.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data92.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... . 393 patterns found. (out of a total of 500 sites) . 101 sites without polymorphism (20.20%). . 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=-7963.047097 . ( 1 sec) [ -7958.8927] [GTR parameters ] . ( 1 sec) [ -7958.7829] [Alpha ][ 0.960038] . ( 1 sec) [ -7958.7829] [Topology ] . ( 2 sec) [ -7935.0414] [Topology ] . ( 2 sec) [ -7932.3359] [Topology ] . ( 3 sec) [ -7931.4845] [Topology ] . ( 4 sec) [ -7931.1483] [Topology ] . ( 5 sec) [ -7931.0049] [Topology ] . ( 6 sec) [ -7930.9412] [Topology ] . ( 7 sec) [ -7930.9121] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7930.912139 . ( 13 sec) [ -7930.7880] [GTR parameters ] . ( 13 sec) [ -7930.6789] [Alpha ][ 0.997965] . ( 13 sec) [ -7930.6789] [Topology ] . ( 14 sec) [ -7930.6511] [Topology ] . ( 15 sec) [ -7930.6388] [Topology ] . ( 16 sec) [ -7930.6332] [Topology ] . ( 16 sec) [ -7930.6306] [Topology ] . ( 17 sec) [ -7930.6294] [Topology ] . ( 18 sec) [ -7930.6289] [Topology ] . Checking for NNIs, optimizing five branches... . ( 24 sec) [ -7930.6285] [Topology ] . Before opt ts/t=1.000000 LK=-7930.628483 . ( 24 sec) [ -7930.6284] [GTR parameters ] . ( 24 sec) [ -7930.6275] [Alpha ][ 1.001552] . ( 24 sec) [ -7930.6275] [Topology ] . ( 25 sec) [ -7930.6271] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7930.627050 . ( 30 sec) [ -7930.6270] [GTR parameters ] . ( 30 sec) [ -7930.6270] [Alpha ][ 1.001552] . ( 30 sec) [ -7930.6270] [Topology ] . ( 31 sec) [ -7930.6269] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 42 sec) [ -7958.8927] [GTR parameters ] . ( 43 sec) [ -7958.7829] [Alpha ][ 0.960038] . ( 43 sec) [ -7957.2802] [ 1555] [depth= 1] . ( 43 sec) [ -7956.7962] [ 1557] [depth= 1] . ( 44 sec) [ -7955.8131] [ 1556] [depth= 1] . ( 44 sec) [ -7954.7418] [ 1557] [depth= 1] . ( 45 sec) [ -7932.3481] [Branch lengths ] . ( 46 sec) [ -7932.2535] [GTR parameters ] . ( 46 sec) [ -7932.2091] [Alpha ][ 0.984254] . ( 46 sec) [ -7932.1151] [ 1556] [depth= 1] . ( 48 sec) [ -7930.7932] [Branch lengths ] . ( 48 sec) [ -7930.7919] [GTR parameters ] . ( 48 sec) [ -7930.7792] [Alpha ][ 0.997891] . ( 51 sec) [ -7930.6444] [Branch lengths ] . ( 70 sec) [ -7930.6304] [Branch lengths ] . ( 70 sec) [ -7930.6304] [Topology ] . ( 70 sec) [ -7930.6292] [Topology ] . ( 71 sec) [ -7930.6288] [Topology ] . ( 72 sec) [ -7930.6283] [GTR parameters ] . ( 72 sec) [ -7930.6273] [Alpha ][ 1.001599] . ( 72 sec) [ -7930.6273] [Topology ] . ( 72 sec) [ -7930.6270] [Topology ] . ( 73 sec) [ -7930.6270] [GTR parameters ] . ( 73 sec) [ -7930.6270] [Alpha ][ 1.001599] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7930.626869 . Log likelihood obtained after SPR moves : -7930.627041 . Log likelihood of the current tree: -7930.626869. . Printing the most likely tree in file 'data92.phy_phyml_tree.txt'... . Time used 0h1m18s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo