.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2638_18x378_2006.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... . 75 patterns found. (out of a total of 378 sites) . 321 sites without polymorphism (84.92%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 3Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -2229.9496] [Alpha ][ 0.500960] . ( 0 sec) [ -2115.8088] [ 122] [depth= 8] . ( 0 sec) [ -2060.2313] [ 117] [depth= 5] . ( 0 sec) [ -2000.1357] [ 110] [depth= 3] . ( 1 sec) [ -1999.7407] [ 110] [depth= 1] . ( 1 sec) [ -1983.6355] [ 109] [depth= 1] . ( 1 sec) [ -1919.6868] [ 108] [depth= 4] . ( 1 sec) [ -1885.2675] [ 102] [depth= 3] . ( 1 sec) [ -1872.5017] [ 102] [depth= 2] . ( 1 sec) [ -1862.6243] [ 103] [depth= 3] . ( 1 sec) [ -1842.2102] [ 100] [depth= 4] . ( 1 sec) [ -1822.5472] [ 97] [depth= 4] . ( 2 sec) [ -1819.5771] [ 97] [depth= 1] . ( 2 sec) [ -1801.4278] [ 97] [depth= 2] . ( 3 sec) [ -1776.9088] [ 97] [depth= 1] . ( 3 sec) [ -1759.6164] [ 95] [depth= 2] . ( 3 sec) [ -1750.4011] [ 93] [depth= 4] . ( 3 sec) [ -1703.1012] [ 84] [depth= 5] . ( 4 sec) [ -1698.5157] [ 83] [depth= 4] . ( 4 sec) [ -1697.0772] [ 82] [depth= 3] . ( 4 sec) [ -1696.9797] [ 82] [depth= 1] . ( 4 sec) [ -1696.9471] [ 82] [depth= 1] . ( 5 sec) [ -1696.8719] [ 82] [depth= 2] . ( 9 sec) [ -1696.5763] [ 82] [depth= 6] . ( 10 sec) [ -1696.1396] [Branch lengths ] . ( 10 sec) [ -1693.5802] [Alpha ][ 0.250961] . ( 15 sec) [ -1692.6945] [ 82] [depth= 1] . ( 17 sec) [ -1692.1865] [ 81] [depth= 1] . ( 17 sec) [ -1692.0940] [ 81] [depth= 1] . ( 31 sec) [ -1691.8269] [Branch lengths ] . ( 31 sec) [ -1691.5033] [Alpha ][ 0.172378] . ( 55 sec) [ -1691.4864] [Branch lengths ] . ( 55 sec) [ -1691.4864] [Topology ] . ( 56 sec) [ -1691.4858] [Topology ] . ( 56 sec) [ -1691.4857] [Alpha ][ 0.170933] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1691.485650. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -2120.5329] [Alpha ][ 0.500960] . ( 1 sec) [ -2044.5220] [ 120] [depth= 4] . ( 1 sec) [ -2006.9636] [ 116] [depth= 1] . ( 1 sec) [ -1992.9460] [ 116] [depth= 1] . ( 1 sec) [ -1982.0521] [ 116] [depth= 1] . ( 1 sec) [ -1946.0961] [ 113] [depth= 6] . ( 1 sec) [ -1933.2877] [ 113] [depth= 3] . ( 1 sec) [ -1910.4187] [ 113] [depth= 1] . ( 1 sec) [ -1880.3235] [ 113] [depth= 1] . ( 1 sec) [ -1869.2980] [ 111] [depth= 1] . ( 1 sec) [ -1832.2677] [ 102] [depth= 6] . ( 1 sec) [ -1823.9275] [ 102] [depth= 1] . ( 1 sec) [ -1792.9625] [ 95] [depth= 4] . ( 2 sec) [ -1789.7383] [ 95] [depth= 5] . ( 2 sec) [ -1781.6814] [ 95] [depth= 2] . ( 3 sec) [ -1753.2301] [ 88] [depth= 1] . ( 3 sec) [ -1747.3767] [ 88] [depth= 1] . ( 4 sec) [ -1745.1167] [ 86] [depth= 3] . ( 4 sec) [ -1740.6862] [ 87] [depth= 1] . ( 4 sec) [ -1732.9635] [ 86] [depth= 1] . ( 4 sec) [ -1732.4131] [ 85] [depth= 2] . ( 4 sec) [ -1731.9592] [ 85] [depth= 1] . ( 4 sec) [ -1716.4197] [ 82] [depth= 2] . ( 5 sec) [ -1713.9321] [ 82] [depth= 1] . ( 5 sec) [ -1712.2238] [ 81] [depth= 1] . ( 7 sec) [ -1709.4240] [ 82] [depth= 1] . ( 7 sec) [ -1705.9982] [ 81] [depth= 1] . ( 9 sec) [ -1705.5176] [ 81] [depth= 1] . ( 9 sec) [ -1701.5287] [ 80] [depth= 1] . ( 9 sec) [ -1701.4158] [ 80] [depth= 1] . ( 10 sec) [ -1694.4178] [Branch lengths ] . ( 10 sec) [ -1692.3251] [Alpha ][ 0.250961] . ( 12 sec) [ -1691.0717] [ 80] [depth= 2] . ( 15 sec) [ -1690.8707] [ 80] [depth= 1] . ( 16 sec) [ -1690.8518] [ 80] [depth= 1] . ( 21 sec) [ -1690.8389] [ 80] [depth= 1] . ( 29 sec) [ -1690.8144] [ 80] [depth= 1] . ( 31 sec) [ -1690.7703] [Branch lengths ] . ( 31 sec) [ -1690.5719] [Alpha ][ 0.187058] . ( 56 sec) [ -1690.5697] [Branch lengths ] . ( 56 sec) [ -1690.5697] [Topology ] . ( 57 sec) [ -1690.5696] [Topology ] . ( 57 sec) [ -1690.5695] [Alpha ][ 0.186079] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1690.569537. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -2191.2618] [Alpha ][ 0.500960] . ( 1 sec) [ -2104.9716] [ 126] [depth= 5] . ( 1 sec) [ -2074.7851] [ 121] [depth= 3] . ( 1 sec) [ -2070.4998] [ 121] [depth= 2] . ( 1 sec) [ -2066.4727] [ 121] [depth= 2] . ( 1 sec) [ -2056.4259] [ 118] [depth= 3] . ( 1 sec) [ -2044.3551] [ 118] [depth= 1] . ( 1 sec) [ -2031.6654] [ 117] [depth= 1] . ( 1 sec) [ -1979.2984] [ 116] [depth= 1] . ( 1 sec) [ -1973.9566] [ 116] [depth= 9] . ( 1 sec) [ -1935.9429] [ 118] [depth= 1] . ( 1 sec) [ -1934.2168] [ 116] [depth= 2] . ( 1 sec) [ -1910.9829] [ 114] [depth= 6] . ( 2 sec) [ -1904.4525] [ 113] [depth= 9] . ( 2 sec) [ -1901.5480] [ 113] [depth= 9] . ( 2 sec) [ -1892.0499] [ 112] [depth= 8] . ( 2 sec) [ -1891.6749] [ 112] [depth= 1] . ( 2 sec) [ -1871.8653] [ 109] [depth= 2] . ( 2 sec) [ -1867.4909] [ 108] [depth= 1] . ( 3 sec) [ -1866.1491] [ 106] [depth= 2] . ( 3 sec) [ -1858.0914] [ 104] [depth= 2] . ( 3 sec) [ -1857.7340] [ 104] [depth= 1] . ( 3 sec) [ -1856.8690] [ 102] [depth= 2] . ( 3 sec) [ -1837.2562] [ 100] [depth= 2] . ( 3 sec) [ -1805.8768] [ 92] [depth= 6] . ( 3 sec) [ -1753.9683] [ 86] [depth= 3] . ( 3 sec) [ -1753.9404] [ 86] [depth= 1] . ( 3 sec) [ -1727.7648] [ 85] [depth= 1] . ( 5 sec) [ -1702.4141] [ 80] [depth= 1] . ( 5 sec) [ -1701.9156] [ 81] [depth= 1] . ( 6 sec) [ -1700.1758] [ 82] [depth= 1] . ( 6 sec) [ -1697.2103] [ 81] [depth= 1] . ( 6 sec) [ -1696.4305] [Branch lengths ] . ( 6 sec) [ -1694.0119] [Alpha ][ 0.250961] . ( 13 sec) [ -1692.9873] [ 82] [depth= 3] . ( 14 sec) [ -1692.8444] [ 82] [depth= 2] . ( 16 sec) [ -1692.3950] [ 81] [depth= 1] . ( 18 sec) [ -1692.3143] [ 81] [depth= 3] . ( 21 sec) [ -1692.2558] [ 81] [depth= 1] . ( 21 sec) [ -1692.2388] [ 81] [depth= 1] . ( 27 sec) [ -1691.8178] [Branch lengths ] . ( 27 sec) [ -1691.4989] [Alpha ][ 0.173052] . ( 51 sec) [ -1691.4864] [Branch lengths ] . ( 51 sec) [ -1691.4864] [Topology ] . ( 52 sec) [ -1691.4860] [Topology ] . ( 52 sec) [ -1691.4857] [Alpha ][ 0.170993] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1691.485721. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -2266.8635] [Alpha ][ 0.500960] . ( 0 sec) [ -2080.7246] [ 122] [depth= 3] . ( 0 sec) [ -1973.3616] [ 116] [depth= 4] . ( 0 sec) [ -1941.5189] [ 115] [depth= 4] . ( 0 sec) [ -1919.1360] [ 110] [depth= 1] . ( 0 sec) [ -1905.7090] [ 109] [depth= 4] . ( 0 sec) [ -1897.6765] [ 107] [depth= 3] . ( 0 sec) [ -1876.8220] [ 106] [depth= 1] . ( 0 sec) [ -1867.1259] [ 106] [depth= 1] . ( 1 sec) [ -1866.3624] [ 106] [depth= 7] . ( 1 sec) [ -1841.3796] [ 100] [depth= 8] . ( 1 sec) [ -1837.2874] [ 100] [depth= 2] . ( 1 sec) [ -1829.0689] [ 100] [depth= 1] . ( 1 sec) [ -1826.9524] [ 99] [depth= 4] . ( 1 sec) [ -1787.9798] [ 92] [depth= 4] . ( 1 sec) [ -1787.9090] [ 92] [depth= 1] . ( 1 sec) [ -1782.0954] [ 92] [depth= 1] . ( 1 sec) [ -1760.2023] [ 90] [depth= 4] . ( 1 sec) [ -1757.7290] [ 89] [depth= 5] . ( 1 sec) [ -1755.4462] [ 89] [depth= 2] . ( 3 sec) [ -1732.2269] [ 84] [depth= 5] . ( 3 sec) [ -1730.9843] [ 84] [depth= 3] . ( 3 sec) [ -1730.0153] [ 83] [depth= 4] . ( 3 sec) [ -1729.9996] [ 83] [depth= 1] . ( 3 sec) [ -1723.4750] [ 83] [depth= 5] . ( 7 sec) [ -1723.1413] [ 83] [depth= 2] . ( 7 sec) [ -1719.4743] [ 84] [depth= 1] . ( 7 sec) [ -1714.4289] [ 83] [depth= 1] . ( 7 sec) [ -1700.7923] [Branch lengths ] . ( 7 sec) [ -1697.9257] [Alpha ][ 0.250961] . ( 13 sec) [ -1694.2865] [ 81] [depth= 3] . ( 14 sec) [ -1691.8227] [ 80] [depth= 2] . ( 14 sec) [ -1690.7028] [ 80] [depth= 1] . ( 29 sec) [ -1690.6511] [Branch lengths ] . ( 29 sec) [ -1690.3333] [Alpha ][ 0.170499] . ( 52 sec) [ -1690.3253] [Branch lengths ] . ( 52 sec) [ -1690.3253] [Topology ] . ( 53 sec) [ -1690.3250] [Topology ] . ( 53 sec) [ -1690.3248] [Alpha ][ 0.168409] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1690.324777. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -2315.1775] [Alpha ][ 0.500960] . ( 0 sec) [ -2178.6766] [ 128] [depth= 4] . ( 0 sec) [ -2063.3872] [ 120] [depth= 4] . ( 0 sec) [ -2051.9623] [ 118] [depth= 1] . ( 1 sec) [ -2048.3645] [ 118] [depth= 2] . ( 1 sec) [ -2041.1150] [ 117] [depth= 1] . ( 1 sec) [ -2037.8218] [ 117] [depth= 3] . ( 1 sec) [ -1893.3908] [ 108] [depth= 8] . ( 1 sec) [ -1883.8141] [ 107] [depth= 3] . ( 1 sec) [ -1877.1719] [ 107] [depth= 1] . ( 2 sec) [ -1845.9818] [ 105] [depth= 5] . ( 2 sec) [ -1835.4044] [ 103] [depth= 5] . ( 2 sec) [ -1834.1092] [ 103] [depth= 3] . ( 2 sec) [ -1799.7479] [ 98] [depth= 1] . ( 2 sec) [ -1784.0456] [ 95] [depth= 6] . ( 3 sec) [ -1750.0868] [ 90] [depth= 1] . ( 3 sec) [ -1749.1768] [ 90] [depth= 2] . ( 3 sec) [ -1744.6450] [ 87] [depth= 2] . ( 3 sec) [ -1744.4262] [ 87] [depth= 3] . ( 3 sec) [ -1733.1526] [ 87] [depth= 2] . ( 3 sec) [ -1729.0080] [ 86] [depth= 2] . ( 3 sec) [ -1725.6151] [ 85] [depth= 1] . ( 4 sec) [ -1725.1294] [ 85] [depth= 1] . ( 4 sec) [ -1712.7548] [ 82] [depth= 1] . ( 4 sec) [ -1711.5923] [ 82] [depth= 2] . ( 8 sec) [ -1704.5725] [ 81] [depth= 1] . ( 9 sec) [ -1704.2834] [ 82] [depth= 1] . ( 9 sec) [ -1704.1756] [ 82] [depth= 1] . ( 9 sec) [ -1703.0651] [ 83] [depth= 4] . ( 9 sec) [ -1698.7461] [ 82] [depth= 1] . ( 10 sec) [ -1696.4559] [Branch lengths ] . ( 10 sec) [ -1693.8405] [Alpha ][ 0.250961] . ( 16 sec) [ -1693.5979] [ 82] [depth= 5] . ( 26 sec) [ -1692.7070] [ 82] [depth= 1] . ( 26 sec) [ -1692.2324] [ 81] [depth= 1] . ( 31 sec) [ -1691.8252] [Branch lengths ] . ( 31 sec) [ -1691.5048] [Alpha ][ 0.172901] . ( 55 sec) [ -1691.4868] [Branch lengths ] . ( 55 sec) [ -1691.4868] [Topology ] . ( 56 sec) [ -1691.4861] [Topology ] . ( 56 sec) [ -1691.4859] [Alpha ][ 0.170985] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1691.485873. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -1700.8671] [Alpha ][ 0.500960] . ( 0 sec) [ -1700.8671] [Topology ] . ( 1 sec) [ -1697.1437] [Topology ] . ( 1 sec) [ -1696.5765] [Topology ] . ( 1 sec) [ -1696.4520] [Topology ] . ( 2 sec) [ -1696.4234] [Topology ] . ( 2 sec) [ -1696.4165] [Topology ] . ( 3 sec) [ -1696.4149] [Topology ] . Checking for NNIs, optimizing five branches... . ( 5 sec) [ -1693.8018] [Alpha ][ 0.250961] . ( 5 sec) [ -1693.8018] [Topology ] . ( 5 sec) [ -1693.7994] [Topology ] . ( 5 sec) [ -1693.7989] [Topology ] . Checking for NNIs, optimizing five branches... . ( 8 sec) [ -1693.3291] [Alpha ][ 0.159379] . ( 8 sec) [ -1693.3291] [Topology ] . ( 8 sec) [ -1693.3244] [Topology ] . ( 8 sec) [ -1693.3235] [Topology ] . Checking for NNIs, optimizing five branches... . ( 10 sec) [ -1693.3234] [Alpha ][ 0.157847] . ( 10 sec) [ -1693.3234] [Topology ] . ( 11 sec) [ -1693.3231] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 15 sec) [ -1700.8671] [Alpha ][ 0.500960] . ( 21 sec) [ -1700.1272] [ 82] [depth= 1] . ( 21 sec) [ -1699.4578] [ 82] [depth= 1] . ( 21 sec) [ -1698.1292] [ 80] [depth= 3] . ( 21 sec) [ -1697.8197] [ 81] [depth= 3] . ( 23 sec) [ -1696.9534] [ 81] [depth= 2] . ( 26 sec) [ -1696.8905] [ 81] [depth= 5] . ( 27 sec) [ -1696.2921] [ 81] [depth= 3] . ( 27 sec) [ -1696.2548] [ 82] [depth= 1] . ( 28 sec) [ -1696.0512] [ 82] [depth= 1] . ( 28 sec) [ -1695.9506] [ 82] [depth= 1] . ( 29 sec) [ -1695.8680] [ 82] [depth= 1] . ( 31 sec) [ -1695.0532] [Branch lengths ] . ( 32 sec) [ -1692.5539] [Alpha ][ 0.250961] . ( 37 sec) [ -1692.0332] [ 81] [depth= 1] . ( 56 sec) [ -1691.8160] [Branch lengths ] . ( 56 sec) [ -1691.4946] [Alpha ][ 0.172623] . ( 80 sec) [ -1691.4860] [Branch lengths ] . ( 80 sec) [ -1691.4860] [Topology ] . ( 80 sec) [ -1691.4857] [Topology ] . ( 81 sec) [ -1691.4855] [Alpha ][ 0.170926] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -1693.323129 . Log likelihood obtained after SPR moves : -1691.485546 . Log likelihood of the current tree: -1691.485546. . Printing the most likely tree in file 'proteic_M2638_18x378_2006.phy_phyml_tree.txt'... . Best log likelihood : -1690.324777 . Time used 0h1m23s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 366.00user 0.00system 6:08.22elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps