.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1382_9x1560_2003.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... . 719 patterns found. (out of a total of 1560 sites) . 822 sites without polymorphism (52.69%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 13Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -13206.0941] [Alpha ][ 0.500960] . ( 0 sec) [ -12970.4266] [ 1696] [depth= 3] . ( 1 sec) [ -12814.8449] [ 1690] [depth= 2] . ( 1 sec) [ -12641.6361] [ 1538] [depth= 1] . ( 2 sec) [ -12602.2684] [ 1542] [depth= 1] . ( 2 sec) [ -12563.7437] [ 1534] [depth= 2] . ( 2 sec) [ -12508.9636] [ 1514] [depth= 3] . ( 2 sec) [ -12445.8222] [ 1516] [depth= 3] . ( 4 sec) [ -12440.1277] [ 1507] [depth= 1] . ( 5 sec) [ -12422.9668] [ 1500] [depth= 2] . ( 6 sec) [ -12348.1925] [Branch lengths ] . ( 6 sec) [ -12346.9163] [Alpha ][ 0.560052] . ( 6 sec) [ -12337.0339] [ 1491] [depth= 1] . ( 10 sec) [ -12335.3389] [Branch lengths ] . ( 10 sec) [ -12335.3333] [Alpha ][ 0.564434] . ( 15 sec) [ -12335.1919] [Branch lengths ] . ( 15 sec) [ -12335.1919] [Topology ] . ( 16 sec) [ -12335.1856] [Topology ] . ( 17 sec) [ -12335.1846] [Topology ] . ( 18 sec) [ -12335.1842] [Topology ] . ( 18 sec) [ -12335.1841] [Alpha ][ 0.563636] . ( 18 sec) [ -12335.1841] [Topology ] . ( 19 sec) [ -12335.1840] [Topology ] . ( 19 sec) [ -12335.1840] [Alpha ][ 0.563636] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12335.184008. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -13205.4747] [Alpha ][ 0.500960] . ( 1 sec) [ -12907.1404] [ 1674] [depth= 3] . ( 1 sec) [ -12795.7239] [ 1629] [depth= 4] . ( 2 sec) [ -12735.7135] [ 1622] [depth= 1] . ( 2 sec) [ -12709.2224] [ 1615] [depth= 1] . ( 3 sec) [ -12672.6877] [ 1612] [depth= 1] . ( 3 sec) [ -12403.4196] [ 1498] [depth= 1] . ( 4 sec) [ -12400.9022] [ 1500] [depth= 1] . ( 4 sec) [ -12393.2473] [ 1492] [depth= 1] . ( 4 sec) [ -12389.2176] [ 1491] [depth= 1] . ( 5 sec) [ -12361.5135] [ 1498] [depth= 1] . ( 6 sec) [ -12343.4722] [Branch lengths ] . ( 6 sec) [ -12341.9192] [Alpha ][ 0.566659] . ( 7 sec) [ -12338.8335] [ 1491] [depth= 1] . ( 11 sec) [ -12335.4146] [Branch lengths ] . ( 11 sec) [ -12335.4112] [Alpha ][ 0.563055] . ( 15 sec) [ -12335.1972] [Branch lengths ] . ( 15 sec) [ -12335.1972] [Topology ] . ( 16 sec) [ -12335.1876] [Topology ] . ( 17 sec) [ -12335.1852] [Topology ] . ( 18 sec) [ -12335.1845] [Topology ] . ( 18 sec) [ -12335.1843] [Alpha ][ 0.563675] . ( 18 sec) [ -12335.1843] [Topology ] . ( 19 sec) [ -12335.1841] [Topology ] . ( 19 sec) [ -12335.1841] [Alpha ][ 0.563675] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12335.184070. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -13882.6374] [Alpha ][ 0.500960] . ( 1 sec) [ -13385.8726] [ 1699] [depth= 3] . ( 1 sec) [ -13365.5724] [ 1691] [depth= 2] . ( 1 sec) [ -12842.4803] [ 1682] [depth= 1] . ( 2 sec) [ -12511.9459] [ 1531] [depth= 4] . ( 2 sec) [ -12506.6600] [ 1528] [depth= 3] . ( 2 sec) [ -12473.3079] [ 1516] [depth= 1] . ( 3 sec) [ -12461.2015] [ 1517] [depth= 3] . ( 3 sec) [ -12443.1275] [ 1503] [depth= 2] . ( 3 sec) [ -12380.6094] [ 1498] [depth= 1] . ( 4 sec) [ -12377.0744] [ 1500] [depth= 2] . ( 5 sec) [ -12374.5657] [ 1500] [depth= 1] . ( 6 sec) [ -12352.4477] [ 1492] [depth= 3] . ( 6 sec) [ -12340.4915] [Branch lengths ] . ( 6 sec) [ -12339.0040] [Alpha ][ 0.565935] . ( 7 sec) [ -12336.9780] [ 1491] [depth= 1] . ( 11 sec) [ -12335.2631] [Branch lengths ] . ( 11 sec) [ -12335.2629] [Alpha ][ 0.564935] . ( 15 sec) [ -12335.1868] [Branch lengths ] . ( 15 sec) [ -12335.1868] [Topology ] . ( 16 sec) [ -12335.1850] [Topology ] . ( 17 sec) [ -12335.1846] [Topology ] . ( 17 sec) [ -12335.1842] [Alpha ][ 0.563639] . ( 17 sec) [ -12335.1842] [Topology ] . ( 18 sec) [ -12335.1840] [Topology ] . ( 18 sec) [ -12335.1840] [Alpha ][ 0.563639] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12335.184030. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -12598.7868] [Alpha ][ 0.500960] . ( 0 sec) [ -12571.3190] [ 1532] [depth= 2] . ( 1 sec) [ -12523.7021] [ 1529] [depth= 1] . ( 1 sec) [ -12483.7240] [ 1518] [depth= 3] . ( 1 sec) [ -12411.4883] [ 1513] [depth= 5] . ( 2 sec) [ -12383.9832] [ 1504] [depth= 4] . ( 4 sec) [ -12364.0622] [ 1492] [depth= 3] . ( 5 sec) [ -12354.8823] [ 1491] [depth= 1] . ( 6 sec) [ -12338.0722] [Branch lengths ] . ( 6 sec) [ -12336.9666] [Alpha ][ 0.557976] . ( 10 sec) [ -12335.2609] [Branch lengths ] . ( 10 sec) [ -12335.2609] [Topology ] . ( 11 sec) [ -12335.2074] [Topology ] . ( 12 sec) [ -12335.1980] [Topology ] . ( 13 sec) [ -12335.1951] [Topology ] . ( 14 sec) [ -12335.1942] [Topology ] . ( 14 sec) [ -12335.1847] [Alpha ][ 0.563736] . ( 14 sec) [ -12335.1847] [Topology ] . ( 15 sec) [ -12335.1842] [Topology ] . ( 15 sec) [ -12335.1842] [Alpha ][ 0.563736] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12335.184164. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -14033.7140] [Alpha ][ 0.500960] . ( 0 sec) [ -13598.4012] [ 1676] [depth= 3] . ( 1 sec) [ -13408.1933] [ 1647] [depth= 2] . ( 1 sec) [ -13376.5198] [ 1642] [depth= 1] . ( 1 sec) [ -12899.6641] [ 1641] [depth= 2] . ( 2 sec) [ -12812.2204] [ 1642] [depth= 1] . ( 2 sec) [ -12519.9765] [ 1522] [depth= 1] . ( 2 sec) [ -12457.0171] [ 1524] [depth= 1] . ( 3 sec) [ -12433.5924] [ 1514] [depth= 2] . ( 3 sec) [ -12391.1820] [ 1503] [depth= 1] . ( 3 sec) [ -12386.6469] [ 1507] [depth= 1] . ( 4 sec) [ -12378.7941] [ 1503] [depth= 1] . ( 4 sec) [ -12353.4277] [ 1498] [depth= 2] . ( 5 sec) [ -12342.2765] [Branch lengths ] . ( 6 sec) [ -12341.1290] [Alpha ][ 0.558657] . ( 7 sec) [ -12339.9729] [ 1491] [depth= 1] . ( 10 sec) [ -12335.5215] [Branch lengths ] . ( 11 sec) [ -12335.5115] [Alpha ][ 0.564595] . ( 15 sec) [ -12335.1945] [Branch lengths ] . ( 15 sec) [ -12335.1945] [Topology ] . ( 16 sec) [ -12335.1863] [Topology ] . ( 17 sec) [ -12335.1848] [Topology ] . ( 18 sec) [ -12335.1843] [Topology ] . ( 18 sec) [ -12335.1841] [Alpha ][ 0.563608] . ( 18 sec) [ -12335.1841] [Topology ] . ( 19 sec) [ -12335.1840] [Topology ] . ( 19 sec) [ -12335.1840] [Alpha ][ 0.563608] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12335.184014. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -12403.8773] [Alpha ][ 0.502812] . ( 1 sec) [ -12403.8773] [Topology ] . ( 2 sec) [ -12365.6388] [Topology ] . ( 3 sec) [ -12360.3449] [Topology ] . ( 4 sec) [ -12346.2642] [Topology ] . ( 4 sec) [ -12337.4402] [Topology ] . ( 5 sec) [ -12336.6549] [Topology ] . ( 6 sec) [ -12336.4916] [Topology ] . ( 7 sec) [ -12336.4489] [Topology ] . ( 8 sec) [ -12336.4372] [Topology ] . ( 9 sec) [ -12336.4339] [Topology ] . Checking for NNIs, optimizing five branches... . ( 16 sec) [ -12335.2103] [Alpha ][ 0.562445] . ( 16 sec) [ -12335.2103] [Topology ] . ( 17 sec) [ -12335.1886] [Topology ] . ( 18 sec) [ -12335.1857] [Topology ] . ( 19 sec) [ -12335.1848] [Topology ] . Checking for NNIs, optimizing five branches... . ( 27 sec) [ -12335.1844] [Alpha ][ 0.563602] . ( 27 sec) [ -12335.1844] [Topology ] . ( 28 sec) [ -12335.1841] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 43 sec) [ -12403.8773] [Alpha ][ 0.502812] . ( 43 sec) [ -12403.7725] [ 1506] [depth= 2] . ( 44 sec) [ -12400.3129] [ 1506] [depth= 1] . ( 44 sec) [ -12362.6208] [ 1504] [depth= 3] . ( 45 sec) [ -12351.1184] [ 1491] [depth= 1] . ( 45 sec) [ -12351.0029] [ 1492] [depth= 1] . ( 45 sec) [ -12350.4677] [ 1491] [depth= 1] . ( 47 sec) [ -12336.9622] [Branch lengths ] . ( 47 sec) [ -12335.8485] [Alpha ][ 0.560134] . ( 52 sec) [ -12335.2172] [Branch lengths ] . ( 52 sec) [ -12335.2172] [Topology ] . ( 53 sec) [ -12335.1961] [Topology ] . ( 53 sec) [ -12335.1905] [Topology ] . ( 54 sec) [ -12335.1887] [Topology ] . ( 55 sec) [ -12335.1881] [Topology ] . ( 56 sec) [ -12335.1844] [Alpha ][ 0.563681] . ( 56 sec) [ -12335.1844] [Topology ] . ( 57 sec) [ -12335.1841] [Topology ] . ( 57 sec) [ -12335.1841] [Alpha ][ 0.563681] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -12335.184105 . Log likelihood obtained after SPR moves : -12335.184099 . Log likelihood of the current tree: -12335.184099. . Printing the most likely tree in file 'proteic_M1382_9x1560_2003.phy_phyml_tree.txt'... . Best log likelihood : -12335.184008 . Time used 0h1m5s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 190.16user 0.00system 3:18.94elapsed 95%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps