.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1373_23x392_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... . 206 patterns found. (out of a total of 392 sites) . 200 sites without polymorphism (51.02%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 11Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -5777.5346] [Alpha ][ 0.500960] . ( 0 sec) [ -4907.4349] [ 588] [depth= 3] . ( 0 sec) [ -4894.6370] [ 586] [depth= 2] . ( 1 sec) [ -4884.1633] [ 586] [depth= 1] . ( 1 sec) [ -4872.0312] [ 586] [depth= 1] . ( 1 sec) [ -4400.2240] [ 586] [depth= 1] . ( 1 sec) [ -4399.0634] [ 586] [depth= 2] . ( 1 sec) [ -4397.6186] [ 586] [depth= 2] . ( 2 sec) [ -4397.5819] [ 586] [depth= 1] . ( 2 sec) [ -4391.1450] [ 586] [depth= 1] . ( 2 sec) [ -4259.2436] [ 585] [depth= 4] . ( 2 sec) [ -4241.9819] [ 585] [depth= 5] . ( 2 sec) [ -4233.9313] [ 584] [depth= 2] . ( 3 sec) [ -4210.5756] [ 582] [depth= 5] . ( 3 sec) [ -4207.0595] [ 583] [depth= 1] . ( 3 sec) [ -4206.5955] [ 582] [depth= 4] . ( 3 sec) [ -4172.4610] [ 577] [depth= 1] . ( 3 sec) [ -4082.2518] [ 573] [depth= 5] . ( 4 sec) [ -3949.6249] [ 548] [depth= 1] . ( 4 sec) [ -3838.2506] [ 546] [depth= 6] . ( 4 sec) [ -3834.7686] [ 544] [depth= 3] . ( 4 sec) [ -3834.3101] [ 545] [depth= 1] . ( 4 sec) [ -3834.1128] [ 545] [depth= 3] . ( 4 sec) [ -3833.7508] [ 545] [depth= 1] . ( 5 sec) [ -3813.6812] [ 541] [depth= 6] . ( 5 sec) [ -3784.6832] [ 542] [depth= 1] . ( 5 sec) [ -3781.8227] [ 541] [depth= 4] . ( 5 sec) [ -3767.3625] [ 513] [depth= 2] . ( 5 sec) [ -3767.0996] [ 511] [depth= 5] . ( 6 sec) [ -3766.9169] [ 511] [depth= 2] . ( 6 sec) [ -3730.4200] [ 511] [depth= 2] . ( 6 sec) [ -3718.4203] [ 498] [depth= 10] . ( 6 sec) [ -3665.7683] [ 484] [depth= 10] . ( 6 sec) [ -3654.4072] [ 484] [depth= 3] . ( 7 sec) [ -3637.9026] [ 479] [depth= 2] . ( 7 sec) [ -3634.8044] [ 480] [depth= 1] . ( 7 sec) [ -3634.4579] [ 476] [depth= 3] . ( 7 sec) [ -3630.2924] [ 475] [depth= 1] . ( 7 sec) [ -3626.8486] [ 474] [depth= 4] . ( 10 sec) [ -3605.8101] [ 473] [depth= 1] . ( 13 sec) [ -3588.9883] [ 469] [depth= 2] . ( 14 sec) [ -3588.7806] [ 469] [depth= 2] . ( 14 sec) [ -3588.7507] [ 468] [depth= 2] . ( 17 sec) [ -3587.3701] [ 468] [depth= 2] . ( 17 sec) [ -3587.0806] [ 467] [depth= 1] . ( 17 sec) [ -3561.7445] [ 457] [depth= 2] . ( 17 sec) [ -3552.5090] [ 459] [depth= 1] . ( 23 sec) [ -3552.4971] [ 459] [depth= 1] . ( 23 sec) [ -3552.0743] [ 459] [depth= 1] . ( 23 sec) [ -3549.0951] [ 454] [depth= 7] . ( 24 sec) [ -3542.6508] [Branch lengths ] . ( 24 sec) [ -3542.6386] [Alpha ][ 0.511009] . ( 29 sec) [ -3535.9722] [ 453] [depth= 1] . ( 30 sec) [ -3535.5947] [ 453] [depth= 1] . ( 30 sec) [ -3534.9706] [ 453] [depth= 1] . ( 37 sec) [ -3534.4064] [ 454] [depth= 9] . ( 41 sec) [ -3534.3888] [ 454] [depth= 2] . ( 44 sec) [ -3534.3748] [ 454] [depth= 1] . ( 85 sec) [ -3534.3373] [ 454] [depth= 1] . ( 90 sec) [ -3533.4521] [ 456] [depth= 2] . ( 90 sec) [ -3532.6635] [Branch lengths ] . ( 91 sec) [ -3532.6635] [Alpha ][ 0.510099] . ( 176 sec) [ -3532.6244] [Branch lengths ] . ( 176 sec) [ -3532.6244] [Topology ] . ( 177 sec) [ -3532.6239] [Topology ] . ( 178 sec) [ -3532.6239] [Alpha ][ 0.509589] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3532.623861. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -6803.5438] [Alpha ][ 0.500960] . ( 0 sec) [ -6775.2303] [ 573] [depth= 3] . ( 1 sec) [ -6764.8673] [ 575] [depth= 1] . ( 1 sec) [ -6735.2764] [ 573] [depth= 4] . ( 1 sec) [ -6607.7987] [ 573] [depth= 4] . ( 1 sec) [ -6595.0058] [ 567] [depth= 1] . ( 1 sec) [ -6549.2223] [ 566] [depth= 3] . ( 1 sec) [ -6545.5947] [ 563] [depth= 2] . ( 2 sec) [ -6539.7658] [ 562] [depth= 5] . ( 2 sec) [ -6539.3872] [ 562] [depth= 2] . ( 2 sec) [ -6539.0759] [ 562] [depth= 1] . ( 2 sec) [ -6530.4668] [ 561] [depth= 5] . ( 2 sec) [ -6449.3397] [ 562] [depth= 1] . ( 3 sec) [ -6424.7261] [ 561] [depth= 3] . ( 3 sec) [ -6412.9571] [ 561] [depth= 1] . ( 3 sec) [ -6405.9730] [ 560] [depth= 3] . ( 3 sec) [ -6399.7855] [ 559] [depth= 1] . ( 3 sec) [ -6398.1451] [ 554] [depth= 5] . ( 3 sec) [ -6397.9286] [ 550] [depth= 5] . ( 4 sec) [ -6397.7813] [ 550] [depth= 2] . ( 4 sec) [ -6395.7455] [ 549] [depth= 4] . ( 5 sec) [ -6388.2428] [ 548] [depth= 2] . ( 5 sec) [ -6386.9685] [ 547] [depth= 3] . ( 5 sec) [ -6336.1358] [ 520] [depth= 11] . ( 5 sec) [ -6329.5143] [ 519] [depth= 3] . ( 5 sec) [ -6311.7124] [ 520] [depth= 2] . ( 5 sec) [ -6292.1263] [ 507] [depth= 2] . ( 6 sec) [ -6288.5509] [ 506] [depth= 3] . ( 6 sec) [ -6281.9869] [ 506] [depth= 3] . ( 7 sec) [ -6277.3629] [ 507] [depth= 1] . ( 9 sec) [ -6276.4914] [ 507] [depth= 1] . ( 9 sec) [ -6276.4807] [ 507] [depth= 2] . ( 9 sec) [ -6276.4626] [ 507] [depth= 1] . ( 12 sec) [ -6275.6000] [ 507] [depth= 1] . ( 15 sec) [ -6246.9440] [ 503] [depth= 6] . ( 15 sec) [ -6246.7097] [ 503] [depth= 2] . ( 15 sec) [ -6246.6910] [ 503] [depth= 2] . ( 19 sec) [ -6246.6793] [ 503] [depth= 1] . ( 19 sec) [ -6218.7683] [ 490] [depth= 9] . ( 19 sec) [ -3808.5615] [ 491] [depth= 1] . ( 19 sec) [ -3790.9864] [ 487] [depth= 10] . ( 19 sec) [ -3790.9643] [ 487] [depth= 1] . ( 20 sec) [ -3703.2967] [ 485] [depth= 1] . ( 23 sec) [ -3698.7484] [ 487] [depth= 1] . ( 23 sec) [ -3698.4815] [ 489] [depth= 1] . ( 24 sec) [ -3564.2158] [ 460] [depth= 7] . ( 24 sec) [ -3549.7179] [ 461] [depth= 8] . ( 24 sec) [ -3549.5399] [ 461] [depth= 1] . ( 25 sec) [ -3545.7203] [Branch lengths ] . ( 25 sec) [ -3545.7185] [Alpha ][ 0.504753] . ( 44 sec) [ -3545.2057] [ 461] [depth= 9] . ( 47 sec) [ -3543.6531] [ 461] [depth= 3] . ( 53 sec) [ -3542.7402] [ 458] [depth= 7] . ( 53 sec) [ -3542.5237] [ 458] [depth= 2] . ( 53 sec) [ -3541.2519] [ 457] [depth= 1] . ( 68 sec) [ -3539.2385] [ 457] [depth= 4] . ( 95 sec) [ -3539.2002] [ 457] [depth= 1] . ( 95 sec) [ -3538.9461] [Branch lengths ] . ( 95 sec) [ -3538.9430] [Alpha ][ 0.509808] . ( 111 sec) [ -3536.8007] [ 457] [depth= 8] . ( 177 sec) [ -3536.7480] [Branch lengths ] . ( 177 sec) [ -3536.7479] [Alpha ][ 0.509298] . ( 263 sec) [ -3536.7471] [Branch lengths ] . ( 263 sec) [ -3536.7471] [Topology ] . ( 264 sec) [ -3536.7471] [Topology ] . ( 264 sec) [ -3536.7471] [Alpha ][ 0.509298] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3536.747055. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -5809.5665] [Alpha ][ 0.500960] . ( 0 sec) [ -5754.6544] [ 581] [depth= 3] . ( 1 sec) [ -5720.8901] [ 580] [depth= 2] . ( 1 sec) [ -5685.4319] [ 579] [depth= 2] . ( 1 sec) [ -5646.5308] [ 576] [depth= 5] . ( 1 sec) [ -5346.8629] [ 551] [depth= 2] . ( 1 sec) [ -5152.8090] [ 550] [depth= 3] . ( 1 sec) [ -5136.8537] [ 545] [depth= 2] . ( 2 sec) [ -4983.3566] [ 541] [depth= 4] . ( 2 sec) [ -4877.1600] [ 540] [depth= 2] . ( 2 sec) [ -4773.0758] [ 540] [depth= 5] . ( 2 sec) [ -4686.3669] [ 517] [depth= 3] . ( 2 sec) [ -4622.8764] [ 515] [depth= 2] . ( 3 sec) [ -4619.5856] [ 515] [depth= 1] . ( 3 sec) [ -4595.0524] [ 514] [depth= 3] . ( 3 sec) [ -4594.0883] [ 514] [depth= 5] . ( 3 sec) [ -4587.2935] [ 513] [depth= 5] . ( 3 sec) [ -4556.4181] [ 486] [depth= 2] . ( 3 sec) [ -4484.4809] [ 480] [depth= 4] . ( 4 sec) [ -4464.4463] [ 480] [depth= 1] . ( 4 sec) [ -4367.7843] [ 474] [depth= 2] . ( 4 sec) [ -3986.3906] [ 468] [depth= 8] . ( 4 sec) [ -3922.3086] [ 477] [depth= 2] . ( 4 sec) [ -3898.1442] [ 477] [depth= 1] . ( 5 sec) [ -3892.7024] [ 476] [depth= 2] . ( 5 sec) [ -3884.7290] [ 475] [depth= 3] . ( 5 sec) [ -3884.0569] [ 475] [depth= 1] . ( 5 sec) [ -3884.0423] [ 475] [depth= 2] . ( 5 sec) [ -3883.9005] [ 475] [depth= 1] . ( 5 sec) [ -3840.5558] [ 476] [depth= 4] . ( 6 sec) [ -3827.5588] [ 475] [depth= 5] . ( 6 sec) [ -3827.1931] [ 475] [depth= 1] . ( 6 sec) [ -3826.7385] [ 473] [depth= 1] . ( 6 sec) [ -3759.2312] [ 475] [depth= 1] . ( 7 sec) [ -3758.3903] [ 474] [depth= 2] . ( 7 sec) [ -3745.3136] [ 472] [depth= 1] . ( 7 sec) [ -3725.6398] [ 462] [depth= 5] . ( 8 sec) [ -3654.0272] [ 464] [depth= 1] . ( 8 sec) [ -3621.0130] [ 465] [depth= 7] . ( 9 sec) [ -3619.9160] [ 465] [depth= 1] . ( 9 sec) [ -3619.8203] [ 465] [depth= 1] . ( 9 sec) [ -3617.3633] [ 465] [depth= 1] . ( 10 sec) [ -3611.2814] [ 463] [depth= 3] . ( 10 sec) [ -3604.9529] [ 462] [depth= 5] . ( 10 sec) [ -3604.4223] [ 462] [depth= 1] . ( 13 sec) [ -3596.1404] [ 460] [depth= 3] . ( 13 sec) [ -3566.5940] [ 455] [depth= 3] . ( 22 sec) [ -3539.5791] [Branch lengths ] . ( 22 sec) [ -3539.5531] [Alpha ][ 0.514930] . ( 28 sec) [ -3538.9744] [ 455] [depth= 1] . ( 29 sec) [ -3537.9355] [ 455] [depth= 4] . ( 30 sec) [ -3537.9144] [ 455] [depth= 2] . ( 42 sec) [ -3537.7742] [ 453] [depth= 7] . ( 56 sec) [ -3537.7502] [ 453] [depth= 1] . ( 57 sec) [ -3535.4503] [ 453] [depth= 2] . ( 87 sec) [ -3534.4148] [Branch lengths ] . ( 88 sec) [ -3534.4140] [Alpha ][ 0.517509] . ( 113 sec) [ -3533.2294] [ 455] [depth= 6] . ( 120 sec) [ -3533.2157] [ 455] [depth= 2] . ( 165 sec) [ -3533.0932] [Branch lengths ] . ( 166 sec) [ -3533.0899] [Alpha ][ 0.512516] . ( 249 sec) [ -3533.0814] [Branch lengths ] . ( 249 sec) [ -3533.0814] [Topology ] . ( 250 sec) [ -3533.0808] [Topology ] . ( 250 sec) [ -3533.0807] [Alpha ][ 0.511636] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3533.080680. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -7415.1810] [Alpha ][ 0.500960] . ( 0 sec) [ -6824.9421] [ 583] [depth= 2] . ( 0 sec) [ -6808.1659] [ 581] [depth= 7] . ( 1 sec) [ -6723.5056] [ 578] [depth= 5] . ( 1 sec) [ -6721.9213] [ 576] [depth= 1] . ( 1 sec) [ -6715.0134] [ 576] [depth= 1] . ( 1 sec) [ -5343.7125] [ 569] [depth= 1] . ( 1 sec) [ -5121.5316] [ 566] [depth= 2] . ( 1 sec) [ -4826.4613] [ 564] [depth= 1] . ( 2 sec) [ -4809.9670] [ 561] [depth= 4] . ( 2 sec) [ -4694.0372] [ 560] [depth= 2] . ( 2 sec) [ -4692.1240] [ 560] [depth= 1] . ( 2 sec) [ -4669.0902] [ 559] [depth= 5] . ( 2 sec) [ -4666.5592] [ 552] [depth= 1] . ( 3 sec) [ -4656.3816] [ 549] [depth= 5] . ( 3 sec) [ -4636.1220] [ 547] [depth= 1] . ( 3 sec) [ -4578.5071] [ 536] [depth= 8] . ( 3 sec) [ -4572.7103] [ 535] [depth= 4] . ( 3 sec) [ -4530.4083] [ 535] [depth= 2] . ( 3 sec) [ -4529.1349] [ 535] [depth= 2] . ( 4 sec) [ -4522.5568] [ 535] [depth= 1] . ( 4 sec) [ -4513.9715] [ 534] [depth= 5] . ( 4 sec) [ -4513.6753] [ 534] [depth= 2] . ( 4 sec) [ -4508.3564] [ 532] [depth= 5] . ( 6 sec) [ -4479.4185] [ 534] [depth= 3] . ( 6 sec) [ -4464.0546] [ 532] [depth= 3] . ( 7 sec) [ -4413.0791] [ 515] [depth= 10] . ( 7 sec) [ -4403.1797] [ 515] [depth= 2] . ( 7 sec) [ -4278.7146] [ 516] [depth= 1] . ( 7 sec) [ -4104.8537] [ 497] [depth= 3] . ( 7 sec) [ -4068.5075] [ 495] [depth= 9] . ( 10 sec) [ -4059.0121] [ 487] [depth= 1] . ( 10 sec) [ -3837.1790] [ 489] [depth= 4] . ( 10 sec) [ -3836.4352] [ 489] [depth= 2] . ( 10 sec) [ -3831.6018] [ 488] [depth= 1] . ( 13 sec) [ -3830.3909] [ 488] [depth= 2] . ( 13 sec) [ -3755.1266] [ 492] [depth= 1] . ( 14 sec) [ -3747.1890] [ 493] [depth= 1] . ( 14 sec) [ -3743.0998] [ 492] [depth= 1] . ( 14 sec) [ -3742.8336] [ 492] [depth= 1] . ( 15 sec) [ -3667.8532] [ 479] [depth= 2] . ( 15 sec) [ -3600.5635] [ 466] [depth= 1] . ( 15 sec) [ -3598.6894] [ 466] [depth= 1] . ( 15 sec) [ -3582.9928] [ 464] [depth= 1] . ( 15 sec) [ -3578.5495] [ 466] [depth= 1] . ( 16 sec) [ -3574.6432] [ 465] [depth= 1] . ( 16 sec) [ -3574.6058] [ 464] [depth= 2] . ( 16 sec) [ -3574.2181] [ 461] [depth= 6] . ( 16 sec) [ -3552.6476] [ 457] [depth= 1] . ( 16 sec) [ -3552.5202] [ 457] [depth= 1] . ( 17 sec) [ -3552.3844] [ 457] [depth= 1] . ( 17 sec) [ -3551.7477] [ 456] [depth= 1] . ( 17 sec) [ -3546.8107] [Branch lengths ] . ( 18 sec) [ -3546.7963] [Alpha ][ 0.511432] . ( 18 sec) [ -3541.6791] [ 455] [depth= 3] . ( 22 sec) [ -3538.8620] [ 455] [depth= 1] . ( 32 sec) [ -3537.8000] [ 456] [depth= 3] . ( 60 sec) [ -3533.5232] [ 455] [depth= 2] . ( 87 sec) [ -3533.4362] [ 455] [depth= 2] . ( 90 sec) [ -3533.0920] [Branch lengths ] . ( 91 sec) [ -3533.0919] [Alpha ][ 0.511943] . ( 173 sec) [ -3533.0811] [Branch lengths ] . ( 173 sec) [ -3533.0811] [Topology ] . ( 174 sec) [ -3533.0806] [Topology ] . ( 174 sec) [ -3533.0806] [Alpha ][ 0.511943] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3533.080625. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -5443.4617] [Alpha ][ 0.500960] . ( 1 sec) [ -5360.6915] [ 582] [depth= 6] . ( 1 sec) [ -5320.6545] [ 578] [depth= 7] . ( 1 sec) [ -5099.6819] [ 575] [depth= 3] . ( 1 sec) [ -5081.3828] [ 574] [depth= 1] . ( 1 sec) [ -5041.6680] [ 572] [depth= 2] . ( 2 sec) [ -5000.4804] [ 570] [depth= 2] . ( 2 sec) [ -4874.8193] [ 570] [depth= 3] . ( 2 sec) [ -4773.3488] [ 568] [depth= 7] . ( 2 sec) [ -4705.1672] [ 568] [depth= 1] . ( 2 sec) [ -4622.1875] [ 561] [depth= 11] . ( 2 sec) [ -4544.9987] [ 561] [depth= 1] . ( 3 sec) [ -4512.0716] [ 560] [depth= 3] . ( 3 sec) [ -4512.0455] [ 560] [depth= 2] . ( 3 sec) [ -4511.9837] [ 560] [depth= 1] . ( 3 sec) [ -4458.9950] [ 559] [depth= 3] . ( 3 sec) [ -4307.0387] [ 531] [depth= 5] . ( 3 sec) [ -4306.1059] [ 531] [depth= 1] . ( 4 sec) [ -4305.8522] [ 531] [depth= 1] . ( 4 sec) [ -4300.8859] [ 530] [depth= 1] . ( 4 sec) [ -4300.5144] [ 536] [depth= 1] . ( 4 sec) [ -4298.5871] [ 536] [depth= 1] . ( 5 sec) [ -4268.2300] [ 530] [depth= 1] . ( 6 sec) [ -4263.1716] [ 529] [depth= 1] . ( 6 sec) [ -3960.2474] [ 529] [depth= 7] . ( 6 sec) [ -3959.3413] [ 528] [depth= 2] . ( 6 sec) [ -3955.6099] [ 527] [depth= 1] . ( 7 sec) [ -3953.5262] [ 529] [depth= 3] . ( 7 sec) [ -3912.5384] [ 501] [depth= 3] . ( 7 sec) [ -3845.1800] [ 474] [depth= 2] . ( 7 sec) [ -3837.4845] [ 473] [depth= 3] . ( 8 sec) [ -3822.1324] [ 471] [depth= 5] . ( 8 sec) [ -3814.7335] [ 470] [depth= 1] . ( 8 sec) [ -3767.2371] [ 468] [depth= 3] . ( 8 sec) [ -3766.9426] [ 468] [depth= 1] . ( 8 sec) [ -3766.0459] [ 468] [depth= 2] . ( 9 sec) [ -3765.8568] [ 469] [depth= 1] . ( 9 sec) [ -3669.9292] [ 470] [depth= 2] . ( 9 sec) [ -3663.7370] [ 468] [depth= 2] . ( 10 sec) [ -3645.6269] [ 458] [depth= 4] . ( 10 sec) [ -3645.5036] [ 458] [depth= 1] . ( 10 sec) [ -3645.4751] [ 456] [depth= 2] . ( 10 sec) [ -3641.2117] [ 454] [depth= 1] . ( 14 sec) [ -3603.3691] [ 469] [depth= 1] . ( 14 sec) [ -3573.8335] [ 454] [depth= 1] . ( 14 sec) [ -3571.7102] [ 453] [depth= 1] . ( 15 sec) [ -3570.9150] [ 453] [depth= 1] . ( 15 sec) [ -3570.8801] [ 453] [depth= 1] . ( 18 sec) [ -3561.6187] [ 455] [depth= 1] . ( 18 sec) [ -3558.1243] [ 455] [depth= 3] . ( 18 sec) [ -3558.0852] [ 455] [depth= 2] . ( 19 sec) [ -3547.1233] [Branch lengths ] . ( 19 sec) [ -3547.1169] [Alpha ][ 0.508315] . ( 25 sec) [ -3547.1033] [ 455] [depth= 1] . ( 25 sec) [ -3547.0885] [ 455] [depth= 1] . ( 28 sec) [ -3543.1992] [ 454] [depth= 2] . ( 56 sec) [ -3541.4233] [ 456] [depth= 8] . ( 58 sec) [ -3540.7639] [ 454] [depth= 1] . ( 61 sec) [ -3540.2437] [ 453] [depth= 1] . ( 61 sec) [ -3540.1475] [ 453] [depth= 1] . ( 62 sec) [ -3540.0762] [ 453] [depth= 1] . ( 66 sec) [ -3538.8027] [ 455] [depth= 7] . ( 72 sec) [ -3538.7661] [ 455] [depth= 1] . ( 81 sec) [ -3534.0188] [Branch lengths ] . ( 81 sec) [ -3534.0184] [Alpha ][ 0.510281] . ( 164 sec) [ -3533.0895] [Branch lengths ] . ( 164 sec) [ -3533.0895] [Topology ] . ( 165 sec) [ -3533.0834] [Topology ] . ( 166 sec) [ -3533.0818] [Topology ] . ( 167 sec) [ -3533.0811] [Topology ] . ( 167 sec) [ -3533.0810] [Alpha ][ 0.511425] . ( 167 sec) [ -3533.0810] [Topology ] . ( 168 sec) [ -3533.0806] [Topology ] . ( 169 sec) [ -3533.0806] [Alpha ][ 0.511425] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3533.080648. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -3571.4717] [Alpha ][ 0.500960] . ( 1 sec) [ -3571.4717] [Topology ] . ( 2 sec) [ -3544.9622] [Topology ] . ( 3 sec) [ -3540.6937] [Topology ] . ( 4 sec) [ -3539.9495] [Topology ] . ( 5 sec) [ -3539.6826] [Topology ] . ( 6 sec) [ -3539.5806] [Topology ] . ( 7 sec) [ -3539.5407] [Topology ] . ( 8 sec) [ -3539.5243] [Topology ] . ( 9 sec) [ -3539.5174] [Topology ] . Checking for NNIs, optimizing five branches... . ( 17 sec) [ -3539.5007] [Alpha ][ 0.512319] . ( 17 sec) [ -3539.5007] [Topology ] . ( 18 sec) [ -3539.4969] [Topology ] . ( 19 sec) [ -3539.4953] [Topology ] . ( 20 sec) [ -3539.4947] [Topology ] . Checking for NNIs, optimizing five branches... . ( 27 sec) [ -3539.4946] [Alpha ][ 0.512900] . ( 27 sec) [ -3539.4946] [Topology ] . ( 28 sec) [ -3539.4943] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 43 sec) [ -3571.4717] [Alpha ][ 0.500960] . ( 44 sec) [ -3555.7984] [ 459] [depth= 1] . ( 46 sec) [ -3555.0067] [ 455] [depth= 8] . ( 49 sec) [ -3548.9171] [ 456] [depth= 1] . ( 50 sec) [ -3547.0823] [ 456] [depth= 1] . ( 51 sec) [ -3543.5837] [ 455] [depth= 2] . ( 65 sec) [ -3542.9287] [ 455] [depth= 1] . ( 70 sec) [ -3542.7076] [ 455] [depth= 1] . ( 70 sec) [ -3542.6975] [ 455] [depth= 1] . ( 70 sec) [ -3542.6463] [ 455] [depth= 1] . ( 77 sec) [ -3542.3849] [ 455] [depth= 1] . ( 91 sec) [ -3542.2916] [ 455] [depth= 1] . ( 99 sec) [ -3535.7494] [Branch lengths ] . ( 99 sec) [ -3535.7440] [Alpha ][ 0.507815] . ( 114 sec) [ -3535.1492] [ 455] [depth= 5] . ( 126 sec) [ -3533.5888] [ 458] [depth= 6] . ( 151 sec) [ -3533.5785] [ 458] [depth= 1] . ( 157 sec) [ -3533.5681] [ 458] [depth= 2] . ( 175 sec) [ -3533.1132] [Branch lengths ] . ( 175 sec) [ -3533.1122] [Alpha ][ 0.504795] . ( 267 sec) [ -3533.0609] [Branch lengths ] . ( 267 sec) [ -3533.0609] [Topology ] . ( 268 sec) [ -3533.0579] [Topology ] . ( 269 sec) [ -3533.0570] [Topology ] . ( 269 sec) [ -3533.0568] [Alpha ][ 0.506275] . ( 270 sec) [ -3533.0568] [Topology ] . ( 271 sec) [ -3533.0564] [Topology ] . ( 271 sec) [ -3533.0564] [Alpha ][ 0.506275] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -3539.494307 . Log likelihood obtained after SPR moves : -3533.056383 . Log likelihood of the current tree: -3533.056383. . Printing the most likely tree in file 'proteic_M1373_23x392_2003.phy_phyml_tree.txt'... . Best log likelihood : -3532.623861 . Time used 0h4m38s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1349.94user 0.00system 22:33.02elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps