.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1383_11x1561_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... . 753 patterns found. (out of a total of 1561 sites) . 798 sites without polymorphism (51.12%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 17Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -17310.5622] [Alpha ][ 0.500960] . ( 1 sec) [ -17196.4059] [ 1908] [depth= 7] . ( 1 sec) [ -16601.7338] [ 1771] [depth= 3] . ( 2 sec) [ -15803.4355] [ 1764] [depth= 1] . ( 2 sec) [ -15748.3610] [ 1772] [depth= 1] . ( 2 sec) [ -15410.9877] [ 1768] [depth= 1] . ( 3 sec) [ -15397.2163] [ 1771] [depth= 1] . ( 3 sec) [ -14909.5675] [ 1766] [depth= 1] . ( 4 sec) [ -14905.7626] [ 1771] [depth= 1] . ( 4 sec) [ -14244.3572] [ 1759] [depth= 5] . ( 4 sec) [ -14232.1726] [ 1768] [depth= 2] . ( 5 sec) [ -14215.7166] [ 1771] [depth= 1] . ( 5 sec) [ -14208.0468] [ 1767] [depth= 1] . ( 6 sec) [ -14192.3212] [ 1756] [depth= 2] . ( 7 sec) [ -14185.1305] [ 1761] [depth= 1] . ( 7 sec) [ -14178.3734] [ 1756] [depth= 1] . ( 7 sec) [ -14175.8036] [ 1752] [depth= 1] . ( 9 sec) [ -13871.9087] [ 1766] [depth= 1] . ( 9 sec) [ -13846.5385] [ 1752] [depth= 1] . ( 9 sec) [ -13713.2828] [Branch lengths ] . ( 10 sec) [ -13713.2611] [Alpha ][ 0.507744] . ( 10 sec) [ -13710.5255] [ 1748] [depth= 1] . ( 19 sec) [ -13705.6240] [Branch lengths ] . ( 19 sec) [ -13705.6166] [Alpha ][ 0.511794] . ( 29 sec) [ -13705.3825] [Branch lengths ] . ( 29 sec) [ -13705.3825] [Topology ] . ( 30 sec) [ -13705.3791] [Topology ] . ( 31 sec) [ -13705.3785] [Topology ] . ( 31 sec) [ -13705.3783] [Alpha ][ 0.512306] . ( 32 sec) [ -13705.3783] [Topology ] . ( 33 sec) [ -13705.3782] [Topology ] . ( 33 sec) [ -13705.3782] [Alpha ][ 0.512306] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -13705.378152. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -14664.0727] [Alpha ][ 0.500960] . ( 1 sec) [ -14482.9354] [ 1948] [depth= 4] . ( 2 sec) [ -14291.6330] [ 1912] [depth= 4] . ( 2 sec) [ -14260.3291] [ 1912] [depth= 1] . ( 2 sec) [ -14168.5999] [ 1905] [depth= 2] . ( 3 sec) [ -14158.6918] [ 1910] [depth= 1] . ( 3 sec) [ -14130.6435] [ 1901] [depth= 1] . ( 3 sec) [ -14101.5656] [ 1883] [depth= 1] . ( 4 sec) [ -14098.2069] [ 1884] [depth= 2] . ( 6 sec) [ -14079.4757] [ 1877] [depth= 1] . ( 6 sec) [ -13843.7758] [ 1764] [depth= 1] . ( 7 sec) [ -13830.4906] [ 1761] [depth= 1] . ( 7 sec) [ -13830.4650] [ 1762] [depth= 2] . ( 8 sec) [ -13821.7241] [ 1762] [depth= 1] . ( 8 sec) [ -13800.0907] [ 1763] [depth= 2] . ( 8 sec) [ -13794.5593] [ 1760] [depth= 4] . ( 9 sec) [ -13758.4853] [ 1750] [depth= 5] . ( 9 sec) [ -13752.6848] [ 1753] [depth= 1] . ( 10 sec) [ -13706.4048] [Branch lengths ] . ( 11 sec) [ -13706.3535] [Alpha ][ 0.511093] . ( 22 sec) [ -13705.8733] [Branch lengths ] . ( 22 sec) [ -13705.8733] [Topology ] . ( 23 sec) [ -13705.8583] [Topology ] . ( 25 sec) [ -13705.8565] [Topology ] . ( 26 sec) [ -13705.8560] [Topology ] . ( 26 sec) [ -13705.8560] [Alpha ][ 0.510582] . ( 27 sec) [ -13705.8560] [Topology ] . ( 28 sec) [ -13705.8558] [Topology ] . ( 28 sec) [ -13705.8558] [Alpha ][ 0.510582] . Checking for NNIs, optimizing five branches... . ( 39 sec) [ -13704.7733] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -13704.773270. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -15527.1463] [Alpha ][ 0.500960] . ( 1 sec) [ -15412.9693] [ 1946] [depth= 5] . ( 1 sec) [ -14497.8337] [ 1907] [depth= 5] . ( 2 sec) [ -14474.5960] [ 1903] [depth= 1] . ( 2 sec) [ -14317.8818] [ 1898] [depth= 1] . ( 2 sec) [ -14278.2406] [ 1894] [depth= 2] . ( 3 sec) [ -14249.4236] [ 1881] [depth= 4] . ( 3 sec) [ -14201.1038] [ 1874] [depth= 3] . ( 4 sec) [ -14197.3019] [ 1880] [depth= 1] . ( 4 sec) [ -14187.9104] [ 1878] [depth= 2] . ( 5 sec) [ -14080.2789] [ 1871] [depth= 4] . ( 6 sec) [ -13810.4792] [ 1760] [depth= 1] . ( 7 sec) [ -13807.8163] [ 1754] [depth= 1] . ( 8 sec) [ -13790.9735] [ 1750] [depth= 2] . ( 9 sec) [ -13717.7142] [Branch lengths ] . ( 9 sec) [ -13717.6767] [Alpha ][ 0.510074] . ( 10 sec) [ -13712.3876] [ 1752] [depth= 3] . ( 11 sec) [ -13710.1176] [ 1752] [depth= 1] . ( 15 sec) [ -13709.9070] [ 1751] [depth= 1] . ( 20 sec) [ -13709.7561] [ 1752] [depth= 1] . ( 22 sec) [ -13707.3131] [ 1756] [depth= 4] . ( 23 sec) [ -13703.0762] [Branch lengths ] . ( 23 sec) [ -13703.0759] [Alpha ][ 0.509137] . ( 38 sec) [ -13702.8413] [Branch lengths ] . ( 38 sec) [ -13702.8413] [Topology ] . ( 39 sec) [ -13702.8343] [Topology ] . ( 40 sec) [ -13702.8328] [Topology ] . ( 42 sec) [ -13702.8322] [Topology ] . ( 42 sec) [ -13702.8314] [Alpha ][ 0.510403] . ( 42 sec) [ -13702.8314] [Topology ] . ( 43 sec) [ -13702.8311] [Topology ] . ( 44 sec) [ -13702.8311] [Alpha ][ 0.510403] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -13702.831112. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -15204.1888] [Alpha ][ 0.500960] . ( 1 sec) [ -15171.4265] [ 1944] [depth= 5] . ( 2 sec) [ -15138.4614] [ 1947] [depth= 2] . ( 2 sec) [ -15132.8018] [ 1944] [depth= 1] . ( 2 sec) [ -14289.0189] [ 1926] [depth= 1] . ( 3 sec) [ -14275.8266] [ 1921] [depth= 2] . ( 3 sec) [ -14170.4760] [ 1934] [depth= 1] . ( 3 sec) [ -14155.2962] [ 1914] [depth= 2] . ( 4 sec) [ -14143.9820] [ 1914] [depth= 1] . ( 4 sec) [ -14137.4324] [ 1907] [depth= 2] . ( 4 sec) [ -14079.0740] [ 1895] [depth= 3] . ( 5 sec) [ -14078.5419] [ 1892] [depth= 1] . ( 6 sec) [ -14030.4006] [ 1876] [depth= 3] . ( 6 sec) [ -13893.6477] [ 1744] [depth= 2] . ( 7 sec) [ -13836.4065] [ 1754] [depth= 1] . ( 7 sec) [ -13806.2560] [ 1744] [depth= 1] . ( 9 sec) [ -13710.3627] [Branch lengths ] . ( 9 sec) [ -13710.2780] [Alpha ][ 0.514121] . ( 10 sec) [ -13708.0023] [ 1748] [depth= 4] . ( 19 sec) [ -13705.4117] [Branch lengths ] . ( 19 sec) [ -13705.4102] [Alpha ][ 0.512134] . ( 29 sec) [ -13705.3788] [Branch lengths ] . ( 29 sec) [ -13705.3788] [Topology ] . ( 30 sec) [ -13705.3782] [Topology ] . ( 30 sec) [ -13705.3782] [Alpha ][ 0.512134] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -13705.378243. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -15844.2632] [Alpha ][ 0.500960] . ( 1 sec) [ -14816.4658] [ 1952] [depth= 7] . ( 2 sec) [ -14517.0500] [ 1923] [depth= 2] . ( 2 sec) [ -14403.5132] [ 1904] [depth= 5] . ( 2 sec) [ -14381.6308] [ 1893] [depth= 1] . ( 3 sec) [ -14343.9405] [ 1887] [depth= 3] . ( 3 sec) [ -14329.7963] [ 1889] [depth= 1] . ( 4 sec) [ -14312.8833] [ 1888] [depth= 1] . ( 4 sec) [ -14090.8807] [ 1885] [depth= 1] . ( 5 sec) [ -14090.6362] [ 1885] [depth= 1] . ( 5 sec) [ -14074.0809] [ 1877] [depth= 2] . ( 6 sec) [ -13766.9050] [ 1765] [depth= 1] . ( 6 sec) [ -13766.5061] [ 1766] [depth= 2] . ( 7 sec) [ -13765.4472] [ 1770] [depth= 2] . ( 8 sec) [ -13765.0049] [ 1771] [depth= 1] . ( 8 sec) [ -13758.6807] [ 1770] [depth= 1] . ( 9 sec) [ -13738.5054] [ 1773] [depth= 7] . ( 9 sec) [ -13735.2959] [ 1768] [depth= 2] . ( 10 sec) [ -13728.1360] [Branch lengths ] . ( 11 sec) [ -13728.1351] [Alpha ][ 0.499498] . ( 11 sec) [ -13725.8185] [ 1761] [depth= 1] . ( 11 sec) [ -13723.1036] [ 1746] [depth= 4] . ( 12 sec) [ -13717.5524] [ 1744] [depth= 1] . ( 13 sec) [ -13717.2088] [ 1752] [depth= 1] . ( 16 sec) [ -13715.4667] [ 1744] [depth= 1] . ( 18 sec) [ -13709.4899] [Branch lengths ] . ( 18 sec) [ -13709.4217] [Alpha ][ 0.511261] . ( 19 sec) [ -13707.1454] [ 1748] [depth= 4] . ( 27 sec) [ -13705.3953] [Branch lengths ] . ( 27 sec) [ -13705.3948] [Alpha ][ 0.512251] . ( 37 sec) [ -13705.3785] [Branch lengths ] . ( 37 sec) [ -13705.3785] [Topology ] . ( 38 sec) [ -13705.3782] [Topology ] . ( 39 sec) [ -13705.3782] [Alpha ][ 0.512251] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -13705.378198. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -13794.2183] [Alpha ][ 0.500960] . ( 1 sec) [ -13794.2183] [Topology ] . ( 2 sec) [ -13736.8319] [Topology ] . ( 3 sec) [ -13731.9263] [Topology ] . ( 5 sec) [ -13730.7630] [Topology ] . ( 6 sec) [ -13730.3890] [Topology ] . ( 7 sec) [ -13730.2582] [Topology ] . ( 8 sec) [ -13730.2107] [Topology ] . Checking for NNIs, optimizing five branches... . ( 18 sec) [ -13730.1591] [Alpha ][ 0.511243] . ( 18 sec) [ -13730.1591] [Topology ] . ( 20 sec) [ -13730.1343] [Topology ] . ( 21 sec) [ -13730.1252] [Topology ] . ( 22 sec) [ -13730.1219] [Topology ] . ( 23 sec) [ -13730.1206] [Topology ] . ( 25 sec) [ -13730.1201] [Topology ] . Checking for NNIs, optimizing five branches... . ( 34 sec) [ -13730.1192] [Alpha ][ 0.512575] . ( 35 sec) [ -13730.1192] [Topology ] . ( 36 sec) [ -13730.1190] [Topology ] . Checking for NNIs, optimizing five branches... . ( 46 sec) [ -13730.1190] [Alpha ][ 0.512575] . ( 46 sec) [ -13730.1190] [Topology ] . ( 47 sec) [ -13730.1189] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 67 sec) [ -13794.2183] [Alpha ][ 0.500960] . ( 68 sec) [ -13782.5689] [ 1759] [depth= 5] . ( 69 sec) [ -13745.2157] [ 1756] [depth= 4] . ( 70 sec) [ -13744.7190] [ 1754] [depth= 1] . ( 70 sec) [ -13742.9184] [ 1759] [depth= 2] . ( 71 sec) [ -13741.4080] [ 1760] [depth= 1] . ( 71 sec) [ -13737.0392] [ 1758] [depth= 1] . ( 72 sec) [ -13732.1008] [ 1753] [depth= 3] . ( 72 sec) [ -13730.2973] [ 1753] [depth= 1] . ( 73 sec) [ -13726.6106] [ 1751] [depth= 1] . ( 73 sec) [ -13721.0602] [ 1750] [depth= 1] . ( 74 sec) [ -13705.6773] [Branch lengths ] . ( 75 sec) [ -13705.6657] [Alpha ][ 0.506004] . ( 85 sec) [ -13704.7725] [Branch lengths ] . ( 85 sec) [ -13704.7725] [Topology ] . ( 87 sec) [ -13704.7277] [Topology ] . ( 88 sec) [ -13704.7155] [Topology ] . ( 89 sec) [ -13704.7110] [Topology ] . ( 90 sec) [ -13704.7092] [Topology ] . ( 92 sec) [ -13704.7085] [Topology ] . ( 92 sec) [ -13704.6985] [Alpha ][ 0.510703] . ( 92 sec) [ -13704.6985] [Topology ] . ( 93 sec) [ -13704.6978] [Topology ] . ( 94 sec) [ -13704.6978] [Alpha ][ 0.510703] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -13730.118863 . Log likelihood obtained after SPR moves : -13704.697769 . Log likelihood of the current tree: -13704.697769. . Printing the most likely tree in file 'proteic_M1383_11x1561_2003.phy_phyml_tree.txt'... . Best log likelihood : -13702.831112 . Time used 0h1m45s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 332.78user 0.00system 5:45.67elapsed 96%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps