.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data82.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... . 304 patterns found. (out of a total of 500 sites) . 178 sites without polymorphism (35.60%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 6Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-4811.134925 . ( 0 sec) [ -4808.5288] [GTR parameters ] . ( 0 sec) [ -4808.5204] [Alpha ][ 0.984728] . ( 0 sec) [ -4808.5204] [Topology ] . ( 1 sec) [ -4795.7810] [Topology ] . ( 2 sec) [ -4793.2976] [Topology ] . ( 2 sec) [ -4792.9706] [Topology ] . ( 3 sec) [ -4792.9122] [Topology ] . ( 3 sec) [ -4792.8936] [Topology ] . ( 4 sec) [ -4792.8867] [Topology ] . ( 5 sec) [ -4792.8841] [Topology ] . ( 5 sec) [ -4792.8831] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4792.883097 . ( 10 sec) [ -4792.8710] [GTR parameters ] . ( 10 sec) [ -4792.8681] [Alpha ][ 0.976547] . ( 10 sec) [ -4792.8681] [Topology ] . ( 11 sec) [ -4792.8678] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4792.867818 . ( 15 sec) [ -4792.8678] [GTR parameters ] . ( 15 sec) [ -4792.8678] [Alpha ][ 0.976547] . ( 15 sec) [ -4792.8678] [Topology ] . ( 16 sec) [ -4792.8677] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 27 sec) [ -4808.5288] [GTR parameters ] . ( 27 sec) [ -4808.5204] [Alpha ][ 0.984728] . ( 27 sec) [ -4808.2950] [ 812] [depth= 1] . ( 28 sec) [ -4806.2962] [ 810] [depth= 1] . ( 28 sec) [ -4805.9249] [ 810] [depth= 1] . ( 28 sec) [ -4805.6271] [ 810] [depth= 1] . ( 28 sec) [ -4805.1660] [ 811] [depth= 2] . ( 28 sec) [ -4804.8692] [ 811] [depth= 1] . ( 29 sec) [ -4803.0042] [ 810] [depth= 1] . ( 29 sec) [ -4802.7890] [ 809] [depth= 1] . ( 29 sec) [ -4801.9850] [ 808] [depth= 1] . ( 29 sec) [ -4800.8108] [ 809] [depth= 1] . ( 30 sec) [ -4800.4726] [ 808] [depth= 1] . ( 30 sec) [ -4800.1933] [ 809] [depth= 2] . ( 30 sec) [ -4799.4029] [ 808] [depth= 2] . ( 30 sec) [ -4799.0610] [ 808] [depth= 1] . ( 30 sec) [ -4799.0508] [ 809] [depth= 1] . ( 30 sec) [ -4798.8624] [ 808] [depth= 1] . ( 30 sec) [ -4794.9716] [Branch lengths ] . ( 30 sec) [ -4794.9555] [GTR parameters ] . ( 30 sec) [ -4794.9507] [Alpha ][ 0.973884] . ( 31 sec) [ -4794.0906] [ 805] [depth= 1] . ( 33 sec) [ -4794.0506] [ 807] [depth= 1] . ( 33 sec) [ -4793.8928] [ 804] [depth= 1] . ( 33 sec) [ -4793.5530] [ 805] [depth= 1] . ( 33 sec) [ -4792.9975] [Branch lengths ] . ( 34 sec) [ -4792.9887] [GTR parameters ] . ( 34 sec) [ -4792.9880] [Alpha ][ 0.977938] . ( 37 sec) [ -4792.9742] [Branch lengths ] . ( 53 sec) [ -4792.9737] [Branch lengths ] . ( 53 sec) [ -4792.9737] [Topology ] . ( 53 sec) [ -4792.9737] [Topology ] . ( 53 sec) [ -4792.9737] [GTR parameters ] . ( 53 sec) [ -4792.9737] [Alpha ][ 0.978916] . Checking for NNIs, optimizing five branches... . ( 57 sec) [ -4792.9730] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -4792.867666 . Log likelihood obtained after SPR moves : -4792.973018 . Log likelihood of the current tree: -4792.867666. . Printing the most likely tree in file 'data82.phy_phyml_tree.txt'... . Time used 0h1m1s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo