.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1380_9x1558_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... . 695 patterns found. (out of a total of 1558 sites) . 832 sites without polymorphism (53.40%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 12Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21460.3164] [Alpha ][ 0.500960] . ( 1 sec) [ -13950.0675] [ 1616] [depth= 5] . ( 1 sec) [ -13437.0694] [ 1589] [depth= 4] . ( 2 sec) [ -13072.6149] [ 1567] [depth= 3] . ( 2 sec) [ -13047.9431] [ 1564] [depth= 1] . ( 2 sec) [ -13018.2433] [ 1557] [depth= 2] . ( 3 sec) [ -12942.7527] [ 1570] [depth= 1] . ( 3 sec) [ -12757.8471] [ 1567] [depth= 3] . ( 3 sec) [ -12400.7121] [ 1455] [depth= 1] . ( 3 sec) [ -12171.3750] [ 1443] [depth= 3] . ( 4 sec) [ -12078.1804] [ 1435] [depth= 1] . ( 4 sec) [ -12065.6455] [ 1432] [depth= 1] . ( 5 sec) [ -12043.6747] [ 1425] [depth= 1] . ( 5 sec) [ -12035.6514] [ 1424] [depth= 1] . ( 6 sec) [ -12008.7515] [Branch lengths ] . ( 6 sec) [ -12007.4606] [Alpha ][ 0.564945] . ( 11 sec) [ -12006.0239] [Branch lengths ] . ( 11 sec) [ -12006.0239] [Topology ] . ( 12 sec) [ -12005.2214] [Topology ] . ( 13 sec) [ -12005.0437] [Topology ] . ( 14 sec) [ -12005.0376] [Topology ] . ( 15 sec) [ -12005.0365] [Topology ] . ( 16 sec) [ -12005.0362] [Topology ] . ( 16 sec) [ -12005.0252] [Alpha ][ 0.571396] . ( 16 sec) [ -12005.0252] [Topology ] . ( 17 sec) [ -12005.0249] [Topology ] . ( 17 sec) [ -12005.0249] [Alpha ][ 0.571396] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12005.024926. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -13386.6818] [Alpha ][ 0.500960] . ( 0 sec) [ -13174.9657] [ 1579] [depth= 3] . ( 1 sec) [ -12550.8830] [ 1547] [depth= 3] . ( 1 sec) [ -12536.5903] [ 1546] [depth= 1] . ( 1 sec) [ -12495.0105] [ 1540] [depth= 1] . ( 2 sec) [ -12179.0290] [ 1435] [depth= 1] . ( 2 sec) [ -12140.9615] [ 1446] [depth= 1] . ( 2 sec) [ -12122.9687] [ 1442] [depth= 1] . ( 2 sec) [ -12122.7075] [ 1443] [depth= 3] . ( 3 sec) [ -12071.9842] [ 1437] [depth= 3] . ( 4 sec) [ -12055.7707] [ 1434] [depth= 2] . ( 5 sec) [ -12051.4419] [ 1438] [depth= 2] . ( 5 sec) [ -12048.6706] [ 1434] [depth= 2] . ( 6 sec) [ -12038.7915] [Branch lengths ] . ( 6 sec) [ -12037.5271] [Alpha ][ 0.562657] . ( 8 sec) [ -12035.4903] [ 1433] [depth= 1] . ( 9 sec) [ -12031.6986] [ 1433] [depth= 1] . ( 11 sec) [ -12016.6383] [ 1430] [depth= 4] . ( 12 sec) [ -12011.6743] [ 1424] [depth= 1] . ( 13 sec) [ -12011.3636] [ 1427] [depth= 1] . ( 13 sec) [ -12005.1355] [Branch lengths ] . ( 14 sec) [ -12005.1157] [Alpha ][ 0.571304] . ( 22 sec) [ -12005.0311] [Branch lengths ] . ( 22 sec) [ -12005.0311] [Topology ] . ( 23 sec) [ -12005.0262] [Topology ] . ( 24 sec) [ -12005.0252] [Topology ] . ( 24 sec) [ -12005.0252] [Alpha ][ 0.571304] . ( 25 sec) [ -12005.0252] [Topology ] . ( 25 sec) [ -12005.0250] [Topology ] . ( 26 sec) [ -12005.0250] [Alpha ][ 0.571304] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12005.024960. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -13799.3361] [Alpha ][ 0.500960] . ( 1 sec) [ -13465.7965] [ 1576] [depth= 3] . ( 1 sec) [ -13266.9719] [ 1575] [depth= 2] . ( 1 sec) [ -12790.9626] [ 1541] [depth= 3] . ( 2 sec) [ -12528.8369] [ 1431] [depth= 1] . ( 2 sec) [ -12457.3286] [ 1433] [depth= 2] . ( 2 sec) [ -12279.9792] [ 1431] [depth= 1] . ( 2 sec) [ -12255.0000] [ 1437] [depth= 2] . ( 3 sec) [ -12247.5282] [ 1447] [depth= 1] . ( 3 sec) [ -12232.6323] [ 1446] [depth= 1] . ( 3 sec) [ -12214.1366] [ 1433] [depth= 2] . ( 4 sec) [ -12168.7696] [ 1435] [depth= 2] . ( 4 sec) [ -12161.9793] [ 1434] [depth= 1] . ( 5 sec) [ -12120.8263] [ 1447] [depth= 1] . ( 5 sec) [ -12075.5696] [ 1434] [depth= 1] . ( 5 sec) [ -12052.4975] [ 1431] [depth= 2] . ( 5 sec) [ -12027.9410] [Branch lengths ] . ( 6 sec) [ -12026.1158] [Alpha ][ 0.575258] . ( 14 sec) [ -12013.2187] [ 1430] [depth= 4] . ( 15 sec) [ -12011.8866] [ 1424] [depth= 1] . ( 15 sec) [ -12010.5935] [ 1427] [depth= 1] . ( 16 sec) [ -12005.0943] [Branch lengths ] . ( 16 sec) [ -12005.0915] [Alpha ][ 0.571840] . ( 25 sec) [ -12005.0293] [Branch lengths ] . ( 25 sec) [ -12005.0293] [Topology ] . ( 26 sec) [ -12005.0258] [Topology ] . ( 27 sec) [ -12005.0252] [Topology ] . ( 27 sec) [ -12005.0251] [Alpha ][ 0.571268] . ( 27 sec) [ -12005.0251] [Topology ] . ( 28 sec) [ -12005.0249] [Topology ] . ( 28 sec) [ -12005.0249] [Alpha ][ 0.571268] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12005.024932. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -13805.6742] [Alpha ][ 0.500960] . ( 1 sec) [ -13525.7071] [ 1604] [depth= 4] . ( 1 sec) [ -13073.9307] [ 1578] [depth= 4] . ( 2 sec) [ -12638.7846] [ 1557] [depth= 1] . ( 2 sec) [ -12535.8520] [ 1556] [depth= 1] . ( 2 sec) [ -12525.8295] [ 1551] [depth= 1] . ( 2 sec) [ -12517.1318] [ 1550] [depth= 1] . ( 3 sec) [ -12405.7690] [ 1546] [depth= 3] . ( 3 sec) [ -12152.0937] [ 1437] [depth= 1] . ( 5 sec) [ -12145.0991] [ 1434] [depth= 1] . ( 6 sec) [ -12124.2463] [ 1429] [depth= 2] . ( 8 sec) [ -12026.0592] [Branch lengths ] . ( 8 sec) [ -12024.2904] [Alpha ][ 0.575893] . ( 13 sec) [ -12007.8456] [ 1427] [depth= 3] . ( 14 sec) [ -12007.2458] [ 1427] [depth= 1] . ( 16 sec) [ -12005.0529] [Branch lengths ] . ( 16 sec) [ -12005.0468] [Alpha ][ 0.570854] . ( 25 sec) [ -12005.0250] [Branch lengths ] . ( 25 sec) [ -12005.0250] [Topology ] . ( 26 sec) [ -12005.0249] [Topology ] . ( 26 sec) [ -12005.0249] [Alpha ][ 0.571424] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12005.024860. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -13887.5047] [Alpha ][ 0.500960] . ( 1 sec) [ -13116.8161] [ 1595] [depth= 1] . ( 1 sec) [ -12509.4992] [ 1543] [depth= 3] . ( 1 sec) [ -12199.2580] [ 1427] [depth= 1] . ( 1 sec) [ -12139.1262] [ 1424] [depth= 1] . ( 2 sec) [ -12120.9930] [ 1429] [depth= 5] . ( 3 sec) [ -12118.8600] [ 1428] [depth= 1] . ( 4 sec) [ -12077.3465] [ 1429] [depth= 1] . ( 4 sec) [ -12076.6554] [ 1432] [depth= 1] . ( 6 sec) [ -12033.9067] [Branch lengths ] . ( 6 sec) [ -12032.3523] [Alpha ][ 0.570242] . ( 8 sec) [ -12029.4725] [ 1431] [depth= 1] . ( 10 sec) [ -12015.1987] [ 1430] [depth= 4] . ( 10 sec) [ -12011.9425] [ 1424] [depth= 1] . ( 11 sec) [ -12011.8490] [ 1427] [depth= 1] . ( 12 sec) [ -12010.4696] [ 1424] [depth= 1] . ( 14 sec) [ -12005.9345] [Branch lengths ] . ( 14 sec) [ -12005.9334] [Alpha ][ 0.572276] . ( 15 sec) [ -12005.7755] [ 1427] [depth= 1] . ( 22 sec) [ -12005.0370] [Branch lengths ] . ( 22 sec) [ -12005.0368] [Alpha ][ 0.571445] . ( 22 sec) [ -12005.0368] [Topology ] . ( 23 sec) [ -12005.0258] [Topology ] . ( 24 sec) [ -12005.0251] [Topology ] . ( 24 sec) [ -12005.0251] [Alpha ][ 0.571445] . ( 24 sec) [ -12005.0251] [Topology ] . ( 25 sec) [ -12005.0249] [Topology ] . ( 25 sec) [ -12005.0249] [Alpha ][ 0.571445] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12005.024899. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -12075.2784] [Alpha ][ 0.513157] . ( 0 sec) [ -12075.2784] [Topology ] . ( 1 sec) [ -12030.4573] [Topology ] . ( 2 sec) [ -12025.7778] [Topology ] . ( 3 sec) [ -12024.9274] [Topology ] . ( 4 sec) [ -12024.6979] [Topology ] . ( 5 sec) [ -12024.6300] [Topology ] . ( 5 sec) [ -12024.6089] [Topology ] . ( 6 sec) [ -12024.6021] [Topology ] . Checking for NNIs, optimizing five branches... . ( 14 sec) [ -12023.4325] [Alpha ][ 0.575059] . ( 14 sec) [ -12023.4325] [Topology ] . ( 15 sec) [ -12023.4045] [Topology ] . ( 16 sec) [ -12023.3999] [Topology ] . ( 16 sec) [ -12023.3985] [Topology ] . ( 17 sec) [ -12023.3981] [Topology ] . Checking for NNIs, optimizing five branches... . ( 25 sec) [ -12023.3976] [Alpha ][ 0.576478] . ( 25 sec) [ -12023.3976] [Topology ] . ( 26 sec) [ -12023.3974] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 40 sec) [ -12075.2784] [Alpha ][ 0.513157] . ( 41 sec) [ -12074.6576] [ 1431] [depth= 1] . ( 41 sec) [ -12063.8515] [ 1431] [depth= 1] . ( 42 sec) [ -12058.0513] [ 1432] [depth= 1] . ( 43 sec) [ -12028.7282] [ 1430] [depth= 5] . ( 45 sec) [ -12028.1801] [ 1424] [depth= 1] . ( 46 sec) [ -12025.6204] [ 1427] [depth= 2] . ( 47 sec) [ -12008.9200] [Branch lengths ] . ( 47 sec) [ -12007.9127] [Alpha ][ 0.570578] . ( 51 sec) [ -12006.7058] [ 1427] [depth= 1] . ( 54 sec) [ -12005.0823] [Branch lengths ] . ( 55 sec) [ -12005.0821] [Alpha ][ 0.571155] . ( 63 sec) [ -12005.0261] [Branch lengths ] . ( 63 sec) [ -12005.0261] [Topology ] . ( 64 sec) [ -12005.0251] [Topology ] . ( 65 sec) [ -12005.0249] [Topology ] . ( 65 sec) [ -12005.0249] [Alpha ][ 0.571155] . ( 65 sec) [ -12005.0249] [Topology ] . ( 66 sec) [ -12005.0249] [Topology ] . ( 66 sec) [ -12005.0249] [Alpha ][ 0.571155] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -12023.397400 . Log likelihood obtained after SPR moves : -12005.024877 . Log likelihood of the current tree: -12005.024877. . Printing the most likely tree in file 'proteic_M1380_9x1558_2003.phy_phyml_tree.txt'... . Best log likelihood : -12005.024860 . Time used 0h1m15s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 232.32user 0.00system 3:59.74elapsed 96%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps