.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data58.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... . 375 patterns found. (out of a total of 500 sites) . 121 sites without polymorphism (24.20%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 8Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-7012.025245 . ( 1 sec) [ -7007.8352] [GTR parameters ] . ( 1 sec) [ -7007.3705] [Alpha ][ 0.916448] . ( 1 sec) [ -7007.3705] [Topology ] . ( 2 sec) [ -6988.1007] [Topology ] . ( 2 sec) [ -6984.6001] [Topology ] . ( 3 sec) [ -6983.9065] [Topology ] . ( 4 sec) [ -6983.6870] [Topology ] . ( 5 sec) [ -6983.6010] [Topology ] . ( 5 sec) [ -6983.5643] [Topology ] . ( 6 sec) [ -6983.5477] [Topology ] . ( 7 sec) [ -6983.5401] [Topology ] . Checking for NNIs, optimizing five branches... . ( 12 sec) [ -6983.5348] [Topology ] . Before opt ts/t=1.000000 LK=-6983.534791 . ( 12 sec) [ -6983.5212] [GTR parameters ] . ( 12 sec) [ -6983.3866] [Alpha ][ 0.958886] . ( 12 sec) [ -6983.3866] [Topology ] . ( 13 sec) [ -6983.3741] [Topology ] . ( 13 sec) [ -6983.3691] [Topology ] . ( 14 sec) [ -6983.3669] [Topology ] . ( 15 sec) [ -6983.3659] [Topology ] . ( 16 sec) [ -6983.3654] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-6983.365373 . ( 20 sec) [ -6983.3652] [GTR parameters ] . ( 20 sec) [ -6983.3646] [Alpha ][ 0.961784] . ( 21 sec) [ -6983.3646] [Topology ] . ( 21 sec) [ -6983.3642] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-6983.364241 . ( 26 sec) [ -6983.3642] [GTR parameters ] . ( 26 sec) [ -6983.3642] [Alpha ][ 0.961784] . ( 26 sec) [ -6983.3642] [Topology ] . ( 27 sec) [ -6983.3641] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6983.364091. . Printing the most likely tree in file 'data58.phy_phyml_tree.txt'... . Time used 0h0m37s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo