.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data14.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... . 387 patterns found. (out of a total of 500 sites) . 105 sites without polymorphism (21.00%). . 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=-7395.141666 . ( 1 sec) [ -7393.3350] [GTR parameters ] . ( 1 sec) [ -7393.1441] [Alpha ][ 0.947123] . ( 1 sec) [ -7393.1441] [Topology ] . ( 2 sec) [ -7351.5864] [Topology ] . ( 3 sec) [ -7345.3795] [Topology ] . ( 4 sec) [ -7343.3033] [Topology ] . ( 5 sec) [ -7342.8241] [Topology ] . ( 5 sec) [ -7342.6261] [Topology ] . ( 6 sec) [ -7342.5346] [Topology ] . ( 7 sec) [ -7342.4901] [Topology ] . ( 7 sec) [ -7342.4678] [Topology ] . ( 8 sec) [ -7342.4564] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7342.456420 . ( 14 sec) [ -7342.4419] [GTR parameters ] . ( 14 sec) [ -7342.4218] [Alpha ][ 0.963635] . ( 14 sec) [ -7342.4218] [Topology ] . ( 14 sec) [ -7342.4135] [Topology ] . ( 15 sec) [ -7342.4095] [Topology ] . ( 16 sec) [ -7342.4075] [Topology ] . ( 16 sec) [ -7342.4065] [Topology ] . ( 17 sec) [ -7342.4060] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7342.405994 . ( 24 sec) [ -7342.4060] [GTR parameters ] . ( 24 sec) [ -7342.4058] [Alpha ][ 0.965001] . ( 24 sec) [ -7342.4058] [Topology ] . ( 25 sec) [ -7342.4055] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 36 sec) [ -7393.3350] [GTR parameters ] . ( 36 sec) [ -7393.1441] [Alpha ][ 0.947123] . ( 36 sec) [ -7389.9580] [ 1489] [depth= 1] . ( 36 sec) [ -7388.2503] [ 1489] [depth= 1] . ( 36 sec) [ -7387.7091] [ 1489] [depth= 1] . ( 36 sec) [ -7387.6434] [ 1489] [depth= 1] . ( 37 sec) [ -7385.8140] [ 1490] [depth= 1] . ( 37 sec) [ -7384.5889] [ 1493] [depth= 1] . ( 37 sec) [ -7383.5378] [ 1490] [depth= 1] . ( 37 sec) [ -7383.1092] [ 1492] [depth= 1] . ( 37 sec) [ -7381.7062] [ 1496] [depth= 3] . ( 37 sec) [ -7380.3578] [ 1492] [depth= 3] . ( 38 sec) [ -7378.9339] [ 1496] [depth= 1] . ( 38 sec) [ -7378.8880] [ 1500] [depth= 1] . ( 38 sec) [ -7378.6404] [ 1492] [depth= 1] . ( 38 sec) [ -7378.1273] [ 1497] [depth= 1] . ( 38 sec) [ -7378.0184] [ 1499] [depth= 1] . ( 38 sec) [ -7377.8882] [ 1501] [depth= 1] . ( 39 sec) [ -7377.3765] [ 1497] [depth= 1] . ( 39 sec) [ -7377.3367] [ 1497] [depth= 1] . ( 39 sec) [ -7377.3191] [ 1497] [depth= 1] . ( 39 sec) [ -7377.0085] [ 1497] [depth= 1] . ( 40 sec) [ -7347.0344] [Branch lengths ] . ( 40 sec) [ -7347.0125] [GTR parameters ] . ( 40 sec) [ -7347.0125] [Alpha ][ 0.948070] . ( 41 sec) [ -7346.8626] [ 1497] [depth= 1] . ( 42 sec) [ -7345.5409] [ 1493] [depth= 1] . ( 44 sec) [ -7343.4209] [Branch lengths ] . ( 44 sec) [ -7343.4146] [GTR parameters ] . ( 44 sec) [ -7343.4054] [Alpha ][ 0.959187] . ( 48 sec) [ -7342.6060] [Branch lengths ] . ( 70 sec) [ -7342.4283] [Branch lengths ] . ( 70 sec) [ -7342.4283] [Topology ] . ( 71 sec) [ -7342.4162] [Topology ] . ( 72 sec) [ -7342.4122] [Topology ] . ( 72 sec) [ -7342.4106] [Topology ] . ( 73 sec) [ -7342.4099] [Topology ] . ( 73 sec) [ -7342.4086] [GTR parameters ] . ( 73 sec) [ -7342.4059] [Alpha ][ 0.965158] . ( 73 sec) [ -7342.4059] [Topology ] . ( 74 sec) [ -7342.4055] [Topology ] . ( 74 sec) [ -7342.4055] [GTR parameters ] . ( 74 sec) [ -7342.4055] [Alpha ][ 0.965158] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7342.405517 . Log likelihood obtained after SPR moves : -7342.405475 . Log likelihood of the current tree: -7342.405475. . Printing the most likely tree in file 'data14.phy_phyml_tree.txt'... . Time used 0h1m19s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo