.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data47.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... . 292 patterns found. (out of a total of 500 sites) . 197 sites without polymorphism (39.40%). . 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=-4367.043375 . ( 1 sec) [ -4364.7703] [GTR parameters ] . ( 1 sec) [ -4364.6848] [Alpha ][ 1.057958] . ( 1 sec) [ -4364.6848] [Topology ] . ( 1 sec) [ -4355.6395] [Topology ] . ( 2 sec) [ -4354.4887] [Topology ] . ( 3 sec) [ -4354.2756] [Topology ] . ( 4 sec) [ -4354.2280] [Topology ] . ( 5 sec) [ -4354.2139] [Topology ] . ( 5 sec) [ -4354.1917] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4354.191669 . ( 9 sec) [ -4354.1882] [GTR parameters ] . ( 9 sec) [ -4354.1779] [Alpha ][ 1.078429] . ( 9 sec) [ -4354.1779] [Topology ] . ( 10 sec) [ -4354.0381] [Topology ] . ( 10 sec) [ -4353.3434] [Topology ] . ( 11 sec) [ -4351.9441] [Topology ] . ( 11 sec) [ -4351.5987] [Topology ] . ( 12 sec) [ -4351.5811] [Topology ] . ( 13 sec) [ -4351.5801] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4351.580143 . ( 16 sec) [ -4351.5775] [GTR parameters ] . ( 16 sec) [ -4351.5766] [Alpha ][ 1.084915] . ( 16 sec) [ -4351.5766] [Topology ] . ( 17 sec) [ -4351.5765] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4351.576504 . ( 20 sec) [ -4351.5765] [GTR parameters ] . ( 21 sec) [ -4351.5765] [Alpha ][ 1.084915] . ( 21 sec) [ -4351.5765] [Topology ] . ( 21 sec) [ -4351.5765] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 32 sec) [ -4364.7703] [GTR parameters ] . ( 32 sec) [ -4364.6848] [Alpha ][ 1.057958] . ( 32 sec) [ -4364.2236] [ 671] [depth= 1] . ( 34 sec) [ -4363.9512] [ 671] [depth= 1] . ( 34 sec) [ -4363.8216] [ 671] [depth= 1] . ( 34 sec) [ -4363.4315] [ 671] [depth= 1] . ( 36 sec) [ -4362.9586] [ 671] [depth= 1] . ( 36 sec) [ -4362.9267] [ 671] [depth= 1] . ( 36 sec) [ -4362.9021] [ 671] [depth= 1] . ( 36 sec) [ -4362.8881] [ 671] [depth= 1] . ( 37 sec) [ -4354.3031] [Branch lengths ] . ( 37 sec) [ -4354.3000] [GTR parameters ] . ( 37 sec) [ -4354.2933] [Alpha ][ 1.075314] . ( 41 sec) [ -4354.2015] [Branch lengths ] . ( 66 sec) [ -4354.1985] [Branch lengths ] . ( 66 sec) [ -4354.1985] [Topology ] . ( 66 sec) [ -4354.1977] [Topology ] . ( 66 sec) [ -4354.1976] [GTR parameters ] . ( 67 sec) [ -4354.1972] [Alpha ][ 1.079401] . ( 67 sec) [ -4354.1972] [Topology ] . ( 68 sec) [ -4354.1918] [Topology ] . ( 69 sec) [ -4354.1515] [Topology ] . ( 69 sec) [ -4353.8833] [Topology ] . ( 70 sec) [ -4352.8552] [Topology ] . ( 71 sec) [ -4351.6429] [Topology ] . ( 72 sec) [ -4351.5846] [Topology ] . ( 72 sec) [ -4351.5818] [GTR parameters ] . ( 72 sec) [ -4351.5811] [Alpha ][ 1.085094] . ( 72 sec) [ -4351.5811] [Topology ] . ( 73 sec) [ -4351.5766] [Topology ] . ( 74 sec) [ -4351.5763] [Topology ] . ( 74 sec) [ -4351.5763] [GTR parameters ] . ( 74 sec) [ -4351.5763] [Alpha ][ 1.085094] . ( 74 sec) [ -4351.5763] [Topology ] . ( 75 sec) [ -4351.5763] [Topology ] . ( 76 sec) [ -4351.5763] [GTR parameters ] . ( 76 sec) [ -4351.5763] [Alpha ][ 1.085094] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -4351.576496 . Log likelihood obtained after SPR moves : -4351.576275 . Log likelihood of the current tree: -4351.576275. . Printing the most likely tree in file 'data47.phy_phyml_tree.txt'... . Time used 0h1m25s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo