.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2344_7x232_2005.phy . Data type : aa . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : WAG . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Amino acid equilibrium frequencies : model . Optimise tree topology : yes . Tree topology search : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : yes . Number of random starting trees : 5 . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 145 patterns found. (out of a total of 232 sites) . 124 sites without polymorphism (53.45%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 2Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -2411.2991] [Alpha ][ 0.500960] . ( 0 sec) [ -2086.8801] [ 187] [depth= 2] . ( 0 sec) [ -2055.1456] [ 175] [depth= 1] . ( 0 sec) [ -1677.7303] [ 181] [depth= 1] . ( 0 sec) [ -1666.8508] [ 178] [depth= 1] . ( 1 sec) [ -1665.0756] [ 181] [depth= 1] . ( 1 sec) [ -1620.3380] [ 175] [depth= 1] . ( 1 sec) [ -1605.1446] [ 172] [depth= 1] . ( 1 sec) [ -1601.1887] [Branch lengths ] . ( 1 sec) [ -1596.5554] [Alpha ][ 1.000067] . ( 2 sec) [ -1591.3823] [ 175] [depth= 1] . ( 2 sec) [ -1587.8928] [ 171] [depth= 1] . ( 2 sec) [ -1584.8406] [ 172] [depth= 1] . ( 3 sec) [ -1583.7133] [Branch lengths ] . ( 3 sec) [ -1583.4977] [Alpha ][ 1.218473] . ( 4 sec) [ -1583.4588] [Branch lengths ] . ( 4 sec) [ -1583.4588] [Topology ] . ( 4 sec) [ -1583.4583] [Topology ] . ( 4 sec) [ -1583.4577] [Alpha ][ 1.231464] . ( 4 sec) [ -1583.4577] [Topology ] . ( 5 sec) [ -1583.4577] [Topology ] . ( 5 sec) [ -1583.4577] [Alpha ][ 1.231464] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1583.457685. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -2557.7803] [Alpha ][ 0.500960] . ( 0 sec) [ -2161.3212] [ 191] [depth= 3] . ( 0 sec) [ -1759.2501] [ 181] [depth= 1] . ( 0 sec) [ -1757.8765] [ 180] [depth= 1] . ( 0 sec) [ -1704.2208] [ 199] [depth= 1] . ( 0 sec) [ -1701.2590] [ 198] [depth= 2] . ( 0 sec) [ -1650.7918] [ 190] [depth= 1] . ( 0 sec) [ -1606.5261] [ 171] [depth= 1] . ( 1 sec) [ -1603.2144] [ 172] [depth= 1] . ( 1 sec) [ -1590.9074] [Branch lengths ] . ( 1 sec) [ -1585.5944] [Alpha ][ 1.000069] . ( 2 sec) [ -1583.7617] [Branch lengths ] . ( 3 sec) [ -1583.7617] [Topology ] . ( 3 sec) [ -1583.6977] [Topology ] . ( 3 sec) [ -1583.6875] [Topology ] . ( 3 sec) [ -1583.6848] [Topology ] . ( 3 sec) [ -1583.6840] [Topology ] . ( 3 sec) [ -1583.4675] [Alpha ][ 1.219606] . ( 3 sec) [ -1583.4675] [Topology ] . ( 4 sec) [ -1583.4591] [Topology ] . ( 4 sec) [ -1583.4583] [Topology ] . ( 4 sec) [ -1583.4580] [Alpha ][ 1.230148] . ( 4 sec) [ -1583.4580] [Topology ] . ( 4 sec) [ -1583.4578] [Topology ] . ( 4 sec) [ -1583.4577] [Alpha ][ 1.231378] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1583.457750. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -2485.4322] [Alpha ][ 0.500960] . ( 0 sec) [ -2226.5854] [ 194] [depth= 1] . ( 1 sec) [ -1916.1984] [ 180] [depth= 2] . ( 1 sec) [ -1805.3808] [ 176] [depth= 1] . ( 1 sec) [ -1683.0429] [ 185] [depth= 1] . ( 1 sec) [ -1646.4194] [ 176] [depth= 1] . ( 1 sec) [ -1606.0861] [ 174] [depth= 2] . ( 1 sec) [ -1601.8612] [ 172] [depth= 1] . ( 1 sec) [ -1600.9013] [ 171] [depth= 1] . ( 1 sec) [ -1596.1694] [ 172] [depth= 1] . ( 1 sec) [ -1589.3210] [Branch lengths ] . ( 1 sec) [ -1583.8239] [Alpha ][ 1.000313] . ( 3 sec) [ -1583.6849] [Branch lengths ] . ( 3 sec) [ -1583.6849] [Topology ] . ( 3 sec) [ -1583.6833] [Topology ] . ( 3 sec) [ -1583.6832] [Topology ] . ( 3 sec) [ -1583.4658] [Alpha ][ 1.220593] . ( 3 sec) [ -1583.4658] [Topology ] . ( 3 sec) [ -1583.4586] [Topology ] . ( 4 sec) [ -1583.4582] [Topology ] . ( 4 sec) [ -1583.4578] [Alpha ][ 1.230358] . ( 4 sec) [ -1583.4578] [Topology ] . ( 4 sec) [ -1583.4577] [Topology ] . ( 4 sec) [ -1583.4577] [Alpha ][ 1.231588] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1583.457714. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -2055.5371] [Alpha ][ 0.500960] . ( 0 sec) [ -1770.5049] [ 188] [depth= 3] . ( 0 sec) [ -1662.8385] [ 175] [depth= 1] . ( 0 sec) [ -1660.5629] [ 171] [depth= 1] . ( 1 sec) [ -1632.7364] [ 176] [depth= 1] . ( 1 sec) [ -1600.9811] [ 171] [depth= 1] . ( 1 sec) [ -1594.8880] [ 172] [depth= 1] . ( 1 sec) [ -1589.3246] [Branch lengths ] . ( 1 sec) [ -1584.0169] [Alpha ][ 1.000308] . ( 3 sec) [ -1583.6928] [Branch lengths ] . ( 3 sec) [ -1583.6928] [Topology ] . ( 3 sec) [ -1583.6845] [Topology ] . ( 3 sec) [ -1583.6834] [Topology ] . ( 4 sec) [ -1583.6832] [Topology ] . ( 4 sec) [ -1583.4659] [Alpha ][ 1.220498] . ( 4 sec) [ -1583.4659] [Topology ] . ( 4 sec) [ -1583.4586] [Topology ] . ( 4 sec) [ -1583.4582] [Topology ] . ( 4 sec) [ -1583.4578] [Alpha ][ 1.230360] . ( 4 sec) [ -1583.4578] [Topology ] . ( 4 sec) [ -1583.4577] [Topology ] . ( 4 sec) [ -1583.4577] [Alpha ][ 1.231590] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1583.457712. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -1992.2305] [Alpha ][ 0.500960] . ( 1 sec) [ -1680.8131] [ 186] [depth= 2] . ( 1 sec) [ -1632.0767] [ 174] [depth= 2] . ( 1 sec) [ -1626.1555] [ 172] [depth= 1] . ( 1 sec) [ -1625.3744] [ 175] [depth= 1] . ( 1 sec) [ -1624.3246] [ 171] [depth= 1] . ( 1 sec) [ -1621.9777] [ 172] [depth= 1] . ( 1 sec) [ -1612.9320] [ 174] [depth= 1] . ( 2 sec) [ -1595.0964] [Branch lengths ] . ( 2 sec) [ -1590.3938] [Alpha ][ 0.999999] . ( 2 sec) [ -1586.5567] [ 172] [depth= 1] . ( 3 sec) [ -1584.6684] [Branch lengths ] . ( 3 sec) [ -1584.4807] [Alpha ][ 1.197379] . ( 5 sec) [ -1584.2529] [Branch lengths ] . ( 5 sec) [ -1584.2529] [Topology ] . ( 5 sec) [ -1583.8082] [Topology ] . ( 5 sec) [ -1583.5700] [Topology ] . ( 5 sec) [ -1583.4945] [Topology ] . ( 5 sec) [ -1583.4713] [Topology ] . ( 6 sec) [ -1583.4644] [Topology ] . ( 6 sec) [ -1583.4623] [Topology ] . ( 6 sec) [ -1583.4585] [Alpha ][ 1.230917] . ( 6 sec) [ -1583.4585] [Topology ] . ( 6 sec) [ -1583.4579] [Topology ] . ( 6 sec) [ -1583.4579] [Alpha ][ 1.232148] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1583.457892. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -1585.9438] [Alpha ][ 1.316624] . ( 1 sec) [ -1585.9438] [Topology ] . ( 1 sec) [ -1583.6530] [Topology ] . ( 1 sec) [ -1583.5036] [Topology ] . ( 1 sec) [ -1583.4820] [Topology ] . ( 1 sec) [ -1583.4784] [Topology ] . ( 1 sec) [ -1583.4778] [Topology ] . Checking for NNIs, optimizing five branches... . ( 3 sec) [ -1583.4588] [Alpha ][ 1.234717] . ( 3 sec) [ -1583.4588] [Topology ] . ( 3 sec) [ -1583.4578] [Topology ] . ( 3 sec) [ -1583.4577] [Topology ] . Checking for NNIs, optimizing five branches... . ( 4 sec) [ -1583.4577] [Alpha ][ 1.231290] . ( 4 sec) [ -1583.4577] [Topology ] . ( 4 sec) [ -1583.4577] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 7 sec) [ -1585.9438] [Alpha ][ 1.316624] . ( 8 sec) [ -1583.5345] [Branch lengths ] . ( 8 sec) [ -1583.5345] [Topology ] . ( 9 sec) [ -1583.4802] [Topology ] . ( 9 sec) [ -1583.4782] [Topology ] . ( 9 sec) [ -1583.4778] [Topology ] . ( 9 sec) [ -1583.4587] [Alpha ][ 1.234442] . ( 9 sec) [ -1583.4587] [Topology ] . ( 9 sec) [ -1583.4578] [Topology ] . ( 9 sec) [ -1583.4578] [Alpha ][ 1.231607] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -1583.457678 . Log likelihood obtained after SPR moves : -1583.457760 . Log likelihood of the current tree: -1583.457678. . Printing the most likely tree in file 'proteic_M2344_7x232_2005.phy_phyml_tree.txt'... . Best log likelihood : -1583.457678 . Time used 0h0m11s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 37.12user 0.00system 0:38.50elapsed 96%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps