.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data88.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... . 401 patterns found. (out of a total of 500 sites) . 94 sites without polymorphism (18.80%). . 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=-7956.615250 . ( 0 sec) [ -7955.1854] [GTR parameters ] . ( 0 sec) [ -7954.9724] [Alpha ][ 1.057884] . ( 0 sec) [ -7954.9724] [Topology ] . ( 1 sec) [ -7939.3506] [Topology ] . ( 2 sec) [ -7937.3186] [Topology ] . ( 3 sec) [ -7936.8134] [Topology ] . ( 4 sec) [ -7936.6150] [Topology ] . ( 5 sec) [ -7936.5279] [Topology ] . ( 6 sec) [ -7936.4882] [Topology ] . ( 7 sec) [ -7936.4695] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7936.469519 . ( 12 sec) [ -7936.4470] [GTR parameters ] . ( 12 sec) [ -7936.2709] [Alpha ][ 1.112677] . ( 12 sec) [ -7936.2709] [Topology ] . ( 13 sec) [ -7936.2498] [Topology ] . ( 14 sec) [ -7936.2412] [Topology ] . ( 14 sec) [ -7936.2372] [Topology ] . ( 15 sec) [ -7936.2354] [Topology ] . ( 16 sec) [ -7936.2346] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7936.234585 . ( 22 sec) [ -7936.2345] [GTR parameters ] . ( 22 sec) [ -7936.2336] [Alpha ][ 1.116587] . ( 22 sec) [ -7936.2336] [Topology ] . ( 23 sec) [ -7936.2331] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7936.233081 . ( 30 sec) [ -7936.2331] [GTR parameters ] . ( 30 sec) [ -7936.2331] [Alpha ][ 1.116587] . ( 30 sec) [ -7936.2331] [Topology ] . ( 31 sec) [ -7936.2328] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 43 sec) [ -7955.1854] [GTR parameters ] . ( 43 sec) [ -7954.9724] [Alpha ][ 1.057884] . ( 44 sec) [ -7954.4398] [ 1559] [depth= 1] . ( 45 sec) [ -7954.2583] [ 1559] [depth= 1] . ( 45 sec) [ -7953.0982] [ 1559] [depth= 1] . ( 45 sec) [ -7951.6454] [ 1563] [depth= 1] . ( 45 sec) [ -7951.0879] [ 1556] [depth= 1] . ( 46 sec) [ -7937.2865] [Branch lengths ] . ( 46 sec) [ -7937.2614] [GTR parameters ] . ( 46 sec) [ -7937.1372] [Alpha ][ 1.104457] . ( 49 sec) [ -7936.3161] [Branch lengths ] . ( 71 sec) [ -7936.2502] [Branch lengths ] . ( 71 sec) [ -7936.2502] [Topology ] . ( 72 sec) [ -7936.2449] [Topology ] . ( 73 sec) [ -7936.2431] [Topology ] . ( 74 sec) [ -7936.2423] [Topology ] . ( 74 sec) [ -7936.2420] [GTR parameters ] . ( 75 sec) [ -7936.2342] [Alpha ][ 1.116562] . ( 75 sec) [ -7936.2342] [Topology ] . ( 76 sec) [ -7936.2333] [Topology ] . ( 76 sec) [ -7936.2333] [GTR parameters ] . ( 76 sec) [ -7936.2333] [Alpha ][ 1.116562] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7936.232830 . Log likelihood obtained after SPR moves : -7936.233301 . Log likelihood of the current tree: -7936.232830. . Printing the most likely tree in file 'data88.phy_phyml_tree.txt'... . Time used 0h1m23s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo