.......................... 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 : Best of NNIs and SPRs . 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 ] . ( 4 sec) [ -8566.0287] [Topology ] . ( 5 sec) [ -8565.9291] [Topology ] . ( 6 sec) [ -8565.8840] [Topology ] . ( 7 sec) [ -8565.8630] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8565.863045 . ( 14 sec) [ -8565.7813] [GTR parameters ] . ( 14 sec) [ -8565.6810] [Alpha ][ 1.165891] . ( 14 sec) [ -8565.6810] [Topology ] . ( 15 sec) [ -8565.6588] [Topology ] . ( 16 sec) [ -8565.6494] [Topology ] . ( 17 sec) [ -8565.6451] [Topology ] . ( 18 sec) [ -8565.6432] [Topology ] . ( 19 sec) [ -8565.6422] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8565.642239 . ( 25 sec) [ -8565.6422] [GTR parameters ] . ( 25 sec) [ -8565.6416] [Alpha ][ 1.169138] . ( 25 sec) [ -8565.6416] [Topology ] . ( 26 sec) [ -8565.6411] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8565.641103 . ( 36 sec) [ -8565.6411] [GTR parameters ] . ( 36 sec) [ -8565.6411] [Alpha ][ 1.169138] . ( 36 sec) [ -8565.6411] [Topology ] . ( 38 sec) [ -8565.6409] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 52 sec) [ -8595.7121] [GTR parameters ] . ( 53 sec) [ -8594.7346] [Alpha ][ 1.123703] . ( 54 sec) [ -8594.6607] [ 1736] [depth= 1] . ( 55 sec) [ -8593.7167] [ 1736] [depth= 1] . ( 56 sec) [ -8592.7299] [ 1741] [depth= 1] . ( 56 sec) [ -8589.3249] [ 1743] [depth= 1] . ( 56 sec) [ -8588.3251] [ 1736] [depth= 1] . ( 56 sec) [ -8586.0362] [ 1736] [depth= 1] . ( 56 sec) [ -8584.7148] [ 1732] [depth= 1] . ( 57 sec) [ -8566.7282] [Branch lengths ] . ( 57 sec) [ -8566.6697] [GTR parameters ] . ( 57 sec) [ -8566.6050] [Alpha ][ 1.157614] . ( 61 sec) [ -8565.7079] [Branch lengths ] . ( 87 sec) [ -8565.6551] [Branch lengths ] . ( 87 sec) [ -8565.6551] [Topology ] . ( 88 sec) [ -8565.6524] [Topology ] . ( 89 sec) [ -8565.6517] [Topology ] . ( 89 sec) [ -8565.6491] [GTR parameters ] . ( 89 sec) [ -8565.6421] [Alpha ][ 1.169175] . ( 89 sec) [ -8565.6421] [Topology ] . ( 90 sec) [ -8565.6413] [Topology ] . ( 91 sec) [ -8565.6413] [GTR parameters ] . ( 91 sec) [ -8565.6413] [Alpha ][ 1.169175] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -8565.640862 . Log likelihood obtained after SPR moves : -8565.641258 . Log likelihood of the current tree: -8565.640862. . Printing the most likely tree in file 'data25.phy_phyml_tree.txt'... . Time used 0h1m37s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo