.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1882_8x705_2004.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... . 524 patterns found. (out of a total of 705 sites) . 233 sites without polymorphism (33.05%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 8Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -9101.6734] [Alpha ][ 0.705839] . ( 0 sec) [ -8748.7487] [ 1113] [depth= 1] . ( 1 sec) [ -7622.2338] [ 1044] [depth= 2] . ( 1 sec) [ -7466.6023] [ 1043] [depth= 1] . ( 1 sec) [ -7128.9013] [ 1030] [depth= 3] . ( 1 sec) [ -6537.1839] [ 950] [depth= 1] . ( 1 sec) [ -6521.6096] [ 939] [depth= 1] . ( 2 sec) [ -6352.6182] [ 953] [depth= 2] . ( 2 sec) [ -6255.2932] [ 949] [depth= 1] . ( 3 sec) [ -6235.6423] [ 953] [depth= 1] . ( 3 sec) [ -6229.1837] [ 957] [depth= 1] . ( 4 sec) [ -6218.9081] [ 932] [depth= 2] . ( 4 sec) [ -6210.1662] [Branch lengths ] . ( 4 sec) [ -6209.0607] [Alpha ][ 0.802573] . ( 7 sec) [ -6204.9215] [Branch lengths ] . ( 7 sec) [ -6204.9215] [Topology ] . ( 8 sec) [ -6202.8913] [Topology ] . ( 9 sec) [ -6199.4565] [Topology ] . ( 10 sec) [ -6194.7335] [Topology ] . ( 11 sec) [ -6193.6646] [Topology ] . ( 11 sec) [ -6193.2782] [Topology ] . ( 12 sec) [ -6193.0943] [Topology ] . ( 12 sec) [ -6192.6640] [Alpha ][ 0.873221] . ( 12 sec) [ -6192.6640] [Topology ] . ( 13 sec) [ -6192.4063] [Topology ] . ( 14 sec) [ -6192.2894] [Topology ] . ( 15 sec) [ -6192.2267] [Topology ] . ( 16 sec) [ -6192.1901] [Topology ] . ( 16 sec) [ -6192.1678] [Topology ] . ( 17 sec) [ -6192.1539] [Topology ] . ( 17 sec) [ -6192.0689] [Alpha ][ 0.907436] . ( 17 sec) [ -6192.0689] [Topology ] . ( 18 sec) [ -6192.0346] [Topology ] . ( 19 sec) [ -6192.0213] [Topology ] . ( 20 sec) [ -6192.0149] [Topology ] . ( 21 sec) [ -6192.0113] [Topology ] . ( 22 sec) [ -6192.0093] [Topology ] . ( 22 sec) [ -6192.0080] [Topology ] . ( 22 sec) [ -6191.9955] [Alpha ][ 0.921539] . ( 23 sec) [ -6191.9955] [Topology ] . ( 23 sec) [ -6191.9910] [Topology ] . ( 24 sec) [ -6191.9894] [Topology ] . ( 25 sec) [ -6191.9887] [Topology ] . ( 25 sec) [ -6191.9877] [Alpha ][ 0.925636] . ( 25 sec) [ -6191.9877] [Topology ] . ( 26 sec) [ -6191.9868] [Topology ] . ( 26 sec) [ -6191.9867] [Alpha ][ 0.926577] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6191.986692. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -8917.5650] [Alpha ][ 0.715201] . ( 1 sec) [ -8370.9038] [ 1046] [depth= 4] . ( 1 sec) [ -7831.5635] [ 1159] [depth= 4] . ( 1 sec) [ -7570.5021] [ 1148] [depth= 1] . ( 1 sec) [ -7133.8004] [ 1147] [depth= 1] . ( 2 sec) [ -6810.8927] [ 1070] [depth= 3] . ( 2 sec) [ -6787.2839] [ 1069] [depth= 2] . ( 2 sec) [ -6482.6861] [ 1032] [depth= 2] . ( 2 sec) [ -6457.7775] [ 932] [depth= 1] . ( 3 sec) [ -6450.9465] [ 939] [depth= 1] . ( 3 sec) [ -6446.6713] [ 939] [depth= 1] . ( 3 sec) [ -6428.8118] [ 939] [depth= 1] . ( 3 sec) [ -6413.3061] [ 932] [depth= 1] . ( 4 sec) [ -6270.2739] [Branch lengths ] . ( 4 sec) [ -6269.8485] [Alpha ][ 0.665799] . ( 4 sec) [ -6226.8618] [ 932] [depth= 1] . ( 5 sec) [ -6221.2314] [ 932] [depth= 1] . ( 5 sec) [ -6218.0610] [ 947] [depth= 1] . ( 6 sec) [ -6209.8163] [ 932] [depth= 1] . ( 7 sec) [ -6197.0805] [Branch lengths ] . ( 7 sec) [ -6194.9733] [Alpha ][ 0.793030] . ( 11 sec) [ -6193.1151] [Branch lengths ] . ( 11 sec) [ -6193.1151] [Topology ] . ( 12 sec) [ -6192.9993] [Topology ] . ( 12 sec) [ -6192.9701] [Topology ] . ( 13 sec) [ -6192.9606] [Topology ] . ( 14 sec) [ -6192.9575] [Topology ] . ( 15 sec) [ -6192.9564] [Topology ] . ( 16 sec) [ -6192.9560] [Topology ] . ( 16 sec) [ -6192.3191] [Alpha ][ 0.879098] . ( 16 sec) [ -6192.3191] [Topology ] . ( 17 sec) [ -6192.1601] [Topology ] . ( 17 sec) [ -6192.1186] [Topology ] . ( 18 sec) [ -6192.1059] [Topology ] . ( 19 sec) [ -6192.1020] [Topology ] . ( 20 sec) [ -6192.1007] [Topology ] . ( 21 sec) [ -6192.1003] [Topology ] . ( 21 sec) [ -6192.0268] [Alpha ][ 0.911453] . ( 21 sec) [ -6192.0268] [Topology ] . ( 22 sec) [ -6192.0067] [Topology ] . ( 23 sec) [ -6192.0014] [Topology ] . ( 23 sec) [ -6191.9998] [Topology ] . ( 24 sec) [ -6191.9993] [Topology ] . ( 24 sec) [ -6191.9916] [Alpha ][ 0.922509] . ( 24 sec) [ -6191.9916] [Topology ] . ( 25 sec) [ -6191.9886] [Topology ] . ( 26 sec) [ -6191.9877] [Topology ] . ( 26 sec) [ -6191.9872] [Alpha ][ 0.925533] . ( 26 sec) [ -6191.9872] [Topology ] . ( 27 sec) [ -6191.9864] [Topology ] . ( 27 sec) [ -6191.9863] [Alpha ][ 0.926592] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6191.986318. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -7585.5774] [Alpha ][ 0.824161] . ( 0 sec) [ -7230.9573] [ 1106] [depth= 3] . ( 1 sec) [ -6885.6237] [ 1044] [depth= 4] . ( 1 sec) [ -6859.2852] [ 1012] [depth= 2] . ( 1 sec) [ -6549.3042] [ 948] [depth= 1] . ( 1 sec) [ -6394.4539] [ 932] [depth= 1] . ( 2 sec) [ -6370.8587] [ 932] [depth= 1] . ( 2 sec) [ -6354.8478] [ 947] [depth= 1] . ( 2 sec) [ -6337.8719] [ 932] [depth= 1] . ( 3 sec) [ -6329.4709] [ 936] [depth= 1] . ( 3 sec) [ -6305.4562] [ 948] [depth= 1] . ( 4 sec) [ -6214.6743] [Branch lengths ] . ( 4 sec) [ -6214.6524] [Alpha ][ 0.809447] . ( 5 sec) [ -6212.6269] [ 944] [depth= 1] . ( 5 sec) [ -6211.4247] [ 944] [depth= 1] . ( 6 sec) [ -6206.2216] [ 932] [depth= 1] . ( 7 sec) [ -6195.5446] [Branch lengths ] . ( 7 sec) [ -6195.3978] [Alpha ][ 0.850318] . ( 11 sec) [ -6193.0152] [Branch lengths ] . ( 11 sec) [ -6193.0152] [Topology ] . ( 11 sec) [ -6192.6888] [Topology ] . ( 12 sec) [ -6192.5328] [Topology ] . ( 13 sec) [ -6192.4412] [Topology ] . ( 14 sec) [ -6192.3836] [Topology ] . ( 15 sec) [ -6192.3472] [Topology ] . ( 15 sec) [ -6192.3240] [Topology ] . ( 16 sec) [ -6192.1157] [Alpha ][ 0.903089] . ( 16 sec) [ -6192.1157] [Topology ] . ( 16 sec) [ -6192.0531] [Topology ] . ( 17 sec) [ -6192.0328] [Topology ] . ( 18 sec) [ -6192.0244] [Topology ] . ( 19 sec) [ -6192.0205] [Topology ] . ( 20 sec) [ -6192.0184] [Topology ] . ( 20 sec) [ -6192.0172] [Topology ] . ( 21 sec) [ -6191.9970] [Alpha ][ 0.920952] . ( 21 sec) [ -6191.9970] [Topology ] . ( 21 sec) [ -6191.9910] [Topology ] . ( 22 sec) [ -6191.9893] [Topology ] . ( 23 sec) [ -6191.9887] [Topology ] . ( 23 sec) [ -6191.9873] [Alpha ][ 0.925719] . ( 23 sec) [ -6191.9873] [Topology ] . ( 24 sec) [ -6191.9864] [Topology ] . ( 24 sec) [ -6191.9863] [Alpha ][ 0.926749] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6191.986297. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -13171.3304] [Alpha ][ 0.500960] . ( 0 sec) [ -7933.3683] [ 1109] [depth= 3] . ( 0 sec) [ -7135.3082] [ 1046] [depth= 3] . ( 1 sec) [ -7112.9396] [ 1044] [depth= 1] . ( 1 sec) [ -6364.5536] [ 956] [depth= 1] . ( 1 sec) [ -6342.4854] [ 932] [depth= 2] . ( 1 sec) [ -6325.4052] [ 949] [depth= 1] . ( 2 sec) [ -6316.1746] [ 955] [depth= 1] . ( 2 sec) [ -6311.9771] [ 939] [depth= 1] . ( 2 sec) [ -6304.4813] [ 932] [depth= 1] . ( 2 sec) [ -6286.8955] [ 932] [depth= 1] . ( 3 sec) [ -6273.3993] [ 932] [depth= 1] . ( 3 sec) [ -6218.7830] [Branch lengths ] . ( 3 sec) [ -6203.6109] [Alpha ][ 0.805033] . ( 4 sec) [ -6199.7165] [ 936] [depth= 1] . ( 4 sec) [ -6196.3948] [ 932] [depth= 1] . ( 7 sec) [ -6193.5825] [Branch lengths ] . ( 7 sec) [ -6193.1440] [Alpha ][ 0.876703] . ( 10 sec) [ -6192.2823] [Branch lengths ] . ( 10 sec) [ -6192.2823] [Topology ] . ( 11 sec) [ -6192.1966] [Topology ] . ( 12 sec) [ -6192.1611] [Topology ] . ( 12 sec) [ -6192.1417] [Topology ] . ( 13 sec) [ -6192.1304] [Topology ] . ( 14 sec) [ -6192.1235] [Topology ] . ( 15 sec) [ -6192.1191] [Topology ] . ( 15 sec) [ -6192.0310] [Alpha ][ 0.911754] . ( 15 sec) [ -6192.0310] [Topology ] . ( 16 sec) [ -6192.0085] [Topology ] . ( 17 sec) [ -6192.0023] [Topology ] . ( 17 sec) [ -6192.0001] [Topology ] . ( 18 sec) [ -6191.9993] [Topology ] . ( 18 sec) [ -6191.9914] [Alpha ][ 0.922972] . ( 18 sec) [ -6191.9914] [Topology ] . ( 19 sec) [ -6191.9883] [Topology ] . ( 20 sec) [ -6191.9875] [Topology ] . ( 20 sec) [ -6191.9869] [Alpha ][ 0.925904] . ( 20 sec) [ -6191.9869] [Topology ] . ( 21 sec) [ -6191.9862] [Topology ] . ( 21 sec) [ -6191.9861] [Alpha ][ 0.926906] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6191.986148. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -8526.4077] [Alpha ][ 1.088716] . ( 0 sec) [ -8079.2420] [ 1022] [depth= 2] . ( 0 sec) [ -7224.6653] [ 953] [depth= 3] . ( 1 sec) [ -7153.8163] [ 950] [depth= 1] . ( 1 sec) [ -6800.1800] [ 932] [depth= 1] . ( 1 sec) [ -6597.4495] [ 939] [depth= 1] . ( 1 sec) [ -6551.4547] [ 939] [depth= 1] . ( 1 sec) [ -6472.9276] [ 932] [depth= 1] . ( 2 sec) [ -6450.2724] [ 944] [depth= 1] . ( 3 sec) [ -6246.3528] [ 932] [depth= 1] . ( 3 sec) [ -6195.4591] [Branch lengths ] . ( 3 sec) [ -6193.7054] [Alpha ][ 0.908817] . ( 7 sec) [ -6192.7613] [Branch lengths ] . ( 7 sec) [ -6192.7613] [Topology ] . ( 7 sec) [ -6192.4188] [Topology ] . ( 8 sec) [ -6192.2583] [Topology ] . ( 9 sec) [ -6192.1622] [Topology ] . ( 10 sec) [ -6192.1033] [Topology ] . ( 11 sec) [ -6192.0664] [Topology ] . ( 11 sec) [ -6192.0432] [Topology ] . ( 12 sec) [ -6192.0288] [Alpha ][ 0.924015] . ( 12 sec) [ -6192.0288] [Topology ] . ( 12 sec) [ -6192.0113] [Topology ] . ( 13 sec) [ -6192.0016] [Topology ] . ( 14 sec) [ -6191.9959] [Topology ] . ( 15 sec) [ -6191.9924] [Topology ] . ( 16 sec) [ -6191.9902] [Topology ] . ( 16 sec) [ -6191.9889] [Topology ] . ( 17 sec) [ -6191.9880] [Alpha ][ 0.927630] . ( 17 sec) [ -6191.9880] [Topology ] . ( 17 sec) [ -6191.9870] [Topology ] . ( 18 sec) [ -6191.9865] [Topology ] . ( 18 sec) [ -6191.9864] [Alpha ][ 0.928558] . ( 18 sec) [ -6191.9864] [Topology ] . ( 19 sec) [ -6191.9861] [Topology ] . ( 19 sec) [ -6191.9861] [Alpha ][ 0.928558] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6191.986060. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -6233.3784] [Alpha ][ 1.337069] . ( 0 sec) [ -6233.3784] [Topology ] . ( 1 sec) [ -6202.1031] [Topology ] . ( 2 sec) [ -6199.6839] [Topology ] . ( 3 sec) [ -6199.1480] [Topology ] . ( 4 sec) [ -6198.9865] [Topology ] . ( 4 sec) [ -6198.9339] [Topology ] . ( 5 sec) [ -6198.9156] [Topology ] . Checking for NNIs, optimizing five branches... . ( 14 sec) [ -6196.3146] [Topology ] . ( 14 sec) [ -6193.2251] [Alpha ][ 1.023146] . ( 14 sec) [ -6193.2251] [Topology ] . ( 15 sec) [ -6192.5234] [Topology ] . ( 16 sec) [ -6192.3736] [Topology ] . ( 17 sec) [ -6192.3359] [Topology ] . ( 17 sec) [ -6192.3259] [Topology ] . ( 18 sec) [ -6192.3231] [Topology ] . ( 19 sec) [ -6192.3222] [Topology ] . Checking for NNIs, optimizing five branches... . ( 27 sec) [ -6192.0976] [Alpha ][ 0.957346] . ( 27 sec) [ -6192.0976] [Topology ] . ( 28 sec) [ -6192.0396] [Topology ] . ( 28 sec) [ -6192.0253] [Topology ] . ( 29 sec) [ -6192.0212] [Topology ] . ( 30 sec) [ -6192.0199] [Topology ] . ( 31 sec) [ -6192.0194] [Topology ] . Checking for NNIs, optimizing five branches... . ( 39 sec) [ -6191.9983] [Alpha ][ 0.938624] . ( 39 sec) [ -6191.9983] [Topology ] . ( 39 sec) [ -6191.9921] [Topology ] . ( 40 sec) [ -6191.9904] [Topology ] . ( 41 sec) [ -6191.9899] [Topology ] . Checking for NNIs, optimizing five branches... . ( 49 sec) [ -6191.9879] [Alpha ][ 0.932536] . ( 49 sec) [ -6191.9879] [Topology ] . ( 50 sec) [ -6191.9867] [Topology ] . ( 51 sec) [ -6191.9863] [Topology ] . Checking for NNIs, optimizing five branches... . ( 58 sec) [ -6191.9861] [Alpha ][ 0.930641] . ( 58 sec) [ -6191.9861] [Topology ] . ( 59 sec) [ -6191.9858] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 75 sec) [ -6233.3784] [Alpha ][ 1.337069] . ( 75 sec) [ -6226.4796] [ 936] [depth= 1] . ( 75 sec) [ -6209.3135] [ 932] [depth= 1] . ( 76 sec) [ -6204.7689] [ 932] [depth= 1] . ( 78 sec) [ -6197.4732] [Branch lengths ] . ( 78 sec) [ -6194.2674] [Alpha ][ 1.019336] . ( 81 sec) [ -6192.4801] [Branch lengths ] . ( 81 sec) [ -6192.4801] [Topology ] . ( 82 sec) [ -6192.3515] [Topology ] . ( 83 sec) [ -6192.3157] [Topology ] . ( 84 sec) [ -6192.3034] [Topology ] . ( 85 sec) [ -6192.2991] [Topology ] . ( 85 sec) [ -6192.2976] [Topology ] . ( 86 sec) [ -6192.2970] [Topology ] . ( 86 sec) [ -6192.0823] [Alpha ][ 0.955316] . ( 86 sec) [ -6192.0823] [Topology ] . ( 87 sec) [ -6192.0315] [Topology ] . ( 88 sec) [ -6192.0193] [Topology ] . ( 89 sec) [ -6192.0159] [Topology ] . ( 90 sec) [ -6192.0149] [Topology ] . ( 90 sec) [ -6191.9979] [Alpha ][ 0.938584] . ( 90 sec) [ -6191.9979] [Topology ] . ( 90 sec) [ -6191.9919] [Topology ] . ( 91 sec) [ -6191.9903] [Topology ] . ( 92 sec) [ -6191.9898] [Topology ] . ( 92 sec) [ -6191.9877] [Alpha ][ 0.932488] . ( 92 sec) [ -6191.9877] [Topology ] . ( 93 sec) [ -6191.9866] [Topology ] . ( 94 sec) [ -6191.9863] [Topology ] . ( 94 sec) [ -6191.9861] [Alpha ][ 0.930603] . ( 94 sec) [ -6191.9861] [Topology ] . ( 95 sec) [ -6191.9858] [Topology ] . ( 95 sec) [ -6191.9858] [Alpha ][ 0.929672] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -6191.985837 . Log likelihood obtained after SPR moves : -6191.985792 . Log likelihood of the current tree: -6191.985792. . Printing the most likely tree in file 'proteic_M1882_8x705_2004.phy_phyml_tree.txt'... . Best log likelihood : -6191.985792 . Time used 0h1m43s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 251.17user 0.00system 4:21.41elapsed 96%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps