.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2641_18x326_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... . 243 patterns found. (out of a total of 326 sites) . 100 sites without polymorphism (30.67%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 10Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -6807.8771] [Alpha ][ 0.500960] . ( 0 sec) [ -6725.5188] [ 1084] [depth= 1] . ( 1 sec) [ -6700.1639] [ 1076] [depth= 5] . ( 1 sec) [ -6686.6348] [ 1075] [depth= 1] . ( 1 sec) [ -6658.3976] [ 1068] [depth= 4] . ( 1 sec) [ -6624.6206] [ 1068] [depth= 2] . ( 1 sec) [ -6547.3883] [ 1057] [depth= 4] . ( 2 sec) [ -6462.2014] [ 1054] [depth= 1] . ( 2 sec) [ -6290.1677] [ 1049] [depth= 3] . ( 2 sec) [ -6099.8737] [ 988] [depth= 4] . ( 2 sec) [ -5797.1510] [ 905] [depth= 5] . ( 2 sec) [ -5777.1438] [ 906] [depth= 1] . ( 2 sec) [ -5679.4026] [ 884] [depth= 2] . ( 3 sec) [ -5677.4489] [ 884] [depth= 1] . ( 3 sec) [ -5676.9711] [ 885] [depth= 1] . ( 3 sec) [ -5642.3362] [ 881] [depth= 1] . ( 3 sec) [ -5539.6100] [ 883] [depth= 3] . ( 4 sec) [ -5472.1056] [ 875] [depth= 1] . ( 4 sec) [ -5459.8166] [ 871] [depth= 1] . ( 4 sec) [ -5459.1145] [ 870] [depth= 1] . ( 5 sec) [ -5325.8276] [ 860] [depth= 1] . ( 5 sec) [ -5288.1821] [ 860] [depth= 1] . ( 5 sec) [ -5263.6453] [ 854] [depth= 2] . ( 5 sec) [ -5244.7474] [ 840] [depth= 1] . ( 5 sec) [ -5211.9003] [ 833] [depth= 1] . ( 6 sec) [ -5207.4406] [ 829] [depth= 1] . ( 6 sec) [ -5203.1251] [ 831] [depth= 1] . ( 8 sec) [ -5198.0537] [ 829] [depth= 1] . ( 8 sec) [ -5165.7808] [Branch lengths ] . ( 8 sec) [ -5161.4317] [Alpha ][ 0.674657] . ( 15 sec) [ -5159.1173] [ 831] [depth= 1] . ( 16 sec) [ -5158.6623] [ 829] [depth= 1] . ( 17 sec) [ -5154.0469] [Branch lengths ] . ( 18 sec) [ -5154.0438] [Alpha ][ 0.680188] . ( 26 sec) [ -5153.6588] [Branch lengths ] . ( 26 sec) [ -5153.6588] [Topology ] . ( 27 sec) [ -5153.6135] [Topology ] . ( 28 sec) [ -5153.5987] [Topology ] . ( 29 sec) [ -5153.5913] [Topology ] . ( 30 sec) [ -5153.5875] [Topology ] . ( 31 sec) [ -5153.5856] [Topology ] . ( 32 sec) [ -5153.5846] [Topology ] . ( 32 sec) [ -5153.5793] [Alpha ][ 0.687403] . ( 32 sec) [ -5153.5793] [Topology ] . ( 33 sec) [ -5153.5784] [Topology ] . ( 33 sec) [ -5153.5784] [Alpha ][ 0.687403] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5153.578422. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -7610.8447] [Alpha ][ 0.500960] . ( 1 sec) [ -7461.2446] [ 1147] [depth= 4] . ( 1 sec) [ -7347.8949] [ 1137] [depth= 6] . ( 1 sec) [ -7300.6039] [ 1126] [depth= 1] . ( 1 sec) [ -6990.9682] [ 1121] [depth= 1] . ( 1 sec) [ -6927.1752] [ 1093] [depth= 4] . ( 1 sec) [ -6820.3616] [ 1077] [depth= 2] . ( 2 sec) [ -6725.1158] [ 1050] [depth= 3] . ( 2 sec) [ -6606.3599] [ 1054] [depth= 10] . ( 2 sec) [ -6354.4794] [ 1026] [depth= 9] . ( 2 sec) [ -6276.0227] [ 1006] [depth= 1] . ( 2 sec) [ -6217.0461] [ 994] [depth= 1] . ( 2 sec) [ -6021.6650] [ 997] [depth= 4] . ( 3 sec) [ -6019.5801] [ 998] [depth= 1] . ( 3 sec) [ -6001.0101] [ 991] [depth= 1] . ( 3 sec) [ -5839.4368] [ 970] [depth= 2] . ( 3 sec) [ -5738.3432] [ 945] [depth= 3] . ( 4 sec) [ -5733.9056] [ 940] [depth= 1] . ( 4 sec) [ -5725.8028] [ 933] [depth= 1] . ( 4 sec) [ -5721.6637] [ 938] [depth= 1] . ( 5 sec) [ -5425.8884] [ 885] [depth= 2] . ( 5 sec) [ -5417.0306] [ 884] [depth= 1] . ( 5 sec) [ -5356.0835] [ 869] [depth= 1] . ( 5 sec) [ -5231.7712] [ 833] [depth= 3] . ( 7 sec) [ -5229.0560] [ 833] [depth= 1] . ( 7 sec) [ -5228.3688] [ 834] [depth= 1] . ( 10 sec) [ -5167.5037] [Branch lengths ] . ( 10 sec) [ -5164.1507] [Alpha ][ 0.650777] . ( 12 sec) [ -5159.7397] [ 831] [depth= 1] . ( 13 sec) [ -5159.0313] [ 829] [depth= 1] . ( 15 sec) [ -5159.0047] [ 829] [depth= 1] . ( 17 sec) [ -5158.9779] [ 829] [depth= 1] . ( 18 sec) [ -5154.3002] [Branch lengths ] . ( 18 sec) [ -5154.2326] [Alpha ][ 0.675978] . ( 27 sec) [ -5153.6936] [Branch lengths ] . ( 27 sec) [ -5153.6936] [Topology ] . ( 28 sec) [ -5153.6323] [Topology ] . ( 29 sec) [ -5153.6122] [Topology ] . ( 30 sec) [ -5153.6023] [Topology ] . ( 31 sec) [ -5153.5973] [Topology ] . ( 31 sec) [ -5153.5947] [Topology ] . ( 32 sec) [ -5153.5934] [Topology ] . ( 32 sec) [ -5153.5803] [Alpha ][ 0.687351] . ( 32 sec) [ -5153.5803] [Topology ] . ( 33 sec) [ -5153.5789] [Topology ] . ( 34 sec) [ -5153.5783] [Topology ] . ( 34 sec) [ -5153.5783] [Alpha ][ 0.687351] . ( 34 sec) [ -5153.5783] [Topology ] . ( 35 sec) [ -5153.5779] [Topology ] . ( 35 sec) [ -5153.5779] [Alpha ][ 0.687351] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5153.577917. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -7412.1314] [Alpha ][ 0.500960] . ( 1 sec) [ -7306.6286] [ 1163] [depth= 6] . ( 1 sec) [ -7063.5934] [ 1143] [depth= 3] . ( 1 sec) [ -7019.6970] [ 1136] [depth= 1] . ( 1 sec) [ -6806.5376] [ 1109] [depth= 5] . ( 1 sec) [ -6712.2330] [ 1083] [depth= 1] . ( 2 sec) [ -6551.5575] [ 1054] [depth= 5] . ( 2 sec) [ -6450.0831] [ 1047] [depth= 1] . ( 2 sec) [ -6442.1644] [ 1043] [depth= 2] . ( 2 sec) [ -6364.8465] [ 1027] [depth= 1] . ( 2 sec) [ -6340.9263] [ 1027] [depth= 1] . ( 2 sec) [ -6205.8443] [ 1003] [depth= 4] . ( 3 sec) [ -6190.9471] [ 1001] [depth= 3] . ( 3 sec) [ -5994.2103] [ 980] [depth= 4] . ( 3 sec) [ -5928.1687] [ 962] [depth= 3] . ( 3 sec) [ -5829.5422] [ 937] [depth= 3] . ( 3 sec) [ -5799.8535] [ 933] [depth= 1] . ( 4 sec) [ -5781.9865] [ 932] [depth= 1] . ( 4 sec) [ -5668.0473] [ 897] [depth= 4] . ( 4 sec) [ -5662.4776] [ 906] [depth= 1] . ( 4 sec) [ -5636.0016] [ 896] [depth= 1] . ( 4 sec) [ -5618.0700] [ 887] [depth= 4] . ( 4 sec) [ -5589.5611] [ 884] [depth= 1] . ( 5 sec) [ -5587.4840] [ 885] [depth= 1] . ( 5 sec) [ -5381.2068] [ 851] [depth= 4] . ( 5 sec) [ -5346.8330] [ 842] [depth= 2] . ( 5 sec) [ -5345.1814] [ 842] [depth= 1] . ( 6 sec) [ -5341.7769] [ 847] [depth= 1] . ( 6 sec) [ -5297.5715] [ 841] [depth= 1] . ( 6 sec) [ -5263.1137] [ 833] [depth= 2] . ( 6 sec) [ -5263.0824] [ 833] [depth= 1] . ( 7 sec) [ -5207.4052] [ 830] [depth= 1] . ( 7 sec) [ -5202.6965] [ 833] [depth= 1] . ( 8 sec) [ -5169.8629] [Branch lengths ] . ( 8 sec) [ -5166.0385] [Alpha ][ 0.662252] . ( 11 sec) [ -5162.7010] [ 829] [depth= 1] . ( 12 sec) [ -5162.6520] [ 829] [depth= 1] . ( 13 sec) [ -5159.4486] [ 831] [depth= 1] . ( 18 sec) [ -5154.9553] [Branch lengths ] . ( 18 sec) [ -5154.9025] [Alpha ][ 0.684497] . ( 31 sec) [ -5154.4661] [Branch lengths ] . ( 31 sec) [ -5154.4661] [Topology ] . ( 32 sec) [ -5153.8693] [Topology ] . ( 33 sec) [ -5153.6481] [Topology ] . ( 34 sec) [ -5153.6065] [Topology ] . ( 35 sec) [ -5153.5917] [Topology ] . ( 35 sec) [ -5153.5851] [Topology ] . ( 36 sec) [ -5153.5819] [Topology ] . ( 37 sec) [ -5153.5803] [Topology ] . ( 37 sec) [ -5153.5795] [Alpha ][ 0.687307] . ( 37 sec) [ -5153.5795] [Topology ] . ( 38 sec) [ -5153.5786] [Topology ] . ( 38 sec) [ -5153.5786] [Alpha ][ 0.687307] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5153.578571. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -7223.6225] [Alpha ][ 0.500960] . ( 1 sec) [ -7043.7436] [ 1112] [depth= 5] . ( 1 sec) [ -6956.9473] [ 1106] [depth= 5] . ( 1 sec) [ -6934.6925] [ 1105] [depth= 1] . ( 1 sec) [ -6750.4665] [ 1093] [depth= 2] . ( 1 sec) [ -6683.1671] [ 1079] [depth= 2] . ( 1 sec) [ -6638.0251] [ 1064] [depth= 3] . ( 2 sec) [ -6417.5568] [ 1047] [depth= 2] . ( 2 sec) [ -6342.0962] [ 1038] [depth= 2] . ( 2 sec) [ -6230.4762] [ 1011] [depth= 1] . ( 2 sec) [ -6223.0680] [ 1008] [depth= 1] . ( 2 sec) [ -6150.1148] [ 1001] [depth= 1] . ( 2 sec) [ -6090.3392] [ 996] [depth= 1] . ( 2 sec) [ -5996.6298] [ 982] [depth= 2] . ( 3 sec) [ -5969.3339] [ 968] [depth= 4] . ( 3 sec) [ -5877.8416] [ 952] [depth= 3] . ( 3 sec) [ -5783.6069] [ 953] [depth= 1] . ( 3 sec) [ -5691.4032] [ 925] [depth= 5] . ( 3 sec) [ -5681.8856] [ 927] [depth= 1] . ( 4 sec) [ -5558.7754] [ 899] [depth= 2] . ( 4 sec) [ -5513.1536] [ 892] [depth= 4] . ( 4 sec) [ -5451.2784] [ 877] [depth= 1] . ( 5 sec) [ -5419.6654] [ 869] [depth= 4] . ( 5 sec) [ -5411.5698] [ 859] [depth= 3] . ( 5 sec) [ -5214.1248] [ 830] [depth= 2] . ( 6 sec) [ -5211.9857] [ 828] [depth= 2] . ( 6 sec) [ -5203.4273] [ 827] [depth= 2] . ( 7 sec) [ -5200.1580] [ 824] [depth= 1] . ( 7 sec) [ -5170.2933] [Branch lengths ] . ( 7 sec) [ -5166.3763] [Alpha ][ 0.666364] . ( 9 sec) [ -5164.9243] [ 829] [depth= 1] . ( 10 sec) [ -5164.8755] [ 829] [depth= 1] . ( 13 sec) [ -5159.3937] [ 829] [depth= 2] . ( 14 sec) [ -5159.1295] [ 831] [depth= 1] . ( 14 sec) [ -5155.0438] [Branch lengths ] . ( 15 sec) [ -5155.0099] [Alpha ][ 0.684115] . ( 28 sec) [ -5154.4738] [Branch lengths ] . ( 28 sec) [ -5154.4738] [Topology ] . ( 29 sec) [ -5153.8716] [Topology ] . ( 29 sec) [ -5153.6491] [Topology ] . ( 30 sec) [ -5153.6071] [Topology ] . ( 31 sec) [ -5153.5922] [Topology ] . ( 32 sec) [ -5153.5855] [Topology ] . ( 33 sec) [ -5153.5823] [Topology ] . ( 34 sec) [ -5153.5806] [Topology ] . ( 34 sec) [ -5153.5796] [Alpha ][ 0.687304] . ( 34 sec) [ -5153.5796] [Topology ] . ( 35 sec) [ -5153.5786] [Topology ] . ( 35 sec) [ -5153.5786] [Alpha ][ 0.687304] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5153.578606. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -7222.4697] [Alpha ][ 0.500960] . ( 1 sec) [ -7105.2973] [ 1137] [depth= 4] . ( 1 sec) [ -7039.4107] [ 1117] [depth= 4] . ( 1 sec) [ -6919.4218] [ 1106] [depth= 2] . ( 1 sec) [ -6918.6525] [ 1107] [depth= 1] . ( 1 sec) [ -6838.3665] [ 1085] [depth= 2] . ( 2 sec) [ -6781.3736] [ 1081] [depth= 2] . ( 2 sec) [ -6691.2303] [ 1064] [depth= 2] . ( 2 sec) [ -6650.0914] [ 1059] [depth= 8] . ( 2 sec) [ -6605.3972] [ 1044] [depth= 1] . ( 3 sec) [ -6600.0887] [ 1038] [depth= 1] . ( 3 sec) [ -6382.5994] [ 1023] [depth= 2] . ( 3 sec) [ -6268.7415] [ 1023] [depth= 1] . ( 3 sec) [ -5958.4502] [ 1009] [depth= 8] . ( 3 sec) [ -5907.8515] [ 985] [depth= 2] . ( 4 sec) [ -5843.4024] [ 958] [depth= 2] . ( 4 sec) [ -5842.0853] [ 958] [depth= 1] . ( 4 sec) [ -5841.8038] [ 958] [depth= 1] . ( 4 sec) [ -5671.1982] [ 916] [depth= 2] . ( 4 sec) [ -5667.0659] [ 915] [depth= 1] . ( 5 sec) [ -5506.3178] [ 890] [depth= 3] . ( 5 sec) [ -5504.2337] [ 883] [depth= 3] . ( 5 sec) [ -5473.5927] [ 875] [depth= 2] . ( 5 sec) [ -5433.3606] [ 869] [depth= 1] . ( 5 sec) [ -5421.3057] [ 866] [depth= 1] . ( 5 sec) [ -5398.0051] [ 857] [depth= 4] . ( 6 sec) [ -5341.9980] [ 839] [depth= 1] . ( 6 sec) [ -5336.2480] [ 849] [depth= 1] . ( 6 sec) [ -5271.9977] [ 839] [depth= 1] . ( 6 sec) [ -5211.3127] [ 828] [depth= 5] . ( 7 sec) [ -5200.6447] [ 825] [depth= 2] . ( 8 sec) [ -5171.7977] [Branch lengths ] . ( 8 sec) [ -5167.3922] [Alpha ][ 0.677105] . ( 9 sec) [ -5166.5888] [ 827] [depth= 1] . ( 9 sec) [ -5166.2806] [ 824] [depth= 1] . ( 9 sec) [ -5164.6359] [ 829] [depth= 1] . ( 13 sec) [ -5159.4608] [ 831] [depth= 1] . ( 15 sec) [ -5159.0486] [ 829] [depth= 1] . ( 17 sec) [ -5154.3142] [Branch lengths ] . ( 17 sec) [ -5154.3142] [Alpha ][ 0.677105] . ( 25 sec) [ -5153.6950] [Branch lengths ] . ( 26 sec) [ -5153.6950] [Topology ] . ( 26 sec) [ -5153.6343] [Topology ] . ( 27 sec) [ -5153.6140] [Topology ] . ( 28 sec) [ -5153.6041] [Topology ] . ( 29 sec) [ -5153.5990] [Topology ] . ( 30 sec) [ -5153.5965] [Topology ] . ( 31 sec) [ -5153.5951] [Topology ] . ( 31 sec) [ -5153.5847] [Alpha ][ 0.687236] . ( 31 sec) [ -5153.5847] [Topology ] . ( 32 sec) [ -5153.5834] [Topology ] . ( 33 sec) [ -5153.5828] [Topology ] . ( 33 sec) [ -5153.5828] [Alpha ][ 0.687236] . ( 33 sec) [ -5153.5828] [Topology ] . ( 34 sec) [ -5153.5825] [Topology ] . ( 34 sec) [ -5153.5825] [Alpha ][ 0.687236] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5153.582517. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -5190.7718] [Alpha ][ 0.607649] . ( 0 sec) [ -5190.7718] [Topology ] . ( 1 sec) [ -5161.6235] [Topology ] . ( 2 sec) [ -5157.1353] [Topology ] . ( 3 sec) [ -5155.5391] [Topology ] . ( 4 sec) [ -5154.9097] [Topology ] . ( 5 sec) [ -5154.6184] [Topology ] . ( 5 sec) [ -5154.4740] [Topology ] . ( 6 sec) [ -5154.4004] [Topology ] . ( 7 sec) [ -5154.3623] [Topology ] . Checking for NNIs, optimizing five branches... . ( 15 sec) [ -5153.6964] [Alpha ][ 0.682511] . ( 15 sec) [ -5153.6964] [Topology ] . ( 16 sec) [ -5153.6349] [Topology ] . ( 17 sec) [ -5153.6081] [Topology ] . ( 18 sec) [ -5153.5946] [Topology ] . ( 19 sec) [ -5153.5877] [Topology ] . ( 20 sec) [ -5153.5842] [Topology ] . ( 20 sec) [ -5153.5823] [Topology ] . Checking for NNIs, optimizing five branches... . ( 28 sec) [ -5153.5800] [Alpha ][ 0.687271] . ( 28 sec) [ -5153.5800] [Topology ] . ( 29 sec) [ -5153.5788] [Topology ] . ( 30 sec) [ -5153.5782] [Topology ] . Checking for NNIs, optimizing five branches... . ( 38 sec) [ -5153.5782] [Alpha ][ 0.687271] . ( 38 sec) [ -5153.5782] [Topology ] . ( 39 sec) [ -5153.5779] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 55 sec) [ -5190.7718] [Alpha ][ 0.607649] . ( 56 sec) [ -5190.4764] [ 831] [depth= 1] . ( 60 sec) [ -5190.3233] [ 829] [depth= 1] . ( 61 sec) [ -5189.8898] [ 830] [depth= 1] . ( 61 sec) [ -5187.4550] [ 829] [depth= 1] . ( 61 sec) [ -5187.2047] [ 830] [depth= 1] . ( 62 sec) [ -5186.1241] [ 826] [depth= 1] . ( 63 sec) [ -5165.8169] [Branch lengths ] . ( 64 sec) [ -5165.2324] [Alpha ][ 0.678849] . ( 68 sec) [ -5164.8412] [ 830] [depth= 1] . ( 68 sec) [ -5163.6275] [ 829] [depth= 1] . ( 71 sec) [ -5158.3547] [ 829] [depth= 2] . ( 73 sec) [ -5153.8689] [Branch lengths ] . ( 73 sec) [ -5153.8680] [Alpha ][ 0.681664] . ( 81 sec) [ -5153.6122] [Branch lengths ] . ( 81 sec) [ -5153.6122] [Topology ] . ( 82 sec) [ -5153.5937] [Topology ] . ( 83 sec) [ -5153.5875] [Topology ] . ( 84 sec) [ -5153.5845] [Topology ] . ( 85 sec) [ -5153.5830] [Topology ] . ( 86 sec) [ -5153.5822] [Topology ] . ( 86 sec) [ -5153.5789] [Alpha ][ 0.687440] . ( 86 sec) [ -5153.5789] [Topology ] . ( 87 sec) [ -5153.5782] [Topology ] . ( 87 sec) [ -5153.5782] [Alpha ][ 0.687440] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -5153.577906 . Log likelihood obtained after SPR moves : -5153.578202 . Log likelihood of the current tree: -5153.577906. . Printing the most likely tree in file 'proteic_M2641_18x326_2006.phy_phyml_tree.txt'... . Best log likelihood : -5153.577906 . Time used 0h1m35s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 307.79user 0.00system 5:10.07elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps