.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data57.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... . 398 patterns found. (out of a total of 500 sites) . 97 sites without polymorphism (19.40%). . 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=-7252.857742 . ( 1 sec) [ -7242.8403] [GTR parameters ] . ( 1 sec) [ -7242.1885] [Alpha ][ 1.109718] . ( 1 sec) [ -7242.1885] [Topology ] . ( 3 sec) [ -7202.1609] [Topology ] . ( 4 sec) [ -7198.2279] [Topology ] . ( 4 sec) [ -7197.5078] [Topology ] . ( 6 sec) [ -7197.2985] [Topology ] . ( 7 sec) [ -7197.2249] [Topology ] . ( 9 sec) [ -7197.1964] [Topology ] . ( 10 sec) [ -7197.1847] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7197.184696 . ( 18 sec) [ -7197.1380] [GTR parameters ] . ( 18 sec) [ -7197.1167] [Alpha ][ 1.131102] . ( 18 sec) [ -7197.1167] [Topology ] . ( 20 sec) [ -7197.1086] [Topology ] . ( 21 sec) [ -7197.1054] [Topology ] . ( 22 sec) [ -7197.1040] [Topology ] . ( 23 sec) [ -7197.1034] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7197.103429 . ( 31 sec) [ -7197.1034] [GTR parameters ] . ( 31 sec) [ -7197.1034] [Alpha ][ 1.132233] . ( 31 sec) [ -7197.1034] [Topology ] . ( 32 sec) [ -7197.1031] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7197.103097. . Printing the most likely tree in file 'data57.phy_phyml_tree.txt'... . Time used 0h0m51s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo