.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data25.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... . 418 patterns found. (out of a total of 500 sites) . 78 sites without polymorphism (15.60%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-8600.808417 . ( 1 sec) [ -8595.7121] [GTR parameters ] . ( 1 sec) [ -8594.7346] [Alpha ][ 1.123703] . ( 1 sec) [ -8594.7346] [Topology ] . ( 2 sec) [ -8569.4203] [Topology ] . ( 3 sec) [ -8566.8728] [Topology ] . ( 4 sec) [ -8566.2596] [Topology ] . ( 5 sec) [ -8566.0287] [Topology ] . ( 6 sec) [ -8565.9291] [Topology ] . ( 7 sec) [ -8565.8840] [Topology ] . ( 8 sec) [ -8565.8630] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8565.863045 . ( 17 sec) [ -8565.7813] [GTR parameters ] . ( 17 sec) [ -8565.6810] [Alpha ][ 1.165891] . ( 18 sec) [ -8565.6810] [Topology ] . ( 19 sec) [ -8565.6588] [Topology ] . ( 20 sec) [ -8565.6494] [Topology ] . ( 21 sec) [ -8565.6451] [Topology ] . ( 22 sec) [ -8565.6432] [Topology ] . ( 23 sec) [ -8565.6422] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8565.642239 . ( 31 sec) [ -8565.6422] [GTR parameters ] . ( 31 sec) [ -8565.6416] [Alpha ][ 1.169138] . ( 31 sec) [ -8565.6416] [Topology ] . ( 32 sec) [ -8565.6411] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8565.641103 . ( 41 sec) [ -8565.6411] [GTR parameters ] . ( 41 sec) [ -8565.6411] [Alpha ][ 1.169138] . ( 41 sec) [ -8565.6411] [Topology ] . ( 42 sec) [ -8565.6409] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8565.640862. . Printing the most likely tree in file 'data25.phy_phyml_tree.txt'... . Time used 0h0m59s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo