.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2345_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) [ -2027.8929] [Alpha ][ 0.500960] . ( 0 sec) [ -1756.8088] [ 195] [depth= 1] . ( 0 sec) [ -1655.1375] [ 182] [depth= 1] . ( 0 sec) [ -1643.2273] [ 178] [depth= 1] . ( 0 sec) [ -1602.4708] [ 171] [depth= 1] . ( 0 sec) [ -1596.7663] [ 172] [depth= 1] . ( 1 sec) [ -1589.4972] [Branch lengths ] . ( 1 sec) [ -1584.1876] [Alpha ][ 1.000255] . ( 3 sec) [ -1583.7039] [Branch lengths ] . ( 3 sec) [ -1583.7039] [Topology ] . ( 3 sec) [ -1583.6867] [Topology ] . ( 3 sec) [ -1583.6842] [Topology ] . ( 3 sec) [ -1583.6835] [Topology ] . ( 3 sec) [ -1583.4671] [Alpha ][ 1.219885] . ( 3 sec) [ -1583.4671] [Topology ] . ( 3 sec) [ -1583.4589] [Topology ] . ( 4 sec) [ -1583.4583] [Topology ] . ( 4 sec) [ -1583.4579] [Alpha ][ 1.230201] . ( 4 sec) [ -1583.4579] [Topology ] . ( 4 sec) [ -1583.4577] [Topology ] . ( 4 sec) [ -1583.4577] [Alpha ][ 1.231431] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1583.457743. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -2061.6575] [Alpha ][ 0.500960] . ( 0 sec) [ -1756.5389] [ 192] [depth= 1] . ( 0 sec) [ -1659.4158] [ 181] [depth= 1] . ( 1 sec) [ -1629.0105] [ 175] [depth= 1] . ( 1 sec) [ -1624.9821] [ 171] [depth= 1] . ( 1 sec) [ -1612.4789] [ 172] [depth= 1] . ( 1 sec) [ -1605.7062] [ 174] [depth= 1] . ( 1 sec) [ -1593.1618] [ 172] [depth= 1] . ( 2 sec) [ -1589.2815] [Branch lengths ] . ( 2 sec) [ -1583.9314] [Alpha ][ 1.000311] . ( 3 sec) [ -1583.6918] [Branch lengths ] . ( 3 sec) [ -1583.6918] [Topology ] . ( 3 sec) [ -1583.6844] [Topology ] . ( 4 sec) [ -1583.6834] [Topology ] . ( 4 sec) [ -1583.4659] [Alpha ][ 1.220651] . ( 4 sec) [ -1583.4659] [Topology ] . ( 4 sec) [ -1583.4586] [Topology ] . ( 4 sec) [ -1583.4582] [Topology ] . ( 4 sec) [ -1583.4579] [Alpha ][ 1.230366] . ( 4 sec) [ -1583.4579] [Topology ] . ( 4 sec) [ -1583.4577] [Topology ] . ( 4 sec) [ -1583.4577] [Alpha ][ 1.231596] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1583.457717. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -2110.9569] [Alpha ][ 0.500960] . ( 1 sec) [ -1802.5533] [ 188] [depth= 2] . ( 1 sec) [ -1772.9666] [ 175] [depth= 1] . ( 1 sec) [ -1699.5235] [ 181] [depth= 1] . ( 1 sec) [ -1648.0130] [ 171] [depth= 2] . ( 1 sec) [ -1646.8380] [ 176] [depth= 1] . ( 1 sec) [ -1625.0952] [ 171] [depth= 1] . ( 1 sec) [ -1595.6657] [ 172] [depth= 1] . ( 1 sec) [ -1594.7670] [ 171] [depth= 1] . ( 1 sec) [ -1592.2580] [Branch lengths ] . ( 2 sec) [ -1586.7539] [Alpha ][ 1.000378] . ( 2 sec) [ -1585.8158] [ 172] [depth= 1] . ( 3 sec) [ -1583.7575] [Branch lengths ] . ( 3 sec) [ -1583.5641] [Alpha ][ 1.204029] . ( 5 sec) [ -1583.4627] [Branch lengths ] . ( 5 sec) [ -1583.4627] [Topology ] . ( 5 sec) [ -1583.4604] [Topology ] . ( 5 sec) [ -1583.4602] [Topology ] . ( 5 sec) [ -1583.4578] [Alpha ][ 1.230285] . ( 5 sec) [ -1583.4578] [Topology ] . ( 5 sec) [ -1583.4577] [Topology ] . ( 5 sec) [ -1583.4577] [Alpha ][ 1.231515] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1583.457696. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -2151.9019] [Alpha ][ 0.500960] . ( 1 sec) [ -1705.0957] [ 189] [depth= 4] . ( 1 sec) [ -1645.1784] [ 175] [depth= 3] . ( 1 sec) [ -1632.8226] [ 171] [depth= 1] . ( 1 sec) [ -1627.0625] [ 176] [depth= 1] . ( 1 sec) [ -1603.2639] [ 171] [depth= 1] . ( 1 sec) [ -1597.9546] [ 172] [depth= 1] . ( 1 sec) [ -1596.9491] [ 171] [depth= 1] . ( 2 sec) [ -1592.2568] [Branch lengths ] . ( 2 sec) [ -1586.7128] [Alpha ][ 1.000362] . ( 2 sec) [ -1584.7056] [ 172] [depth= 1] . ( 3 sec) [ -1583.7230] [Branch lengths ] . ( 3 sec) [ -1583.5111] [Alpha ][ 1.216745] . ( 5 sec) [ -1583.4598] [Branch lengths ] . ( 5 sec) [ -1583.4598] [Topology ] . ( 5 sec) [ -1583.4586] [Topology ] . ( 5 sec) [ -1583.4584] [Topology ] . ( 5 sec) [ -1583.4578] [Alpha ][ 1.230841] . ( 5 sec) [ -1583.4578] [Topology ] . ( 5 sec) [ -1583.4577] [Topology ] . ( 5 sec) [ -1583.4577] [Alpha ][ 1.230841] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1583.457709. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -2303.2587] [Alpha ][ 0.500960] . ( 1 sec) [ -2149.7347] [ 194] [depth= 1] . ( 1 sec) [ -1744.2050] [ 181] [depth= 2] . ( 1 sec) [ -1699.1775] [ 198] [depth= 1] . ( 1 sec) [ -1696.3575] [ 196] [depth= 2] . ( 1 sec) [ -1648.4530] [ 190] [depth= 1] . ( 1 sec) [ -1601.0576] [ 171] [depth= 1] . ( 1 sec) [ -1598.4330] [ 172] [depth= 1] . ( 2 sec) [ -1590.4709] [Branch lengths ] . ( 2 sec) [ -1585.1262] [Alpha ][ 1.000103] . ( 3 sec) [ -1583.7129] [Branch lengths ] . ( 3 sec) [ -1583.7129] [Topology ] . ( 3 sec) [ -1583.6863] [Topology ] . ( 4 sec) [ -1583.6841] [Topology ] . ( 4 sec) [ -1583.6837] [Topology ] . ( 4 sec) [ -1583.4665] [Alpha ][ 1.219962] . ( 4 sec) [ -1583.4665] [Topology ] . ( 4 sec) [ -1583.4587] [Topology ] . ( 4 sec) [ -1583.4582] [Topology ] . ( 4 sec) [ -1583.4579] [Alpha ][ 1.230299] . ( 4 sec) [ -1583.4579] [Topology ] . ( 4 sec) [ -1583.4577] [Topology ] . ( 4 sec) [ -1583.4577] [Alpha ][ 1.231529] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1583.457711. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -1585.9438] [Alpha ][ 1.316624] . ( 0 sec) [ -1585.9438] [Topology ] . ( 0 sec) [ -1583.6530] [Topology ] . ( 0 sec) [ -1583.5036] [Topology ] . ( 0 sec) [ -1583.4820] [Topology ] . ( 1 sec) [ -1583.4784] [Topology ] . ( 1 sec) [ -1583.4778] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2 sec) [ -1583.4588] [Alpha ][ 1.234717] . ( 2 sec) [ -1583.4588] [Topology ] . ( 2 sec) [ -1583.4578] [Topology ] . ( 2 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)... . ( 6 sec) [ -1585.9438] [Alpha ][ 1.316624] . ( 8 sec) [ -1583.5345] [Branch lengths ] . ( 8 sec) [ -1583.5345] [Topology ] . ( 8 sec) [ -1583.4802] [Topology ] . ( 8 sec) [ -1583.4782] [Topology ] . ( 8 sec) [ -1583.4778] [Topology ] . ( 8 sec) [ -1583.4587] [Alpha ][ 1.234442] . ( 8 sec) [ -1583.4587] [Topology ] . ( 8 sec) [ -1583.4578] [Topology ] . ( 8 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_M2345_7x232_2005.phy_phyml_tree.txt'... . Best log likelihood : -1583.457678 . Time used 0h0m10s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 36.82user 0.00system 0:38.15elapsed 96%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps