.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data46.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... . 436 patterns found. (out of a total of 500 sites) . 62 sites without polymorphism (12.40%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-10431.263771 . ( 1 sec) [ -10427.9988] [GTR parameters ] . ( 1 sec) [ -10427.3751] [Alpha ][ 0.921352] . ( 1 sec) [ -10427.3751] [Topology ] . ( 2 sec) [ -10366.0401] [Topology ] . ( 3 sec) [ -10358.1689] [Topology ] . ( 3 sec) [ -10355.5306] [Topology ] . ( 4 sec) [ -10353.9275] [Topology ] . ( 5 sec) [ -10353.3427] [Topology ] . ( 6 sec) [ -10353.0657] [Topology ] . ( 8 sec) [ -10352.9283] [Topology ] . ( 9 sec) [ -10352.8601] [Topology ] . ( 11 sec) [ -10352.8259] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10352.825858 . ( 21 sec) [ -10352.7481] [GTR parameters ] . ( 21 sec) [ -10352.5836] [Alpha ][ 0.959089] . ( 21 sec) [ -10352.5836] [Topology ] . ( 23 sec) [ -10352.5521] [Topology ] . ( 24 sec) [ -10352.5389] [Topology ] . ( 25 sec) [ -10352.5323] [Topology ] . ( 27 sec) [ -10352.5289] [Topology ] . ( 28 sec) [ -10352.5271] [Topology ] . ( 29 sec) [ -10352.5261] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10352.526138 . ( 40 sec) [ -10352.5259] [GTR parameters ] . ( 40 sec) [ -10352.5246] [Alpha ][ 0.962592] . ( 40 sec) [ -10352.5246] [Topology ] . ( 41 sec) [ -10352.5240] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10352.523974 . ( 52 sec) [ -10352.5239] [GTR parameters ] . ( 52 sec) [ -10352.5239] [Alpha ][ 0.962592] . ( 52 sec) [ -10352.5239] [Topology ] . ( 54 sec) [ -10352.5236] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 78 sec) [ -10427.9988] [GTR parameters ] . ( 78 sec) [ -10427.3751] [Alpha ][ 0.921352] . ( 78 sec) [ -10427.3254] [ 2361] [depth= 1] . ( 79 sec) [ -10427.1830] [ 2359] [depth= 1] . ( 80 sec) [ -10427.0571] [ 2374] [depth= 1] . ( 80 sec) [ -10424.6917] [ 2359] [depth= 1] . ( 80 sec) [ -10422.3320] [ 2362] [depth= 1] . ( 80 sec) [ -10420.1469] [ 2367] [depth= 1] . ( 80 sec) [ -10410.4417] [ 2370] [depth= 1] . ( 81 sec) [ -10408.2363] [ 2366] [depth= 1] . ( 81 sec) [ -10408.0992] [ 2368] [depth= 1] . ( 81 sec) [ -10404.7814] [ 2366] [depth= 1] . ( 82 sec) [ -10404.7115] [ 2366] [depth= 1] . ( 83 sec) [ -10400.7572] [ 2372] [depth= 1] . ( 83 sec) [ -10398.0205] [ 2367] [depth= 1] . ( 84 sec) [ -10397.9246] [ 2372] [depth= 1] . ( 84 sec) [ -10361.0283] [Branch lengths ] . ( 85 sec) [ -10360.9881] [GTR parameters ] . ( 85 sec) [ -10360.9449] [Alpha ][ 0.941265] . ( 85 sec) [ -10360.3662] [ 2374] [depth= 1] . ( 87 sec) [ -10359.7577] [ 2368] [depth= 1] . ( 89 sec) [ -10358.4052] [ 2363] [depth= 1] . ( 90 sec) [ -10353.1655] [Branch lengths ] . ( 90 sec) [ -10353.1529] [GTR parameters ] . ( 90 sec) [ -10353.1049] [Alpha ][ 0.962539] . ( 95 sec) [ -10352.7296] [Branch lengths ] . ( 125 sec) [ -10352.6924] [Branch lengths ] . ( 125 sec) [ -10352.6924] [Topology ] . ( 126 sec) [ -10352.6896] [Topology ] . ( 127 sec) [ -10352.6887] [Topology ] . ( 128 sec) [ -10352.6886] [GTR parameters ] . ( 128 sec) [ -10352.6886] [Alpha ][ 0.962539] . ( 128 sec) [ -10352.6886] [Topology ] . ( 129 sec) [ -10352.6882] [Topology ] . ( 129 sec) [ -10352.6882] [GTR parameters ] . ( 129 sec) [ -10352.6882] [Alpha ][ 0.962539] . Checking for NNIs, optimizing five branches... . ( 136 sec) [ -10352.5259] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10352.523643 . Log likelihood obtained after SPR moves : -10352.525919 . Log likelihood of the current tree: -10352.523643. . Printing the most likely tree in file 'data46.phy_phyml_tree.txt'... . Time used 0h2m24s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo