. Sum=1.000003 . Scaling frequencies... .......................... 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 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: 1301370627 . Subtree patterns aliasing: no . Version: 20100824-SM04.101103 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 318 patterns found (out of a total of 1112 sites). . 0 sites without polymorphism (0.00%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 7 Mo of memory space. . ( 1 sec) [ -6671.4121] [Branch lengths ] . ( 1 sec) [ -6666.7450] [Selective constraints on amino acids ][0.385234 * aa_fitness(a,b) + -1.870604 * (1-delta(a,b))] . ( 2 sec) [ -6666.7197] [Branch lengths ] . ( 2 sec) [ -6666.7197] [Selective constraints on amino acids ][0.385234 * aa_fitness(a,b) + -1.870604 * (1-delta(a,b))] . ( 3 sec) [ -6666.7195] [Branch lengths ] . ( 4 sec) [ -6666.7195] [Selective constraints on amino acids ][0.385234 * aa_fitness(a,b) + -1.870604 * (1-delta(a,b))] . ( 4 sec) [ -6666.7195] [Selective constraints on amino acids ][0.385234 * aa_fitness(a,b) + -1.870604 * (1-delta(a,b))] . Log likelihood of the current tree: -6666.719451. . Printing the most likely tree in file 'input.phy_phyml_tree.txt'... . Time used 0h0m5s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo