.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2302_24x365_2005.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 . 19 sites are made from completely undetermined states ('X', '-', '?')... . Compressing sequences... . 261 patterns found. (out of a total of 365 sites) . 103 sites without polymorphism (28.22%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 15Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -7556.6424] [Alpha ][ 0.500960] . ( 0 sec) [ -7426.1638] [ 936] [depth= 3] . ( 1 sec) [ -7038.6282] [ 908] [depth= 3] . ( 1 sec) [ -7037.1241] [ 908] [depth= 1] . ( 1 sec) [ -7030.0887] [ 908] [depth= 1] . ( 2 sec) [ -7027.0751] [ 908] [depth= 2] . ( 2 sec) [ -6967.3629] [ 908] [depth= 3] . ( 2 sec) [ -6937.8704] [ 906] [depth= 3] . ( 3 sec) [ -6652.5755] [ 906] [depth= 1] . ( 3 sec) [ -6617.1041] [ 895] [depth= 4] . ( 3 sec) [ -6591.6579] [ 895] [depth= 1] . ( 3 sec) [ -6358.1215] [ 857] [depth= 7] . ( 3 sec) [ -5906.0735] [ 835] [depth= 1] . ( 4 sec) [ -5495.1431] [ 813] [depth= 1] . ( 4 sec) [ -5364.4324] [ 811] [depth= 4] . ( 4 sec) [ -5254.7680] [ 778] [depth= 2] . ( 4 sec) [ -5064.9404] [ 724] [depth= 6] . ( 5 sec) [ -5030.0281] [ 720] [depth= 8] . ( 5 sec) [ -4955.6527] [ 714] [depth= 7] . ( 5 sec) [ -4952.1750] [ 714] [depth= 6] . ( 6 sec) [ -4927.1646] [ 704] [depth= 2] . ( 6 sec) [ -4907.5229] [ 696] [depth= 6] . ( 6 sec) [ -4907.0456] [ 695] [depth= 2] . ( 6 sec) [ -4903.5314] [ 695] [depth= 4] . ( 7 sec) [ -4767.9458] [ 682] [depth= 6] . ( 7 sec) [ -4657.3708] [ 664] [depth= 7] . ( 7 sec) [ -4591.5619] [ 646] [depth= 1] . ( 7 sec) [ -4589.9689] [ 646] [depth= 4] . ( 8 sec) [ -4588.6945] [ 646] [depth= 5] . ( 9 sec) [ -4585.6025] [ 645] [depth= 4] . ( 9 sec) [ -4584.3354] [ 642] [depth= 3] . ( 9 sec) [ -4584.0350] [ 642] [depth= 1] . ( 9 sec) [ -4550.9500] [ 636] [depth= 1] . ( 10 sec) [ -4502.9266] [ 623] [depth= 1] . ( 10 sec) [ -4400.3020] [ 605] [depth= 1] . ( 11 sec) [ -4397.3845] [ 605] [depth= 1] . ( 11 sec) [ -4397.2515] [ 605] [depth= 2] . ( 13 sec) [ -4397.2397] [ 605] [depth= 3] . ( 14 sec) [ -4397.1991] [ 605] [depth= 1] . ( 14 sec) [ -4319.7758] [ 606] [depth= 3] . ( 15 sec) [ -4319.7590] [ 606] [depth= 4] . ( 15 sec) [ -4319.7238] [ 606] [depth= 3] . ( 16 sec) [ -4296.9391] [Branch lengths ] . ( 16 sec) [ -4272.0756] [Alpha ][ 1.000694] . ( 17 sec) [ -4250.3447] [ 605] [depth= 5] . ( 18 sec) [ -4250.1984] [ 605] [depth= 3] . ( 18 sec) [ -4249.5272] [ 604] [depth= 2] . ( 21 sec) [ -4227.0654] [ 594] [depth= 6] . ( 30 sec) [ -4220.2241] [ 593] [depth= 4] . ( 30 sec) [ -4219.7820] [ 593] [depth= 2] . ( 30 sec) [ -4219.3624] [ 593] [depth= 1] . ( 31 sec) [ -4219.2411] [ 593] [depth= 1] . ( 31 sec) [ -4211.6120] [ 592] [depth= 1] . ( 31 sec) [ -4211.5760] [ 592] [depth= 2] . ( 32 sec) [ -4210.8302] [ 592] [depth= 1] . ( 32 sec) [ -4210.6614] [ 592] [depth= 3] . ( 52 sec) [ -4206.9416] [Branch lengths ] . ( 53 sec) [ -4204.9849] [Alpha ][ 1.338663] . ( 104 sec) [ -4204.5517] [Branch lengths ] . ( 104 sec) [ -4204.5517] [Topology ] . ( 105 sec) [ -4204.5382] [Topology ] . ( 107 sec) [ -4204.5359] [Topology ] . ( 108 sec) [ -4204.5353] [Topology ] . ( 109 sec) [ -4204.5257] [Alpha ][ 1.368035] . ( 109 sec) [ -4204.5257] [Topology ] . ( 110 sec) [ -4204.5251] [Topology ] . ( 110 sec) [ -4204.5251] [Alpha ][ 1.369403] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4204.525113. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -8492.2161] [Alpha ][ 0.500960] . ( 1 sec) [ -8277.5741] [ 961] [depth= 6] . ( 1 sec) [ -8144.7140] [ 936] [depth= 7] . ( 1 sec) [ -8113.9764] [ 936] [depth= 1] . ( 1 sec) [ -7261.6347] [ 936] [depth= 1] . ( 2 sec) [ -7246.1587] [ 935] [depth= 2] . ( 2 sec) [ -7162.4717] [ 935] [depth= 2] . ( 2 sec) [ -7077.2958] [ 934] [depth= 7] . ( 2 sec) [ -7026.4868] [ 933] [depth= 6] . ( 3 sec) [ -7021.1403] [ 932] [depth= 5] . ( 3 sec) [ -6916.2046] [ 932] [depth= 1] . ( 3 sec) [ -6535.1635] [ 927] [depth= 1] . ( 8 sec) [ -6406.8518] [ 896] [depth= 1] . ( 8 sec) [ -6378.1906] [ 894] [depth= 8] . ( 8 sec) [ -6313.1082] [ 879] [depth= 3] . ( 8 sec) [ -6205.1947] [ 881] [depth= 2] . ( 9 sec) [ -5550.0975] [ 875] [depth= 3] . ( 9 sec) [ -5102.2092] [ 812] [depth= 1] . ( 9 sec) [ -5039.3308] [ 811] [depth= 5] . ( 9 sec) [ -5025.6882] [ 813] [depth= 2] . ( 10 sec) [ -4881.3553] [ 753] [depth= 9] . ( 10 sec) [ -4879.4829] [ 752] [depth= 6] . ( 10 sec) [ -4859.5121] [ 750] [depth= 7] . ( 10 sec) [ -4856.5057] [ 749] [depth= 3] . ( 11 sec) [ -4770.1922] [ 732] [depth= 1] . ( 11 sec) [ -4726.2348] [ 729] [depth= 6] . ( 11 sec) [ -4723.9334] [ 729] [depth= 5] . ( 11 sec) [ -4723.7063] [ 729] [depth= 2] . ( 12 sec) [ -4702.9903] [ 729] [depth= 3] . ( 12 sec) [ -4690.4912] [ 727] [depth= 6] . ( 12 sec) [ -4432.5946] [ 642] [depth= 10] . ( 13 sec) [ -4413.3871] [ 639] [depth= 8] . ( 13 sec) [ -4412.3494] [ 639] [depth= 1] . ( 13 sec) [ -4408.5374] [ 639] [depth= 5] . ( 13 sec) [ -4370.2623] [ 611] [depth= 7] . ( 14 sec) [ -4324.1180] [ 604] [depth= 3] . ( 14 sec) [ -4324.0465] [ 604] [depth= 5] . ( 14 sec) [ -4323.1671] [ 604] [depth= 1] . ( 15 sec) [ -4323.0514] [ 603] [depth= 5] . ( 15 sec) [ -4322.8010] [ 603] [depth= 1] . ( 18 sec) [ -4320.7347] [ 604] [depth= 1] . ( 18 sec) [ -4320.5975] [ 604] [depth= 3] . ( 18 sec) [ -4319.8671] [ 604] [depth= 4] . ( 18 sec) [ -4319.8171] [ 604] [depth= 2] . ( 19 sec) [ -4288.1503] [ 592] [depth= 11] . ( 20 sec) [ -4260.6869] [Branch lengths ] . ( 20 sec) [ -4237.6867] [Alpha ][ 1.000552] . ( 26 sec) [ -4237.6520] [ 592] [depth= 2] . ( 42 sec) [ -4237.6394] [ 592] [depth= 4] . ( 67 sec) [ -4237.3085] [Branch lengths ] . ( 67 sec) [ -4236.2766] [Alpha ][ 1.226420] . ( 119 sec) [ -4236.2453] [Branch lengths ] . ( 119 sec) [ -4236.2453] [Topology ] . ( 120 sec) [ -4236.2435] [Topology ] . ( 122 sec) [ -4236.2430] [Topology ] . ( 122 sec) [ -4236.2423] [Alpha ][ 1.233527] . ( 122 sec) [ -4236.2423] [Topology ] . ( 124 sec) [ -4236.2416] [Topology ] . ( 124 sec) [ -4236.2416] [Alpha ][ 1.233527] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4236.241556. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -7797.6554] [Alpha ][ 0.500960] . ( 1 sec) [ -7412.2202] [ 961] [depth= 6] . ( 1 sec) [ -7290.2353] [ 935] [depth= 7] . ( 2 sec) [ -7280.0666] [ 938] [depth= 1] . ( 2 sec) [ -6944.2364] [ 936] [depth= 4] . ( 2 sec) [ -6873.5049] [ 904] [depth= 2] . ( 2 sec) [ -6836.2841] [ 904] [depth= 1] . ( 3 sec) [ -6835.7217] [ 903] [depth= 4] . ( 3 sec) [ -6790.6024] [ 903] [depth= 4] . ( 3 sec) [ -6727.7874] [ 895] [depth= 2] . ( 3 sec) [ -6720.2862] [ 892] [depth= 6] . ( 3 sec) [ -6667.4723] [ 892] [depth= 1] . ( 4 sec) [ -6643.7168] [ 890] [depth= 6] . ( 4 sec) [ -6634.8769] [ 889] [depth= 1] . ( 4 sec) [ -6229.2576] [ 885] [depth= 8] . ( 5 sec) [ -6207.4308] [ 886] [depth= 5] . ( 5 sec) [ -6037.1930] [ 873] [depth= 2] . ( 5 sec) [ -6034.7293] [ 871] [depth= 5] . ( 5 sec) [ -5966.3757] [ 848] [depth= 3] . ( 5 sec) [ -5943.5901] [ 859] [depth= 2] . ( 6 sec) [ -5884.7144] [ 845] [depth= 1] . ( 6 sec) [ -5626.7785] [ 768] [depth= 2] . ( 6 sec) [ -5608.6155] [ 767] [depth= 1] . ( 6 sec) [ -5553.3736] [ 754] [depth= 5] . ( 7 sec) [ -5334.9979] [ 753] [depth= 5] . ( 7 sec) [ -5298.1865] [ 753] [depth= 1] . ( 7 sec) [ -4663.5385] [ 749] [depth= 4] . ( 7 sec) [ -4532.8483] [ 686] [depth= 1] . ( 7 sec) [ -4511.3677] [ 683] [depth= 4] . ( 8 sec) [ -4475.7424] [ 677] [depth= 3] . ( 8 sec) [ -4472.7697] [ 679] [depth= 1] . ( 8 sec) [ -4457.0069] [ 679] [depth= 2] . ( 8 sec) [ -4455.6219] [ 679] [depth= 2] . ( 8 sec) [ -4443.1681] [ 678] [depth= 3] . ( 9 sec) [ -4442.8899] [ 678] [depth= 1] . ( 9 sec) [ -4421.1972] [ 678] [depth= 1] . ( 9 sec) [ -4355.8697] [ 635] [depth= 13] . ( 10 sec) [ -4355.8279] [ 635] [depth= 1] . ( 10 sec) [ -4354.6037] [ 635] [depth= 2] . ( 13 sec) [ -4352.3761] [ 636] [depth= 6] . ( 14 sec) [ -4352.2321] [ 636] [depth= 2] . ( 14 sec) [ -4352.1582] [ 636] [depth= 2] . ( 14 sec) [ -4327.8587] [ 611] [depth= 5] . ( 15 sec) [ -4327.8008] [ 611] [depth= 2] . ( 15 sec) [ -4327.4917] [ 611] [depth= 1] . ( 15 sec) [ -4327.4509] [ 611] [depth= 4] . ( 16 sec) [ -4327.3014] [ 611] [depth= 2] . ( 19 sec) [ -4287.0891] [Branch lengths ] . ( 20 sec) [ -4265.1901] [Alpha ][ 1.000287] . ( 21 sec) [ -4253.3206] [ 609] [depth= 1] . ( 24 sec) [ -4253.0518] [ 604] [depth= 1] . ( 24 sec) [ -4253.0396] [ 604] [depth= 3] . ( 25 sec) [ -4252.9623] [ 604] [depth= 1] . ( 25 sec) [ -4252.9502] [ 604] [depth= 1] . ( 26 sec) [ -4252.9212] [ 604] [depth= 1] . ( 27 sec) [ -4247.8187] [ 603] [depth= 1] . ( 28 sec) [ -4247.7351] [ 604] [depth= 1] . ( 28 sec) [ -4242.6835] [ 598] [depth= 7] . ( 29 sec) [ -4237.3156] [ 596] [depth= 2] . ( 29 sec) [ -4234.4821] [ 596] [depth= 4] . ( 32 sec) [ -4217.2248] [ 593] [depth= 6] . ( 32 sec) [ -4216.7453] [ 593] [depth= 1] . ( 33 sec) [ -4216.2608] [ 593] [depth= 1] . ( 34 sec) [ -4216.2195] [ 593] [depth= 2] . ( 35 sec) [ -4216.1580] [ 593] [depth= 3] . ( 35 sec) [ -4216.1230] [ 593] [depth= 1] . ( 37 sec) [ -4215.9361] [ 593] [depth= 1] . ( 38 sec) [ -4215.9186] [ 593] [depth= 1] . ( 45 sec) [ -4209.0998] [Branch lengths ] . ( 45 sec) [ -4207.2910] [Alpha ][ 1.319312] . ( 51 sec) [ -4205.2930] [ 592] [depth= 3] . ( 95 sec) [ -4204.5778] [Branch lengths ] . ( 95 sec) [ -4204.5560] [Alpha ][ 1.363530] . ( 147 sec) [ -4204.5261] [Branch lengths ] . ( 147 sec) [ -4204.5261] [Topology ] . ( 148 sec) [ -4204.5254] [Topology ] . ( 148 sec) [ -4204.5250] [Alpha ][ 1.369039] . ( 149 sec) [ -4204.5250] [Topology ] . ( 150 sec) [ -4204.5249] [Topology ] . ( 150 sec) [ -4204.5249] [Alpha ][ 1.369039] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4204.524885. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -7744.5301] [Alpha ][ 0.500960] . ( 1 sec) [ -7700.3775] [ 919] [depth= 3] . ( 1 sec) [ -7166.6559] [ 902] [depth= 6] . ( 1 sec) [ -7046.1833] [ 889] [depth= 2] . ( 2 sec) [ -6938.2987] [ 891] [depth= 1] . ( 2 sec) [ -6797.1761] [ 870] [depth= 2] . ( 2 sec) [ -6729.4400] [ 855] [depth= 9] . ( 2 sec) [ -6365.6773] [ 809] [depth= 2] . ( 3 sec) [ -6223.8023] [ 806] [depth= 1] . ( 3 sec) [ -5997.6734] [ 778] [depth= 1] . ( 3 sec) [ -5938.4332] [ 778] [depth= 2] . ( 3 sec) [ -5900.8880] [ 771] [depth= 1] . ( 4 sec) [ -5706.1333] [ 715] [depth= 5] . ( 4 sec) [ -5678.2483] [ 714] [depth= 1] . ( 4 sec) [ -5602.3631] [ 699] [depth= 6] . ( 4 sec) [ -5580.3594] [ 698] [depth= 3] . ( 4 sec) [ -5555.2064] [ 696] [depth= 7] . ( 5 sec) [ -5499.3055] [ 691] [depth= 8] . ( 5 sec) [ -5484.3056] [ 691] [depth= 3] . ( 6 sec) [ -4819.9171] [ 665] [depth= 8] . ( 6 sec) [ -4569.1318] [ 638] [depth= 9] . ( 6 sec) [ -4565.8614] [ 637] [depth= 3] . ( 6 sec) [ -4565.6714] [ 637] [depth= 1] . ( 6 sec) [ -4464.7742] [ 637] [depth= 2] . ( 7 sec) [ -4462.4639] [ 637] [depth= 3] . ( 7 sec) [ -4461.1517] [ 637] [depth= 3] . ( 7 sec) [ -4459.2140] [ 637] [depth= 6] . ( 7 sec) [ -4446.0902] [ 638] [depth= 1] . ( 8 sec) [ -4441.7550] [ 637] [depth= 1] . ( 8 sec) [ -4440.8842] [ 639] [depth= 1] . ( 8 sec) [ -4400.3363] [ 633] [depth= 2] . ( 8 sec) [ -4383.4676] [ 621] [depth= 4] . ( 9 sec) [ -4380.6689] [ 619] [depth= 1] . ( 9 sec) [ -4373.3858] [ 616] [depth= 4] . ( 9 sec) [ -4364.1741] [ 616] [depth= 3] . ( 10 sec) [ -4364.1329] [ 616] [depth= 6] . ( 10 sec) [ -4348.9955] [ 616] [depth= 1] . ( 10 sec) [ -4305.9502] [ 615] [depth= 1] . ( 13 sec) [ -4301.9814] [ 613] [depth= 4] . ( 13 sec) [ -4294.4057] [ 613] [depth= 3] . ( 13 sec) [ -4294.0499] [ 613] [depth= 1] . ( 15 sec) [ -4292.6201] [ 613] [depth= 2] . ( 15 sec) [ -4292.2822] [ 613] [depth= 1] . ( 16 sec) [ -4290.5409] [ 613] [depth= 1] . ( 16 sec) [ -4290.4924] [ 613] [depth= 4] . ( 17 sec) [ -4261.5135] [Branch lengths ] . ( 17 sec) [ -4238.3240] [Alpha ][ 1.000506] . ( 19 sec) [ -4233.7139] [ 612] [depth= 2] . ( 20 sec) [ -4232.6894] [ 613] [depth= 1] . ( 21 sec) [ -4232.6432] [ 614] [depth= 2] . ( 24 sec) [ -4230.7365] [ 613] [depth= 2] . ( 25 sec) [ -4214.2066] [ 592] [depth= 2] . ( 28 sec) [ -4214.1910] [ 592] [depth= 4] . ( 34 sec) [ -4214.1437] [ 592] [depth= 2] . ( 62 sec) [ -4206.8979] [Branch lengths ] . ( 62 sec) [ -4204.9540] [Alpha ][ 1.338927] . ( 114 sec) [ -4204.5483] [Branch lengths ] . ( 114 sec) [ -4204.5483] [Topology ] . ( 116 sec) [ -4204.5368] [Topology ] . ( 117 sec) [ -4204.5352] [Topology ] . ( 119 sec) [ -4204.5348] [Topology ] . ( 119 sec) [ -4204.5253] [Alpha ][ 1.368144] . ( 119 sec) [ -4204.5253] [Topology ] . ( 120 sec) [ -4204.5249] [Topology ] . ( 121 sec) [ -4204.5249] [Alpha ][ 1.369512] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4204.524895. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -8341.5521] [Alpha ][ 0.500960] . ( 1 sec) [ -8140.5949] [ 918] [depth= 2] . ( 1 sec) [ -8073.7389] [ 904] [depth= 5] . ( 2 sec) [ -7977.5616] [ 903] [depth= 3] . ( 2 sec) [ -7935.5948] [ 904] [depth= 1] . ( 2 sec) [ -7721.2602] [ 904] [depth= 3] . ( 2 sec) [ -7135.4624] [ 816] [depth= 4] . ( 2 sec) [ -6981.2307] [ 792] [depth= 7] . ( 3 sec) [ -6876.8907] [ 791] [depth= 7] . ( 3 sec) [ -6796.3952] [ 777] [depth= 7] . ( 4 sec) [ -6791.9551] [ 777] [depth= 4] . ( 4 sec) [ -6378.4223] [ 777] [depth= 1] . ( 4 sec) [ -6344.6653] [ 775] [depth= 9] . ( 4 sec) [ -6226.6676] [ 775] [depth= 2] . ( 5 sec) [ -5084.1856] [ 709] [depth= 10] . ( 5 sec) [ -4969.6211] [ 654] [depth= 1] . ( 5 sec) [ -4968.4606] [ 653] [depth= 7] . ( 5 sec) [ -4923.7345] [ 667] [depth= 1] . ( 5 sec) [ -4817.2276] [ 648] [depth= 2] . ( 6 sec) [ -4808.9967] [ 646] [depth= 1] . ( 6 sec) [ -4749.3027] [ 636] [depth= 5] . ( 6 sec) [ -4740.0972] [ 634] [depth= 5] . ( 7 sec) [ -4738.6425] [ 634] [depth= 1] . ( 7 sec) [ -4706.1467] [ 634] [depth= 2] . ( 7 sec) [ -4700.1254] [ 644] [depth= 1] . ( 7 sec) [ -4403.5352] [ 622] [depth= 1] . ( 7 sec) [ -4397.3991] [ 622] [depth= 1] . ( 8 sec) [ -4379.7868] [ 622] [depth= 3] . ( 8 sec) [ -4378.8809] [ 623] [depth= 5] . ( 8 sec) [ -4372.5599] [ 621] [depth= 4] . ( 8 sec) [ -4364.9146] [ 620] [depth= 4] . ( 9 sec) [ -4363.3898] [ 619] [depth= 1] . ( 9 sec) [ -4352.7339] [ 619] [depth= 1] . ( 9 sec) [ -4351.9910] [ 618] [depth= 1] . ( 9 sec) [ -4351.8954] [ 618] [depth= 2] . ( 10 sec) [ -4351.7660] [ 618] [depth= 2] . ( 10 sec) [ -4344.4418] [ 618] [depth= 1] . ( 10 sec) [ -4344.3886] [ 618] [depth= 3] . ( 11 sec) [ -4340.7318] [ 609] [depth= 2] . ( 11 sec) [ -4340.7182] [ 609] [depth= 2] . ( 12 sec) [ -4337.2649] [ 610] [depth= 1] . ( 12 sec) [ -4336.6007] [ 610] [depth= 2] . ( 12 sec) [ -4336.5136] [ 610] [depth= 4] . ( 13 sec) [ -4336.3601] [ 610] [depth= 5] . ( 13 sec) [ -4336.1963] [ 610] [depth= 4] . ( 13 sec) [ -4336.1551] [ 610] [depth= 2] . ( 14 sec) [ -4329.1393] [ 594] [depth= 1] . ( 14 sec) [ -4274.1132] [Branch lengths ] . ( 14 sec) [ -4251.4327] [Alpha ][ 1.000506] . ( 16 sec) [ -4249.6021] [ 595] [depth= 1] . ( 17 sec) [ -4247.6343] [ 594] [depth= 2] . ( 17 sec) [ -4247.6069] [ 594] [depth= 3] . ( 17 sec) [ -4246.9884] [ 592] [depth= 1] . ( 18 sec) [ -4246.9228] [ 592] [depth= 2] . ( 18 sec) [ -4246.3055] [ 594] [depth= 1] . ( 22 sec) [ -4246.2828] [ 594] [depth= 2] . ( 23 sec) [ -4242.4192] [ 592] [depth= 1] . ( 23 sec) [ -4242.2193] [ 592] [depth= 1] . ( 23 sec) [ -4242.1128] [ 592] [depth= 2] . ( 33 sec) [ -4242.0863] [ 592] [depth= 2] . ( 34 sec) [ -4242.0437] [ 592] [depth= 1] . ( 36 sec) [ -4241.9207] [ 592] [depth= 2] . ( 51 sec) [ -4237.4222] [Branch lengths ] . ( 52 sec) [ -4236.4112] [Alpha ][ 1.224655] . ( 104 sec) [ -4236.2505] [Branch lengths ] . ( 104 sec) [ -4236.2505] [Topology ] . ( 106 sec) [ -4236.2448] [Topology ] . ( 107 sec) [ -4236.2437] [Topology ] . ( 108 sec) [ -4236.2429] [Topology ] . ( 109 sec) [ -4236.2416] [Alpha ][ 1.233775] . ( 109 sec) [ -4236.2416] [Topology ] . ( 110 sec) [ -4236.2373] [Topology ] . ( 111 sec) [ -4236.2041] [Topology ] . ( 113 sec) [ -4235.9501] [Topology ] . ( 114 sec) [ -4234.1226] [Topology ] . ( 116 sec) [ -4224.6480] [Topology ] . ( 117 sec) [ -4209.8338] [Topology ] . ( 117 sec) [ -4209.7754] [Alpha ][ 1.298693] . ( 117 sec) [ -4209.7754] [Topology ] . ( 119 sec) [ -4205.5947] [Topology ] . ( 120 sec) [ -4204.7790] [Topology ] . ( 122 sec) [ -4204.6248] [Topology ] . ( 123 sec) [ -4204.5914] [Topology ] . ( 125 sec) [ -4204.5832] [Topology ] . ( 126 sec) [ -4204.5809] [Topology ] . ( 126 sec) [ -4204.5281] [Alpha ][ 1.366731] . ( 126 sec) [ -4204.5281] [Topology ] . ( 128 sec) [ -4204.5255] [Topology ] . ( 129 sec) [ -4204.5251] [Topology ] . ( 129 sec) [ -4204.5250] [Alpha ][ 1.368971] . ( 129 sec) [ -4204.5250] [Topology ] . ( 131 sec) [ -4204.5249] [Topology ] . ( 131 sec) [ -4204.5249] [Alpha ][ 1.368971] . Checking for NNIs, optimizing five branches... . ( 139 sec) [ -4204.5248] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4204.524754. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -4218.6216] [Alpha ][ 1.394511] . ( 0 sec) [ -4218.6216] [Topology ] . ( 2 sec) [ -4207.3938] [Topology ] . ( 4 sec) [ -4205.0043] [Topology ] . ( 6 sec) [ -4204.6545] [Topology ] . ( 7 sec) [ -4204.5667] [Topology ] . ( 9 sec) [ -4204.5412] [Topology ] . ( 10 sec) [ -4204.5337] [Topology ] . ( 12 sec) [ -4204.5316] [Topology ] . Checking for NNIs, optimizing five branches... . ( 20 sec) [ -4204.5258] [Alpha ][ 1.370680] . ( 20 sec) [ -4204.5258] [Topology ] . ( 22 sec) [ -4204.5250] [Topology ] . Checking for NNIs, optimizing five branches... . ( 31 sec) [ -4204.5250] [Alpha ][ 1.370680] . ( 31 sec) [ -4204.5250] [Topology ] . ( 32 sec) [ -4204.5248] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 50 sec) [ -4218.6216] [Alpha ][ 1.394511] . ( 52 sec) [ -4216.6126] [ 592] [depth= 1] . ( 56 sec) [ -4216.4084] [ 592] [depth= 1] . ( 56 sec) [ -4216.3831] [ 592] [depth= 1] . ( 57 sec) [ -4216.2531] [ 592] [depth= 1] . ( 57 sec) [ -4216.2399] [ 592] [depth= 2] . ( 57 sec) [ -4216.2290] [ 592] [depth= 2] . ( 71 sec) [ -4215.8317] [ 592] [depth= 1] . ( 71 sec) [ -4215.7582] [ 592] [depth= 3] . ( 72 sec) [ -4215.6970] [ 592] [depth= 1] . ( 72 sec) [ -4215.5894] [ 592] [depth= 3] . ( 73 sec) [ -4215.5269] [ 592] [depth= 3] . ( 73 sec) [ -4215.3859] [ 592] [depth= 1] . ( 74 sec) [ -4215.3518] [ 592] [depth= 4] . ( 76 sec) [ -4215.3341] [ 592] [depth= 4] . ( 81 sec) [ -4204.6858] [Branch lengths ] . ( 81 sec) [ -4204.6845] [Alpha ][ 1.383700] . ( 132 sec) [ -4204.5317] [Branch lengths ] . ( 132 sec) [ -4204.5317] [Topology ] . ( 133 sec) [ -4204.5276] [Topology ] . ( 135 sec) [ -4204.5269] [Topology ] . ( 135 sec) [ -4204.5251] [Alpha ][ 1.370749] . ( 135 sec) [ -4204.5251] [Topology ] . ( 136 sec) [ -4204.5248] [Topology ] . ( 137 sec) [ -4204.5248] [Alpha ][ 1.369378] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -4204.524817 . Log likelihood obtained after SPR moves : -4204.524808 . Log likelihood of the current tree: -4204.524808. . Printing the most likely tree in file 'proteic_M2302_24x365_2005.phy_phyml_tree.txt'... . Best log likelihood : -4204.524754 . Time used 0h2m25s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 822.31user 0.00system 13:53.80elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps