.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data16.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... . 251 patterns found. (out of a total of 500 sites) . 238 sites without polymorphism (47.60%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 5Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-3809.279994 . ( 1 sec) [ -3808.5219] [GTR parameters ] . ( 1 sec) [ -3807.9062] [Alpha ][ 0.847346] . ( 1 sec) [ -3807.9062] [Topology ] . ( 2 sec) [ -3796.9317] [Topology ] . ( 3 sec) [ -3795.7445] [Topology ] . ( 3 sec) [ -3795.4946] [Topology ] . ( 4 sec) [ -3795.4363] [Topology ] . ( 5 sec) [ -3795.4223] [Topology ] . ( 5 sec) [ -3795.4188] [Topology ] . ( 6 sec) [ -3795.4177] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-3795.417742 . ( 11 sec) [ -3795.4124] [GTR parameters ] . ( 11 sec) [ -3795.3950] [Alpha ][ 0.870219] . ( 12 sec) [ -3795.3950] [Topology ] . ( 12 sec) [ -3795.3941] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-3795.394058 . ( 17 sec) [ -3795.3940] [GTR parameters ] . ( 18 sec) [ -3795.3940] [Alpha ][ 0.871089] . ( 18 sec) [ -3795.3940] [Topology ] . ( 18 sec) [ -3795.3938] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 28 sec) [ -3808.5219] [GTR parameters ] . ( 28 sec) [ -3807.9062] [Alpha ][ 0.847346] . ( 30 sec) [ -3807.6298] [ 547] [depth= 1] . ( 30 sec) [ -3807.3767] [ 547] [depth= 1] . ( 30 sec) [ -3806.9838] [ 547] [depth= 1] . ( 30 sec) [ -3806.7381] [ 547] [depth= 1] . ( 30 sec) [ -3806.6602] [ 547] [depth= 2] . ( 30 sec) [ -3805.4762] [ 547] [depth= 1] . ( 31 sec) [ -3804.7192] [ 547] [depth= 1] . ( 31 sec) [ -3804.6972] [ 547] [depth= 1] . ( 31 sec) [ -3802.7599] [ 546] [depth= 1] . ( 32 sec) [ -3802.3854] [ 545] [depth= 1] . ( 32 sec) [ -3802.3261] [ 545] [depth= 1] . ( 32 sec) [ -3801.3034] [ 546] [depth= 1] . ( 32 sec) [ -3801.2044] [ 545] [depth= 1] . ( 33 sec) [ -3800.7823] [ 545] [depth= 1] . ( 33 sec) [ -3800.7458] [ 545] [depth= 1] . ( 33 sec) [ -3799.8680] [ 544] [depth= 1] . ( 33 sec) [ -3798.2351] [ 544] [depth= 1] . ( 34 sec) [ -3798.2201] [ 545] [depth= 1] . ( 35 sec) [ -3798.1735] [ 545] [depth= 1] . ( 35 sec) [ -3797.9463] [ 545] [depth= 1] . ( 35 sec) [ -3795.4241] [Branch lengths ] . ( 35 sec) [ -3795.4188] [GTR parameters ] . ( 35 sec) [ -3795.4031] [Alpha ][ 0.869009] . ( 42 sec) [ -3795.3941] [Branch lengths ] . ( 64 sec) [ -3795.3937] [Branch lengths ] . ( 64 sec) [ -3795.3937] [Topology ] . ( 65 sec) [ -3795.3937] [Topology ] . ( 65 sec) [ -3795.3937] [GTR parameters ] . ( 65 sec) [ -3795.3935] [Alpha ][ 0.870982] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -3795.393804 . Log likelihood obtained after SPR moves : -3795.393526 . Log likelihood of the current tree: -3795.393526. . Printing the most likely tree in file 'data16.phy_phyml_tree.txt'... . Time used 0h1m10s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo