.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data34.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . Optimise tree topology : yes . Tree topology search : NNIs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 357 patterns found. (out of a total of 500 sites) . 130 sites without polymorphism (26.00%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 7Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-5915.368272 . ( 1 sec) [ -5914.3337] [GTR parameters ] . ( 1 sec) [ -5914.2453] [Alpha ][ 1.044120] . ( 1 sec) [ -5914.2453] [Topology ] . ( 2 sec) [ -5884.5145] [Topology ] . ( 3 sec) [ -5879.8822] [Topology ] . ( 5 sec) [ -5878.8229] [Topology ] . ( 6 sec) [ -5878.5145] [Topology ] . ( 6 sec) [ -5878.4132] [Topology ] . ( 7 sec) [ -5878.3768] [Topology ] . ( 8 sec) [ -5878.3628] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-5878.362839 . ( 14 sec) [ -5878.3580] [GTR parameters ] . ( 15 sec) [ -5878.2915] [Alpha ][ 1.083518] . ( 15 sec) [ -5878.2915] [Topology ] . ( 15 sec) [ -5878.2828] [Topology ] . ( 16 sec) [ -5878.2795] [Topology ] . ( 17 sec) [ -5878.2782] [Topology ] . ( 17 sec) [ -5878.2777] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-5878.277650 . ( 22 sec) [ -5878.2776] [GTR parameters ] . ( 23 sec) [ -5878.2775] [Alpha ][ 1.084814] . ( 23 sec) [ -5878.2775] [Topology ] . ( 24 sec) [ -5878.2772] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5878.277241. . Printing the most likely tree in file 'data34.phy_phyml_tree.txt'... . Time used 0h0m36s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo