.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1381_9x1557_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 1557 sites) . 829 sites without polymorphism (53.24%). . [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)... . ( 0 sec) [ -14516.8866] [Alpha ][ 0.500960] . ( 0 sec) [ -13272.3376] [ 1620] [depth= 4] . ( 1 sec) [ -12718.1042] [ 1589] [depth= 3] . ( 1 sec) [ -12615.3983] [ 1582] [depth= 2] . ( 1 sec) [ -12573.1970] [ 1576] [depth= 3] . ( 2 sec) [ -12546.2078] [ 1579] [depth= 1] . ( 2 sec) [ -12518.7717] [ 1573] [depth= 4] . ( 2 sec) [ -12501.8652] [ 1569] [depth= 1] . ( 3 sec) [ -12130.9700] [ 1445] [depth= 1] . ( 3 sec) [ -12119.2279] [ 1446] [depth= 1] . ( 5 sec) [ -12093.4017] [ 1439] [depth= 3] . ( 6 sec) [ -12079.5986] [Branch lengths ] . ( 6 sec) [ -12078.1281] [Alpha ][ 0.568003] . ( 11 sec) [ -12078.0028] [Branch lengths ] . ( 12 sec) [ -12078.0028] [Topology ] . ( 12 sec) [ -12077.9989] [Topology ] . ( 13 sec) [ -12077.9981] [Topology ] . ( 14 sec) [ -12077.9976] [Alpha ][ 0.569282] . ( 14 sec) [ -12077.9976] [Topology ] . ( 15 sec) [ -12077.9974] [Topology ] . ( 15 sec) [ -12077.9974] [Alpha ][ 0.569282] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12077.997366. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -15185.4666] [Alpha ][ 0.500960] . ( 1 sec) [ -13997.3837] [ 1603] [depth= 1] . ( 1 sec) [ -13665.3739] [ 1609] [depth= 1] . ( 2 sec) [ -13378.1650] [ 1458] [depth= 4] . ( 2 sec) [ -13363.5214] [ 1461] [depth= 1] . ( 2 sec) [ -13270.7682] [ 1460] [depth= 2] . ( 3 sec) [ -13126.7155] [ 1447] [depth= 4] . ( 3 sec) [ -12768.6077] [ 1454] [depth= 1] . ( 3 sec) [ -12751.0110] [ 1449] [depth= 1] . ( 4 sec) [ -12732.9579] [ 1449] [depth= 1] . ( 4 sec) [ -12589.8603] [ 1446] [depth= 1] . ( 4 sec) [ -12570.6422] [ 1439] [depth= 3] . ( 5 sec) [ -12382.6484] [ 1559] [depth= 1] . ( 5 sec) [ -12171.2158] [ 1439] [depth= 1] . ( 7 sec) [ -12080.3243] [Branch lengths ] . ( 7 sec) [ -12078.9895] [Alpha ][ 0.565315] . ( 12 sec) [ -12078.0408] [Branch lengths ] . ( 12 sec) [ -12078.0408] [Topology ] . ( 13 sec) [ -12078.0100] [Topology ] . ( 14 sec) [ -12078.0043] [Topology ] . ( 15 sec) [ -12078.0026] [Topology ] . ( 16 sec) [ -12078.0021] [Topology ] . ( 16 sec) [ -12077.9976] [Alpha ][ 0.569354] . ( 16 sec) [ -12077.9976] [Topology ] . ( 17 sec) [ -12077.9973] [Topology ] . ( 17 sec) [ -12077.9973] [Alpha ][ 0.569354] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12077.997350. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -14789.2489] [Alpha ][ 0.500960] . ( 0 sec) [ -13951.2735] [ 1640] [depth= 3] . ( 1 sec) [ -12749.5503] [ 1608] [depth= 3] . ( 1 sec) [ -12702.8163] [ 1596] [depth= 2] . ( 1 sec) [ -12667.0672] [ 1601] [depth= 1] . ( 2 sec) [ -12655.3014] [ 1594] [depth= 1] . ( 2 sec) [ -12383.8470] [ 1478] [depth= 1] . ( 2 sec) [ -12334.4700] [ 1470] [depth= 1] . ( 2 sec) [ -12293.4899] [ 1459] [depth= 4] . ( 3 sec) [ -12245.4982] [ 1449] [depth= 2] . ( 3 sec) [ -12233.5268] [ 1450] [depth= 1] . ( 3 sec) [ -12206.6881] [ 1442] [depth= 1] . ( 4 sec) [ -12197.5493] [ 1435] [depth= 1] . ( 5 sec) [ -12178.8153] [Branch lengths ] . ( 5 sec) [ -12178.6866] [Alpha ][ 0.519176] . ( 6 sec) [ -12177.8062] [ 1439] [depth= 1] . ( 7 sec) [ -12102.7693] [ 1446] [depth= 2] . ( 9 sec) [ -12100.1218] [ 1450] [depth= 1] . ( 9 sec) [ -12100.0584] [ 1441] [depth= 2] . ( 10 sec) [ -12094.9682] [Branch lengths ] . ( 11 sec) [ -12094.2764] [Alpha ][ 0.565482] . ( 11 sec) [ -12092.2486] [ 1445] [depth= 1] . ( 12 sec) [ -12088.6649] [ 1435] [depth= 1] . ( 12 sec) [ -12082.0198] [ 1439] [depth= 1] . ( 16 sec) [ -12078.0273] [Branch lengths ] . ( 16 sec) [ -12078.0237] [Alpha ][ 0.569071] . ( 21 sec) [ -12077.9984] [Branch lengths ] . ( 21 sec) [ -12077.9984] [Topology ] . ( 22 sec) [ -12077.9975] [Topology ] . ( 22 sec) [ -12077.9975] [Alpha ][ 0.569640] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12077.997542. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -17810.9371] [Alpha ][ 0.500960] . ( 1 sec) [ -17128.5169] [ 1482] [depth= 3] . ( 1 sec) [ -13833.8154] [ 1470] [depth= 2] . ( 1 sec) [ -13241.3811] [ 1458] [depth= 1] . ( 2 sec) [ -13223.4211] [ 1450] [depth= 1] . ( 2 sec) [ -13171.8748] [ 1450] [depth= 1] . ( 2 sec) [ -12931.8811] [ 1450] [depth= 1] . ( 3 sec) [ -12874.7843] [ 1445] [depth= 2] . ( 3 sec) [ -12574.5557] [ 1445] [depth= 1] . ( 3 sec) [ -12236.4974] [ 1445] [depth= 1] . ( 4 sec) [ -12173.0822] [ 1443] [depth= 2] . ( 4 sec) [ -12154.8588] [ 1445] [depth= 1] . ( 5 sec) [ -12104.9401] [Branch lengths ] . ( 6 sec) [ -12103.2772] [Alpha ][ 0.571808] . ( 8 sec) [ -12101.9945] [ 1446] [depth= 1] . ( 9 sec) [ -12079.8167] [ 1439] [depth= 3] . ( 12 sec) [ -12078.0519] [Branch lengths ] . ( 12 sec) [ -12078.0498] [Alpha ][ 0.568905] . ( 17 sec) [ -12077.9984] [Branch lengths ] . ( 18 sec) [ -12077.9984] [Topology ] . ( 18 sec) [ -12077.9975] [Topology ] . ( 19 sec) [ -12077.9975] [Alpha ][ 0.569474] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12077.997462. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -15430.4311] [Alpha ][ 0.500960] . ( 1 sec) [ -13191.6035] [ 1615] [depth= 3] . ( 1 sec) [ -12760.1194] [ 1574] [depth= 4] . ( 2 sec) [ -12743.1738] [ 1580] [depth= 1] . ( 2 sec) [ -12670.5810] [ 1593] [depth= 1] . ( 2 sec) [ -12623.5237] [ 1586] [depth= 1] . ( 3 sec) [ -12589.9039] [ 1594] [depth= 1] . ( 3 sec) [ -12562.8374] [ 1582] [depth= 3] . ( 3 sec) [ -12538.8349] [ 1570] [depth= 4] . ( 4 sec) [ -12256.2456] [ 1458] [depth= 1] . ( 4 sec) [ -12225.6962] [ 1449] [depth= 1] . ( 4 sec) [ -12219.0483] [ 1445] [depth= 2] . ( 5 sec) [ -12194.3271] [ 1441] [depth= 4] . ( 6 sec) [ -12182.5314] [Branch lengths ] . ( 6 sec) [ -12182.4257] [Alpha ][ 0.517211] . ( 7 sec) [ -12180.9700] [ 1435] [depth= 2] . ( 8 sec) [ -12105.3468] [ 1441] [depth= 1] . ( 10 sec) [ -12088.9688] [ 1435] [depth= 1] . ( 11 sec) [ -12084.6498] [Branch lengths ] . ( 11 sec) [ -12083.6897] [Alpha ][ 0.572406] . ( 12 sec) [ -12079.2700] [ 1439] [depth= 1] . ( 16 sec) [ -12078.0333] [Branch lengths ] . ( 16 sec) [ -12078.0311] [Alpha ][ 0.569400] . ( 22 sec) [ -12077.9974] [Branch lengths ] . ( 22 sec) [ -12077.9974] [Topology ] . ( 23 sec) [ -12077.9973] [Topology ] . ( 23 sec) [ -12077.9973] [Alpha ][ 0.569400] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12077.997276. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -12145.2942] [Alpha ][ 0.516381] . ( 1 sec) [ -12145.2942] [Topology ] . ( 1 sec) [ -12105.5625] [Topology ] . ( 2 sec) [ -12101.4516] [Topology ] . ( 3 sec) [ -12100.5701] [Topology ] . ( 4 sec) [ -12100.3221] [Topology ] . ( 5 sec) [ -12100.2474] [Topology ] . ( 6 sec) [ -12100.2239] [Topology ] . Checking for NNIs, optimizing five branches... . ( 13 sec) [ -12099.2600] [Alpha ][ 0.572384] . ( 13 sec) [ -12099.2600] [Topology ] . ( 14 sec) [ -12099.2253] [Topology ] . ( 15 sec) [ -12099.2175] [Topology ] . ( 16 sec) [ -12099.2152] [Topology ] . ( 17 sec) [ -12099.2145] [Topology ] . Checking for NNIs, optimizing five branches... . ( 24 sec) [ -12099.2138] [Alpha ][ 0.573859] . ( 24 sec) [ -12099.2138] [Topology ] . ( 25 sec) [ -12099.2136] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 39 sec) [ -12145.2942] [Alpha ][ 0.516381] . ( 42 sec) [ -12144.5726] [ 1445] [depth= 1] . ( 42 sec) [ -12137.3493] [ 1446] [depth= 1] . ( 43 sec) [ -12136.2702] [ 1449] [depth= 1] . ( 44 sec) [ -12109.0248] [ 1447] [depth= 4] . ( 44 sec) [ -12107.1936] [ 1435] [depth= 2] . ( 45 sec) [ -12104.4152] [ 1441] [depth= 1] . ( 45 sec) [ -12096.2444] [ 1435] [depth= 1] . ( 46 sec) [ -12085.3919] [Branch lengths ] . ( 46 sec) [ -12084.5912] [Alpha ][ 0.567344] . ( 48 sec) [ -12081.3240] [ 1439] [depth= 1] . ( 51 sec) [ -12078.1403] [Branch lengths ] . ( 51 sec) [ -12078.1389] [Alpha ][ 0.569594] . ( 56 sec) [ -12078.0023] [Branch lengths ] . ( 57 sec) [ -12078.0023] [Topology ] . ( 57 sec) [ -12077.9982] [Topology ] . ( 58 sec) [ -12077.9975] [Topology ] . ( 59 sec) [ -12077.9975] [Alpha ][ 0.569594] . ( 59 sec) [ -12077.9975] [Topology ] . ( 60 sec) [ -12077.9973] [Topology ] . ( 60 sec) [ -12077.9973] [Alpha ][ 0.569594] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -12099.213554 . Log likelihood obtained after SPR moves : -12077.997340 . Log likelihood of the current tree: -12077.997340. . Printing the most likely tree in file 'proteic_M1381_9x1557_2003.phy_phyml_tree.txt'... . Best log likelihood : -12077.997276 . Time used 0h1m9s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 199.22user 0.00system 3:27.08elapsed 96%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps