.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1372_23x394_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 . 3 sites are made from completely undetermined states ('X', '-', '?')... . Compressing sequences... . 246 patterns found. (out of a total of 394 sites) . 162 sites without polymorphism (41.12%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 13Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -6731.6685] [Alpha ][ 0.500960] . ( 1 sec) [ -6656.8790] [ 869] [depth= 2] . ( 1 sec) [ -6244.4128] [ 862] [depth= 8] . ( 1 sec) [ -6163.6437] [ 858] [depth= 2] . ( 2 sec) [ -5874.9287] [ 859] [depth= 1] . ( 2 sec) [ -5858.3963] [ 853] [depth= 1] . ( 2 sec) [ -5857.8701] [ 855] [depth= 1] . ( 2 sec) [ -5828.5381] [ 842] [depth= 1] . ( 2 sec) [ -5680.1534] [ 843] [depth= 1] . ( 3 sec) [ -5641.0946] [ 814] [depth= 1] . ( 3 sec) [ -5248.0168] [ 774] [depth= 9] . ( 3 sec) [ -5198.4507] [ 769] [depth= 5] . ( 3 sec) [ -5168.7268] [ 756] [depth= 4] . ( 3 sec) [ -5141.8752] [ 750] [depth= 4] . ( 4 sec) [ -5139.4540] [ 749] [depth= 1] . ( 4 sec) [ -5137.4706] [ 750] [depth= 1] . ( 4 sec) [ -5125.2869] [ 749] [depth= 3] . ( 4 sec) [ -5050.4965] [ 737] [depth= 8] . ( 5 sec) [ -4988.3783] [ 724] [depth= 7] . ( 5 sec) [ -4972.8736] [ 723] [depth= 12] . ( 5 sec) [ -4964.3206] [ 725] [depth= 7] . ( 5 sec) [ -4957.0487] [ 722] [depth= 1] . ( 5 sec) [ -4911.8619] [ 722] [depth= 2] . ( 6 sec) [ -4877.0773] [ 718] [depth= 5] . ( 6 sec) [ -4864.4475] [ 717] [depth= 1] . ( 6 sec) [ -4828.5909] [ 713] [depth= 5] . ( 6 sec) [ -4826.4932] [ 713] [depth= 2] . ( 7 sec) [ -4815.5107] [ 710] [depth= 3] . ( 7 sec) [ -4811.1089] [ 709] [depth= 2] . ( 7 sec) [ -4800.8252] [ 709] [depth= 2] . ( 7 sec) [ -4790.7160] [ 703] [depth= 2] . ( 8 sec) [ -4755.1885] [ 683] [depth= 1] . ( 8 sec) [ -4749.6831] [ 681] [depth= 1] . ( 8 sec) [ -4679.3197] [ 680] [depth= 2] . ( 8 sec) [ -4674.4027] [ 679] [depth= 1] . ( 9 sec) [ -4638.6485] [ 679] [depth= 1] . ( 9 sec) [ -4631.7377] [ 679] [depth= 1] . ( 12 sec) [ -4620.7739] [ 680] [depth= 1] . ( 12 sec) [ -4618.2288] [ 680] [depth= 2] . ( 12 sec) [ -4605.0145] [ 678] [depth= 2] . ( 13 sec) [ -4604.8953] [ 678] [depth= 1] . ( 13 sec) [ -4557.5283] [ 674] [depth= 12] . ( 13 sec) [ -4538.5056] [ 659] [depth= 11] . ( 13 sec) [ -4535.6579] [ 661] [depth= 1] . ( 19 sec) [ -4497.9630] [Branch lengths ] . ( 19 sec) [ -4496.0520] [Alpha ][ 0.614364] . ( 23 sec) [ -4495.9907] [ 661] [depth= 1] . ( 28 sec) [ -4495.9456] [ 661] [depth= 1] . ( 33 sec) [ -4491.6041] [ 660] [depth= 3] . ( 33 sec) [ -4484.1507] [ 650] [depth= 7] . ( 39 sec) [ -4484.1354] [ 649] [depth= 1] . ( 39 sec) [ -4482.3178] [ 647] [depth= 1] . ( 44 sec) [ -4481.6634] [ 647] [depth= 1] . ( 44 sec) [ -4480.9111] [ 645] [depth= 2] . ( 48 sec) [ -4480.3528] [ 647] [depth= 2] . ( 50 sec) [ -4479.4527] [ 649] [depth= 1] . ( 51 sec) [ -4479.4324] [ 649] [depth= 1] . ( 51 sec) [ -4479.2714] [ 649] [depth= 1] . ( 56 sec) [ -4478.9671] [ 649] [depth= 1] . ( 59 sec) [ -4470.0499] [ 651] [depth= 8] . ( 64 sec) [ -4465.3676] [Branch lengths ] . ( 64 sec) [ -4465.3500] [Alpha ][ 0.626960] . ( 92 sec) [ -4460.9657] [ 650] [depth= 2] . ( 116 sec) [ -4460.2614] [Branch lengths ] . ( 116 sec) [ -4460.2611] [Alpha ][ 0.625171] . ( 167 sec) [ -4460.2356] [Branch lengths ] . ( 167 sec) [ -4460.2356] [Topology ] . ( 169 sec) [ -4460.1391] [Topology ] . ( 170 sec) [ -4459.6677] [Topology ] . ( 172 sec) [ -4459.2009] [Topology ] . ( 173 sec) [ -4459.1544] [Topology ] . ( 174 sec) [ -4459.1496] [Topology ] . ( 176 sec) [ -4459.1490] [Topology ] . ( 176 sec) [ -4459.1490] [Alpha ][ 0.625797] . ( 176 sec) [ -4459.1490] [Topology ] . ( 177 sec) [ -4459.1489] [Topology ] . ( 177 sec) [ -4459.1489] [Alpha ][ 0.625797] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4459.148928. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -6209.3373] [Alpha ][ 0.500960] . ( 0 sec) [ -6045.3459] [ 854] [depth= 4] . ( 0 sec) [ -5998.7116] [ 849] [depth= 3] . ( 1 sec) [ -5824.6488] [ 850] [depth= 1] . ( 1 sec) [ -5772.9507] [ 846] [depth= 3] . ( 1 sec) [ -5758.8534] [ 819] [depth= 2] . ( 1 sec) [ -5735.0792] [ 816] [depth= 1] . ( 1 sec) [ -5732.7215] [ 814] [depth= 5] . ( 2 sec) [ -5650.5532] [ 814] [depth= 3] . ( 2 sec) [ -5648.8854] [ 815] [depth= 1] . ( 2 sec) [ -5645.3975] [ 811] [depth= 3] . ( 2 sec) [ -5623.4248] [ 810] [depth= 5] . ( 3 sec) [ -5597.7032] [ 809] [depth= 2] . ( 3 sec) [ -5587.8349] [ 805] [depth= 3] . ( 3 sec) [ -5584.9653] [ 805] [depth= 3] . ( 3 sec) [ -5332.6949] [ 805] [depth= 1] . ( 3 sec) [ -5258.5735] [ 806] [depth= 3] . ( 4 sec) [ -5219.0086] [ 797] [depth= 4] . ( 4 sec) [ -5212.6749] [ 796] [depth= 3] . ( 4 sec) [ -5211.2747] [ 795] [depth= 1] . ( 4 sec) [ -5206.2458] [ 796] [depth= 1] . ( 4 sec) [ -5190.3420] [ 797] [depth= 3] . ( 5 sec) [ -5141.6790] [ 772] [depth= 3] . ( 5 sec) [ -5093.6187] [ 757] [depth= 10] . ( 5 sec) [ -5030.2573] [ 748] [depth= 4] . ( 5 sec) [ -4873.4263] [ 746] [depth= 1] . ( 5 sec) [ -4804.8997] [ 747] [depth= 1] . ( 6 sec) [ -4795.1741] [ 744] [depth= 2] . ( 6 sec) [ -4793.5567] [ 743] [depth= 1] . ( 6 sec) [ -4775.6189] [ 726] [depth= 7] . ( 6 sec) [ -4758.1366] [ 725] [depth= 1] . ( 6 sec) [ -4747.2995] [ 722] [depth= 7] . ( 7 sec) [ -4591.4241] [ 680] [depth= 8] . ( 7 sec) [ -4588.6409] [ 680] [depth= 1] . ( 13 sec) [ -4586.9083] [ 679] [depth= 1] . ( 13 sec) [ -4585.3414] [ 681] [depth= 1] . ( 13 sec) [ -4584.0327] [ 680] [depth= 1] . ( 14 sec) [ -4571.2022] [ 678] [depth= 1] . ( 15 sec) [ -4570.9361] [ 678] [depth= 1] . ( 15 sec) [ -4569.8162] [ 679] [depth= 1] . ( 18 sec) [ -4557.7498] [ 675] [depth= 3] . ( 21 sec) [ -4532.7039] [ 677] [depth= 1] . ( 26 sec) [ -4530.1591] [ 677] [depth= 1] . ( 26 sec) [ -4522.1125] [ 673] [depth= 3] . ( 26 sec) [ -4517.3645] [ 670] [depth= 3] . ( 27 sec) [ -4505.2607] [Branch lengths ] . ( 28 sec) [ -4503.9660] [Alpha ][ 0.592785] . ( 29 sec) [ -4501.4732] [ 658] [depth= 2] . ( 29 sec) [ -4500.0236] [ 657] [depth= 3] . ( 29 sec) [ -4497.0932] [ 655] [depth= 4] . ( 30 sec) [ -4496.7824] [ 655] [depth= 1] . ( 31 sec) [ -4495.8694] [ 655] [depth= 1] . ( 32 sec) [ -4490.7537] [ 655] [depth= 1] . ( 35 sec) [ -4488.7594] [ 654] [depth= 2] . ( 38 sec) [ -4488.6967] [ 654] [depth= 1] . ( 42 sec) [ -4482.4441] [ 655] [depth= 4] . ( 47 sec) [ -4480.4341] [ 655] [depth= 2] . ( 48 sec) [ -4479.4410] [ 655] [depth= 1] . ( 52 sec) [ -4479.2905] [ 655] [depth= 1] . ( 58 sec) [ -4477.7696] [ 647] [depth= 9] . ( 58 sec) [ -4472.4475] [ 645] [depth= 4] . ( 58 sec) [ -4465.0420] [Branch lengths ] . ( 59 sec) [ -4464.6389] [Alpha ][ 0.654754] . ( 60 sec) [ -4463.1494] [ 646] [depth= 1] . ( 67 sec) [ -4461.7321] [ 646] [depth= 1] . ( 106 sec) [ -4461.6069] [ 651] [depth= 8] . ( 108 sec) [ -4460.3641] [Branch lengths ] . ( 109 sec) [ -4460.2728] [Alpha ][ 0.624181] . ( 110 sec) [ -4459.1966] [ 650] [depth= 1] . ( 159 sec) [ -4459.1512] [Branch lengths ] . ( 159 sec) [ -4459.1510] [Alpha ][ 0.625316] . ( 210 sec) [ -4459.1492] [Branch lengths ] . ( 210 sec) [ -4459.1492] [Topology ] . ( 212 sec) [ -4459.1491] [Topology ] . ( 212 sec) [ -4459.1491] [Alpha ][ 0.625316] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4459.149114. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -5963.7336] [Alpha ][ 0.500960] . ( 0 sec) [ -5861.8301] [ 864] [depth= 3] . ( 1 sec) [ -5812.0120] [ 858] [depth= 5] . ( 1 sec) [ -5800.1526] [ 856] [depth= 1] . ( 1 sec) [ -5773.3023] [ 855] [depth= 2] . ( 1 sec) [ -5753.2378] [ 853] [depth= 1] . ( 1 sec) [ -5747.6994] [ 851] [depth= 1] . ( 1 sec) [ -5745.4315] [ 851] [depth= 1] . ( 2 sec) [ -5737.1963] [ 845] [depth= 8] . ( 2 sec) [ -5734.9362] [ 844] [depth= 1] . ( 2 sec) [ -5617.2597] [ 837] [depth= 9] . ( 2 sec) [ -5612.8502] [ 837] [depth= 3] . ( 3 sec) [ -5515.3602] [ 824] [depth= 3] . ( 3 sec) [ -5339.7407] [ 796] [depth= 4] . ( 3 sec) [ -5248.5010] [ 798] [depth= 4] . ( 5 sec) [ -5175.5548] [ 763] [depth= 3] . ( 5 sec) [ -5173.1393] [ 762] [depth= 1] . ( 5 sec) [ -5132.0259] [ 745] [depth= 2] . ( 5 sec) [ -5128.1576] [ 746] [depth= 1] . ( 5 sec) [ -5104.3723] [ 745] [depth= 7] . ( 8 sec) [ -4878.3978] [ 750] [depth= 7] . ( 8 sec) [ -4712.4807] [ 697] [depth= 5] . ( 8 sec) [ -4700.3104] [ 696] [depth= 1] . ( 8 sec) [ -4677.2267] [ 683] [depth= 2] . ( 8 sec) [ -4647.6461] [ 674] [depth= 3] . ( 9 sec) [ -4628.5319] [ 672] [depth= 1] . ( 9 sec) [ -4626.7634] [ 668] [depth= 1] . ( 9 sec) [ -4602.1957] [ 669] [depth= 2] . ( 9 sec) [ -4575.3053] [ 662] [depth= 1] . ( 9 sec) [ -4561.3007] [ 661] [depth= 6] . ( 10 sec) [ -4556.9050] [ 665] [depth= 1] . ( 10 sec) [ -4551.7101] [ 661] [depth= 1] . ( 10 sec) [ -4542.8286] [ 661] [depth= 1] . ( 10 sec) [ -4538.7259] [ 659] [depth= 2] . ( 11 sec) [ -4536.7889] [ 659] [depth= 1] . ( 11 sec) [ -4522.8298] [ 653] [depth= 1] . ( 12 sec) [ -4495.1550] [ 648] [depth= 4] . ( 12 sec) [ -4493.5756] [ 648] [depth= 1] . ( 17 sec) [ -4487.6285] [ 647] [depth= 2] . ( 17 sec) [ -4482.7441] [ 645] [depth= 3] . ( 18 sec) [ -4481.6306] [ 646] [depth= 3] . ( 22 sec) [ -4480.6974] [ 646] [depth= 1] . ( 24 sec) [ -4465.5920] [Branch lengths ] . ( 24 sec) [ -4462.8594] [Alpha ][ 0.649145] . ( 29 sec) [ -4462.6415] [ 646] [depth= 1] . ( 36 sec) [ -4462.6091] [ 646] [depth= 1] . ( 40 sec) [ -4462.5972] [ 646] [depth= 1] . ( 69 sec) [ -4461.9173] [Branch lengths ] . ( 69 sec) [ -4461.9100] [Alpha ][ 0.658335] . ( 69 sec) [ -4461.9100] [Topology ] . ( 71 sec) [ -4461.8266] [Topology ] . ( 72 sec) [ -4461.7901] [Topology ] . ( 73 sec) [ -4461.7800] [Topology ] . ( 75 sec) [ -4461.7773] [Topology ] . ( 76 sec) [ -4461.7764] [Topology ] . ( 76 sec) [ -4461.7762] [Alpha ][ 0.659582] . ( 76 sec) [ -4461.7762] [Topology ] . ( 77 sec) [ -4461.7759] [Topology ] . ( 78 sec) [ -4461.7759] [Alpha ][ 0.659582] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4461.775870. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -6453.4382] [Alpha ][ 0.500960] . ( 0 sec) [ -6373.2580] [ 815] [depth= 7] . ( 1 sec) [ -5981.0938] [ 804] [depth= 6] . ( 1 sec) [ -5949.1850] [ 802] [depth= 5] . ( 1 sec) [ -5895.4898] [ 792] [depth= 1] . ( 1 sec) [ -5821.3713] [ 791] [depth= 7] . ( 1 sec) [ -5761.6635] [ 792] [depth= 1] . ( 2 sec) [ -5542.5446] [ 789] [depth= 2] . ( 2 sec) [ -5528.4600] [ 787] [depth= 4] . ( 2 sec) [ -5480.6786] [ 782] [depth= 2] . ( 2 sec) [ -5111.8553] [ 754] [depth= 5] . ( 2 sec) [ -5028.0709] [ 743] [depth= 3] . ( 2 sec) [ -5027.9250] [ 748] [depth= 1] . ( 3 sec) [ -4958.8530] [ 746] [depth= 10] . ( 3 sec) [ -4946.8424] [ 745] [depth= 6] . ( 3 sec) [ -4940.6733] [ 737] [depth= 1] . ( 3 sec) [ -4874.7257] [ 722] [depth= 7] . ( 4 sec) [ -4797.0177] [ 691] [depth= 1] . ( 4 sec) [ -4796.7996] [ 690] [depth= 5] . ( 4 sec) [ -4790.0584] [ 689] [depth= 3] . ( 4 sec) [ -4749.9676] [ 685] [depth= 1] . ( 4 sec) [ -4743.5597] [ 684] [depth= 2] . ( 5 sec) [ -4742.5850] [ 682] [depth= 2] . ( 5 sec) [ -4732.0962] [ 687] [depth= 1] . ( 5 sec) [ -4725.8927] [ 686] [depth= 1] . ( 5 sec) [ -4710.2953] [ 677] [depth= 6] . ( 6 sec) [ -4705.8618] [ 685] [depth= 2] . ( 6 sec) [ -4648.9625] [ 679] [depth= 1] . ( 6 sec) [ -4647.8961] [ 680] [depth= 1] . ( 6 sec) [ -4645.5231] [ 679] [depth= 1] . ( 7 sec) [ -4625.1974] [ 680] [depth= 1] . ( 7 sec) [ -4616.4827] [ 680] [depth= 5] . ( 7 sec) [ -4551.3320] [ 662] [depth= 1] . ( 7 sec) [ -4549.9359] [ 662] [depth= 1] . ( 8 sec) [ -4549.0641] [ 662] [depth= 1] . ( 9 sec) [ -4547.6374] [ 661] [depth= 1] . ( 9 sec) [ -4529.9850] [ 658] [depth= 4] . ( 11 sec) [ -4527.3822] [ 658] [depth= 1] . ( 11 sec) [ -4521.2612] [ 655] [depth= 1] . ( 11 sec) [ -4519.6093] [ 656] [depth= 1] . ( 14 sec) [ -4516.3635] [ 656] [depth= 1] . ( 14 sec) [ -4511.6747] [ 655] [depth= 3] . ( 15 sec) [ -4509.3869] [ 654] [depth= 2] . ( 15 sec) [ -4508.5366] [ 654] [depth= 3] . ( 17 sec) [ -4506.0125] [ 653] [depth= 4] . ( 19 sec) [ -4489.2485] [Branch lengths ] . ( 20 sec) [ -4486.3046] [Alpha ][ 0.652320] . ( 20 sec) [ -4481.8969] [ 652] [depth= 1] . ( 28 sec) [ -4481.8678] [ 652] [depth= 3] . ( 29 sec) [ -4474.2448] [ 650] [depth= 2] . ( 31 sec) [ -4472.3539] [ 646] [depth= 5] . ( 31 sec) [ -4472.3329] [ 646] [depth= 1] . ( 53 sec) [ -4467.8185] [ 644] [depth= 3] . ( 55 sec) [ -4467.6379] [ 644] [depth= 1] . ( 58 sec) [ -4466.9702] [ 646] [depth= 8] . ( 61 sec) [ -4463.1882] [Branch lengths ] . ( 61 sec) [ -4463.1658] [Alpha ][ 0.667978] . ( 61 sec) [ -4462.2335] [ 647] [depth= 7] . ( 71 sec) [ -4462.2178] [ 646] [depth= 5] . ( 79 sec) [ -4461.4741] [ 650] [depth= 7] . ( 87 sec) [ -4460.8530] [ 650] [depth= 1] . ( 109 sec) [ -4459.4166] [Branch lengths ] . ( 109 sec) [ -4459.2413] [Alpha ][ 0.624919] . ( 161 sec) [ -4459.1599] [Branch lengths ] . ( 161 sec) [ -4459.1599] [Topology ] . ( 162 sec) [ -4459.1528] [Topology ] . ( 164 sec) [ -4459.1508] [Topology ] . ( 165 sec) [ -4459.1499] [Topology ] . ( 165 sec) [ -4459.1499] [Alpha ][ 0.625544] . ( 165 sec) [ -4459.1499] [Topology ] . ( 167 sec) [ -4459.1494] [Topology ] . ( 167 sec) [ -4459.1494] [Alpha ][ 0.625544] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4459.149432. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -6145.0117] [Alpha ][ 0.500960] . ( 1 sec) [ -6031.3013] [ 846] [depth= 5] . ( 1 sec) [ -5971.0878] [ 839] [depth= 8] . ( 1 sec) [ -5970.9121] [ 841] [depth= 1] . ( 2 sec) [ -5942.7992] [ 835] [depth= 4] . ( 2 sec) [ -5937.8761] [ 833] [depth= 2] . ( 2 sec) [ -5872.5513] [ 829] [depth= 2] . ( 2 sec) [ -5799.3720] [ 831] [depth= 1] . ( 2 sec) [ -5789.7884] [ 828] [depth= 1] . ( 3 sec) [ -5776.0446] [ 826] [depth= 2] . ( 3 sec) [ -5737.1381] [ 827] [depth= 3] . ( 3 sec) [ -5558.7426] [ 796] [depth= 7] . ( 3 sec) [ -5511.1097] [ 794] [depth= 5] . ( 3 sec) [ -5474.3405] [ 796] [depth= 1] . ( 4 sec) [ -5468.2118] [ 794] [depth= 1] . ( 4 sec) [ -5291.8567] [ 791] [depth= 6] . ( 4 sec) [ -5287.2714] [ 788] [depth= 3] . ( 4 sec) [ -5136.2192] [ 786] [depth= 2] . ( 6 sec) [ -5102.1874] [ 785] [depth= 2] . ( 6 sec) [ -5094.9603] [ 782] [depth= 1] . ( 6 sec) [ -4958.2405] [ 753] [depth= 2] . ( 6 sec) [ -4944.5749] [ 751] [depth= 1] . ( 6 sec) [ -4941.7785] [ 751] [depth= 1] . ( 7 sec) [ -4939.2188] [ 751] [depth= 2] . ( 7 sec) [ -4938.1793] [ 753] [depth= 1] . ( 7 sec) [ -4922.0416] [ 754] [depth= 6] . ( 9 sec) [ -4827.6395] [ 738] [depth= 7] . ( 13 sec) [ -4823.3593] [ 736] [depth= 1] . ( 14 sec) [ -4747.3623] [ 716] [depth= 3] . ( 14 sec) [ -4716.8608] [ 716] [depth= 3] . ( 14 sec) [ -4714.3390] [ 708] [depth= 3] . ( 14 sec) [ -4714.0984] [ 701] [depth= 1] . ( 15 sec) [ -4710.6063] [ 702] [depth= 1] . ( 15 sec) [ -4706.6866] [ 701] [depth= 8] . ( 15 sec) [ -4706.5527] [ 700] [depth= 1] . ( 15 sec) [ -4656.4942] [ 676] [depth= 3] . ( 16 sec) [ -4533.2893] [ 658] [depth= 1] . ( 16 sec) [ -4525.4929] [ 657] [depth= 1] . ( 18 sec) [ -4518.1356] [ 654] [depth= 1] . ( 18 sec) [ -4516.1345] [ 653] [depth= 2] . ( 19 sec) [ -4514.3816] [ 653] [depth= 1] . ( 20 sec) [ -4514.2474] [ 653] [depth= 1] . ( 21 sec) [ -4513.9997] [ 653] [depth= 1] . ( 22 sec) [ -4498.7785] [Branch lengths ] . ( 22 sec) [ -4496.8992] [Alpha ][ 0.620131] . ( 23 sec) [ -4496.5839] [ 653] [depth= 1] . ( 28 sec) [ -4487.0571] [ 654] [depth= 1] . ( 31 sec) [ -4486.8734] [ 652] [depth= 1] . ( 33 sec) [ -4486.2413] [ 652] [depth= 1] . ( 39 sec) [ -4484.3817] [ 655] [depth= 7] . ( 52 sec) [ -4483.0557] [ 657] [depth= 5] . ( 53 sec) [ -4480.6749] [ 649] [depth= 9] . ( 54 sec) [ -4478.9538] [ 649] [depth= 1] . ( 59 sec) [ -4478.9401] [ 648] [depth= 1] . ( 63 sec) [ -4478.6679] [ 648] [depth= 1] . ( 65 sec) [ -4469.8527] [Branch lengths ] . ( 65 sec) [ -4469.7883] [Alpha ][ 0.645357] . ( 66 sec) [ -4468.8854] [ 650] [depth= 1] . ( 70 sec) [ -4463.8661] [ 646] [depth= 6] . ( 77 sec) [ -4463.6224] [ 646] [depth= 1] . ( 94 sec) [ -4462.8807] [ 646] [depth= 6] . ( 109 sec) [ -4460.5293] [Branch lengths ] . ( 110 sec) [ -4460.5121] [Alpha ][ 0.658704] . ( 159 sec) [ -4460.4713] [Branch lengths ] . ( 159 sec) [ -4460.4713] [Topology ] . ( 161 sec) [ -4460.4700] [Topology ] . ( 162 sec) [ -4460.4699] [Topology ] . ( 162 sec) [ -4460.4699] [Alpha ][ 0.659363] . ( 162 sec) [ -4460.4699] [Topology ] . ( 163 sec) [ -4460.4698] [Topology ] . ( 164 sec) [ -4460.4698] [Alpha ][ 0.659363] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4460.469835. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -4512.1912] [Alpha ][ 0.596203] . ( 0 sec) [ -4512.1912] [Topology ] . ( 1 sec) [ -4483.0594] [Topology ] . ( 3 sec) [ -4477.9104] [Topology ] . ( 4 sec) [ -4476.3403] [Topology ] . ( 6 sec) [ -4475.2627] [Topology ] . ( 7 sec) [ -4474.9882] [Topology ] . ( 8 sec) [ -4474.9096] [Topology ] . ( 9 sec) [ -4474.8846] [Topology ] . ( 11 sec) [ -4474.8756] [Topology ] . ( 12 sec) [ -4474.8722] [Topology ] . Checking for NNIs, optimizing five branches... . ( 21 sec) [ -4474.5121] [Alpha ][ 0.655762] . ( 21 sec) [ -4474.5121] [Topology ] . ( 22 sec) [ -4474.4958] [Topology ] . ( 24 sec) [ -4474.4919] [Topology ] . ( 25 sec) [ -4474.4903] [Topology ] . ( 26 sec) [ -4474.4896] [Topology ] . Checking for NNIs, optimizing five branches... . ( 35 sec) [ -4474.4890] [Alpha ][ 0.658482] . ( 35 sec) [ -4474.4890] [Topology ] . ( 37 sec) [ -4474.4886] [Topology ] . Checking for NNIs, optimizing five branches... . ( 46 sec) [ -4474.4886] [Alpha ][ 0.658482] . ( 46 sec) [ -4474.4886] [Topology ] . ( 47 sec) [ -4474.4884] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 66 sec) [ -4512.1912] [Alpha ][ 0.596203] . ( 66 sec) [ -4510.7574] [ 648] [depth= 2] . ( 67 sec) [ -4509.8214] [ 651] [depth= 1] . ( 69 sec) [ -4507.5758] [ 648] [depth= 1] . ( 69 sec) [ -4504.4834] [ 648] [depth= 2] . ( 70 sec) [ -4494.0203] [ 645] [depth= 5] . ( 70 sec) [ -4493.9133] [ 646] [depth= 1] . ( 70 sec) [ -4493.5419] [ 643] [depth= 4] . ( 70 sec) [ -4492.5401] [ 643] [depth= 1] . ( 71 sec) [ -4492.0982] [ 643] [depth= 1] . ( 71 sec) [ -4491.8533] [ 643] [depth= 1] . ( 71 sec) [ -4491.6218] [ 643] [depth= 1] . ( 71 sec) [ -4490.2200] [ 643] [depth= 1] . ( 81 sec) [ -4487.3781] [ 644] [depth= 1] . ( 82 sec) [ -4485.5060] [ 643] [depth= 2] . ( 84 sec) [ -4485.3798] [ 643] [depth= 1] . ( 87 sec) [ -4483.1302] [ 643] [depth= 1] . ( 88 sec) [ -4483.0009] [ 643] [depth= 1] . ( 89 sec) [ -4482.7074] [ 643] [depth= 1] . ( 93 sec) [ -4473.1385] [Branch lengths ] . ( 93 sec) [ -4472.7653] [Alpha ][ 0.657460] . ( 94 sec) [ -4469.6521] [ 645] [depth= 2] . ( 100 sec) [ -4468.8713] [ 647] [depth= 1] . ( 100 sec) [ -4467.9178] [ 648] [depth= 7] . ( 101 sec) [ -4466.7216] [ 648] [depth= 6] . ( 101 sec) [ -4464.9578] [ 647] [depth= 1] . ( 138 sec) [ -4463.3848] [Branch lengths ] . ( 138 sec) [ -4463.3839] [Alpha ][ 0.660589] . ( 143 sec) [ -4462.6943] [ 648] [depth= 6] . ( 146 sec) [ -4461.7266] [ 648] [depth= 7] . ( 151 sec) [ -4461.0059] [ 648] [depth= 1] . ( 185 sec) [ -4460.4822] [Branch lengths ] . ( 185 sec) [ -4460.4765] [Alpha ][ 0.652976] . ( 239 sec) [ -4460.4577] [Branch lengths ] . ( 239 sec) [ -4460.4577] [Topology ] . ( 240 sec) [ -4460.4567] [Topology ] . ( 241 sec) [ -4460.4567] [Alpha ][ 0.653629] . ( 241 sec) [ -4460.4567] [Topology ] . ( 242 sec) [ -4460.4564] [Topology ] . ( 242 sec) [ -4460.4564] [Alpha ][ 0.653629] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -4474.488419 . Log likelihood obtained after SPR moves : -4460.456367 . Log likelihood of the current tree: -4460.456367. . Printing the most likely tree in file 'proteic_M1372_23x394_2003.phy_phyml_tree.txt'... . Best log likelihood : -4459.148928 . Time used 0h4m13s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1098.86user 0.00system 18:21.79elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps