/usr/local/phylogeny/phyml/bin/phyml -i input_files/20110203_154455.txt -d codon -b 0 -f e --mechanistic "/usr/local/phylogeny/phyml/dat/Wmatrix_with_EI-11_JTT EI-11" -c 1 --mechanistic_opt 01000 -o lr --mechanistic_params "1.0 0.0 0.0 0.0 1.0 1.0 1.0 1.0 1.0 0.25 0.25 0.25" . Sum=1.000003 . Scaling frequencies... .......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename: 20110203_154455.txt . 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: no . Run ID: none . Random seed: 1296715496 . Subtree patterns aliasing: no . Version: 20100824-SM04.101103 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 80 patterns found (out of a total of 81 sites). . 0 sites without polymorphism (0.00%). . Computing pairwise distances... . Building BioNJ tree... . ( 0 sec) [ -1023.3543] [Branch lengths ] . ( 0 sec) [ -1020.8254] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -0.546303] . ( 0 sec) [ -1016.7033] [Branch lengths ] . ( 0 sec) [ -1016.6561] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -0.478491] . ( 0 sec) [ -1016.6026] [Branch lengths ] . ( 0 sec) [ -1016.6014] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -0.467479] . ( 0 sec) [ -1016.5996] [Branch lengths ] . ( 1 sec) [ -1016.5996] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -0.466590] . ( 1 sec) [ -1016.5994] [Branch lengths ] . ( 1 sec) [ -1016.5994] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -0.467749] . ( 1 sec) [ -1016.5994] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -0.467749] . Log likelihood of the current tree: -1016.599406. . Printing the most likely tree in file '20110203_154455.txt_phyml_tree.txt'... . Time used 0h0m1s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo