equlibrium freqs.][ACGT: 0.384084 0.201855 0.269335 0.144727] . ( 10 sec) [ -3735.2155] [Branch lengths ] . ( 10 sec) [ -3735.2049] [Selective constraints on amino acids ][0.764274 * aa_fitness(a,b) + -1.789405 * (1-delta(a,b))] . ( 11 sec) [ -3735.2049] [GTR parameters ][rr_val: 0.118184 1.544273 1.000000 1.000000 1.000000 1.000000] . ( 11 sec) [ -3735.2046] [Nucleotide equlibrium freqs.][ACGT: 0.384104 0.200992 0.269865 0.145038] . ( 11 sec) [ -3735.2046] [Branch lengths ] . ( 12 sec) [ -3735.1992] [Selective constraints on amino acids ][0.756948 * aa_fitness(a,b) + -1.797333 * (1-delta(a,b))] . ( 12 sec) [ -3735.1992] [GTR parameters ][rr_val: 0.117588 1.545850 1.000000 1.000000 1.000000 1.000000] . ( 12 sec) [ -3735.1991] [Nucleotide equlibrium freqs.][ACGT: 0.384029 0.200373 0.270321 0.145277] . ( 13 sec) [ -3735.1991] [Branch lengths ] . ( 13 sec) [ -3735.1964] [Selective constraints on amino acids ][0.751618 * aa_fitness(a,b) + -1.802716 * (1-delta(a,b))] . ( 13 sec) [ -3735.1963] [GTR parameters ][rr_val: 0.117161 1.545850 1.000000 1.000000 1.000000 1.000000] . ( 14 sec) [ -3735.1963] [Nucleotide equlibrium freqs.][ACGT: 0.383931 0.199938 0.270680 0.145451] . ( 14 sec) [ -3735.1963] [Branch lengths ] . ( 14 sec) [ -3735.1949] [Selective constraints on amino acids ][0.747740 * aa_fitness(a,b) + -1.806230 * (1-delta(a,b))] . ( 14 sec) [ -3735.1949] [GTR parameters ][rr_val: 0.116878 1.547835 1.000000 1.000000 1.000000 1.000000] . ( 15 sec) [ -3735.1949] [Nucleotide equlibrium freqs.][ACGT: 0.383834 0.199631 0.270938 0.145597] . ( 15 sec) [ -3735.1948] [Branch lengths ] . ( 15 sec) [ -3735.1942] [Selective constraints on amino acids ][0.744905 * aa_fitness(a,b) + -1.809626 * (1-delta(a,b))] . ( 16 sec) [ -3735.1942] [GTR parameters ][rr_val: 0.117002 1.547835 1.000000 1.000000 1.000000 1.000000] . ( 16 sec) [ -3735.1942] [Nucleotide equlibrium freqs.][ACGT: 0.383737 0.199525 0.271001 0.145737] . ( 16 sec) [ -3735.1940] [Selective constraints on amino acids ][0.743047 * aa_fitness(a,b) + -1.809626 * (1-delta(a,b))] . ( 16 sec) [ -3735.1939] [GTR parameters ][rr_val: 0.116200 1.547835 1.000000 1.000000 1.000000 1.000000] . ( 17 sec) [ -3735.1939] [Nucleotide equlibrium freqs.][ACGT: 0.383822 0.199219 0.271180 0.145780] . Log likelihood of the current tree: -3735.193909. . 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 0h0m17s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo