.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data49.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . 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... . 248 patterns found. (out of a total of 500 sites) . 240 sites without polymorphism (48.00%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 5Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -7840.0548] [GTR parameters ] . ( 1 sec) [ -7692.7141] [Alpha ][ 0.500960] . ( 1 sec) [ -7555.1794] [ 1197] [depth= 8] . ( 1 sec) [ -7492.2809] [ 1195] [depth= 6] . ( 1 sec) [ -7402.4404] [ 1190] [depth= 4] . ( 1 sec) [ -7351.0071] [ 1190] [depth= 5] . ( 1 sec) [ -7155.2170] [ 1174] [depth= 6] . ( 1 sec) [ -7149.7561] [ 1174] [depth= 1] . ( 1 sec) [ -7133.2555] [ 1171] [depth= 11] . ( 1 sec) [ -7071.0169] [ 1176] [depth= 1] . ( 1 sec) [ -7068.7465] [ 1176] [depth= 1] . ( 1 sec) [ -7046.0667] [ 1173] [depth= 2] . ( 2 sec) [ -7008.7752] [ 1187] [depth= 2] . ( 2 sec) [ -6812.6824] [ 1136] [depth= 12] . ( 2 sec) [ -6783.5442] [ 1130] [depth= 15] . ( 2 sec) [ -6709.0538] [ 1117] [depth= 15] . ( 2 sec) [ -6700.0159] [ 1117] [depth= 1] . ( 2 sec) [ -6679.0571] [ 1117] [depth= 3] . ( 2 sec) [ -6652.1041] [ 1117] [depth= 3] . ( 2 sec) [ -6651.9180] [ 1117] [depth= 1] . ( 2 sec) [ -6550.2522] [ 1081] [depth= 2] . ( 2 sec) [ -6456.7696] [ 1081] [depth= 2] . ( 2 sec) [ -6382.6758] [ 1069] [depth= 9] . ( 2 sec) [ -6260.0756] [ 1021] [depth= 17] . ( 2 sec) [ -6028.3492] [ 1020] [depth= 1] . ( 2 sec) [ -5947.1769] [ 1016] [depth= 17] . ( 2 sec) [ -5906.9340] [ 985] [depth= 10] . ( 2 sec) [ -5890.1370] [ 990] [depth= 13] . ( 2 sec) [ -5838.2137] [ 990] [depth= 3] . ( 2 sec) [ -5824.6942] [ 990] [depth= 16] . ( 2 sec) [ -5780.2582] [ 990] [depth= 11] . ( 2 sec) [ -5672.7158] [ 969] [depth= 10] . ( 2 sec) [ -5574.1739] [ 968] [depth= 7] . ( 2 sec) [ -5561.8087] [ 971] [depth= 1] . ( 2 sec) [ -5553.7326] [ 969] [depth= 2] . ( 2 sec) [ -5350.6095] [ 948] [depth= 12] . ( 2 sec) [ -5133.7249] [ 884] [depth= 6] . ( 3 sec) [ -5021.2288] [ 854] [depth= 12] . ( 3 sec) [ -4803.4339] [ 825] [depth= 1] . ( 3 sec) [ -4658.2728] [ 787] [depth= 9] . ( 3 sec) [ -4556.3248] [ 757] [depth= 10] . ( 3 sec) [ -4503.0599] [ 752] [depth= 6] . ( 3 sec) [ -4477.7466] [ 738] [depth= 10] . ( 3 sec) [ -4433.7536] [ 724] [depth= 1] . ( 3 sec) [ -4431.8881] [ 721] [depth= 4] . ( 3 sec) [ -4397.3170] [ 704] [depth= 6] . ( 3 sec) [ -4319.5796] [ 696] [depth= 2] . ( 3 sec) [ -4237.8319] [ 689] [depth= 5] . ( 3 sec) [ -4235.1020] [ 689] [depth= 1] . ( 3 sec) [ -4235.0178] [ 671] [depth= 3] . ( 3 sec) [ -4225.0815] [ 671] [depth= 1] . ( 3 sec) [ -4205.0523] [ 671] [depth= 5] . ( 3 sec) [ -4201.6723] [ 670] [depth= 1] . ( 3 sec) [ -4153.3360] [ 644] [depth= 1] . ( 4 sec) [ -4148.2335] [ 644] [depth= 1] . ( 4 sec) [ -4117.5158] [ 626] [depth= 1] . ( 4 sec) [ -4116.2646] [ 626] [depth= 2] . ( 4 sec) [ -4115.9851] [ 626] [depth= 1] . ( 4 sec) [ -4113.7372] [ 626] [depth= 2] . ( 4 sec) [ -4070.9454] [ 618] [depth= 3] . ( 4 sec) [ -4063.7189] [ 619] [depth= 9] . ( 4 sec) [ -4063.2794] [ 619] [depth= 1] . ( 4 sec) [ -4060.3085] [ 619] [depth= 1] . ( 4 sec) [ -4060.1642] [ 619] [depth= 3] . ( 4 sec) [ -4059.8780] [ 619] [depth= 2] . ( 4 sec) [ -4058.2749] [ 621] [depth= 2] . ( 4 sec) [ -4048.2979] [ 620] [depth= 3] . ( 4 sec) [ -3996.2138] [ 614] [depth= 6] . ( 4 sec) [ -3939.8388] [ 598] [depth= 2] . ( 4 sec) [ -3932.2730] [ 597] [depth= 3] . ( 4 sec) [ -3928.6058] [ 595] [depth= 1] . ( 5 sec) [ -3891.4115] [ 591] [depth= 1] . ( 5 sec) [ -3884.1687] [ 590] [depth= 9] . ( 5 sec) [ -3824.9541] [ 574] [depth= 8] . ( 5 sec) [ -3816.6481] [ 570] [depth= 7] . ( 5 sec) [ -3803.2483] [ 569] [depth= 4] . ( 5 sec) [ -3795.4663] [ 572] [depth= 1] . ( 5 sec) [ -3795.3493] [ 572] [depth= 1] . ( 5 sec) [ -3777.3321] [ 564] [depth= 1] . ( 5 sec) [ -3776.6515] [ 562] [depth= 1] . ( 5 sec) [ -3770.4400] [ 561] [depth= 2] . ( 6 sec) [ -3739.9573] [Branch lengths ] . ( 6 sec) [ -3738.6010] [GTR parameters ] . ( 6 sec) [ -3733.3776] [Alpha ][ 0.748383] . ( 6 sec) [ -3681.1416] [ 550] [depth= 3] . ( 6 sec) [ -3680.6237] [ 551] [depth= 1] . ( 7 sec) [ -3633.0172] [ 529] [depth= 1] . ( 7 sec) [ -3608.3310] [ 522] [depth= 3] . ( 7 sec) [ -3596.9268] [ 518] [depth= 2] . ( 7 sec) [ -3573.8347] [ 511] [depth= 1] . ( 7 sec) [ -3573.7672] [ 507] [depth= 3] . ( 7 sec) [ -3570.5195] [ 506] [depth= 3] . ( 7 sec) [ -3558.2935] [ 508] [depth= 1] . ( 7 sec) [ -3521.8725] [ 494] [depth= 1] . ( 7 sec) [ -3521.8532] [ 494] [depth= 1] . ( 7 sec) [ -3514.7569] [ 491] [depth= 1] . ( 8 sec) [ -3512.8782] [ 492] [depth= 2] . ( 8 sec) [ -3510.8083] [ 490] [depth= 1] . ( 8 sec) [ -3504.4637] [ 486] [depth= 1] . ( 8 sec) [ -3504.4150] [ 486] [depth= 2] . ( 8 sec) [ -3504.3991] [ 486] [depth= 2] . ( 8 sec) [ -3503.6793] [ 486] [depth= 1] . ( 9 sec) [ -3496.4049] [Branch lengths ] . ( 10 sec) [ -3495.7644] [GTR parameters ] . ( 10 sec) [ -3492.7607] [Alpha ][ 1.110265] . ( 13 sec) [ -3490.2227] [Branch lengths ] . ( 13 sec) [ -3490.1181] [ 486] [depth= 1] . ( 27 sec) [ -3490.0535] [ 486] [depth= 1] . ( 35 sec) [ -3485.5159] [Branch lengths ] . ( 36 sec) [ -3485.4933] [GTR parameters ] . ( 36 sec) [ -3485.4905] [Alpha ][ 1.125430] . ( 36 sec) [ -3485.1779] [ 486] [depth= 1] . ( 59 sec) [ -3484.7929] [Branch lengths ] . ( 60 sec) [ -3484.7929] [GTR parameters ] . ( 60 sec) [ -3484.7929] [Alpha ][ 1.126556] . ( 60 sec) [ -3484.7929] [Topology ] . ( 61 sec) [ -3484.7926] [Topology ] . ( 61 sec) [ -3484.7926] [GTR parameters ] . ( 61 sec) [ -3484.7926] [Alpha ][ 1.126556] . Checking for NNIs, optimizing five branches... . ( 66 sec) [ -3484.7921] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3484.792069. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -9565.0485] [GTR parameters ] . ( 1 sec) [ -9373.6157] [Alpha ][ 0.500960] . ( 1 sec) [ -9225.7529] [ 1300] [depth= 3] . ( 1 sec) [ -8921.8934] [ 1271] [depth= 3] . ( 1 sec) [ -8918.2028] [ 1265] [depth= 3] . ( 1 sec) [ -8823.6788] [ 1265] [depth= 2] . ( 1 sec) [ -8724.5802] [ 1248] [depth= 5] . ( 1 sec) [ -8635.3464] [ 1244] [depth= 7] . ( 2 sec) [ -8551.7530] [ 1235] [depth= 3] . ( 2 sec) [ -8514.4541] [ 1221] [depth= 1] . ( 2 sec) [ -8378.9152] [ 1198] [depth= 2] . ( 2 sec) [ -8351.6498] [ 1197] [depth= 2] . ( 2 sec) [ -8338.5760] [ 1197] [depth= 3] . ( 2 sec) [ -8062.0772] [ 1167] [depth= 5] . ( 2 sec) [ -7873.6174] [ 1167] [depth= 6] . ( 2 sec) [ -7461.4219] [ 1113] [depth= 11] . ( 2 sec) [ -7365.8217] [ 1094] [depth= 3] . ( 2 sec) [ -7033.3439] [ 1050] [depth= 19] . ( 2 sec) [ -6809.1681] [ 1049] [depth= 3] . ( 2 sec) [ -6798.4907] [ 1051] [depth= 1] . ( 2 sec) [ -6595.0884] [ 1004] [depth= 12] . ( 3 sec) [ -6530.2138] [ 992] [depth= 7] . ( 3 sec) [ -6447.7585] [ 976] [depth= 1] . ( 3 sec) [ -6357.7778] [ 978] [depth= 9] . ( 3 sec) [ -6353.3822] [ 978] [depth= 5] . ( 3 sec) [ -6309.2552] [ 968] [depth= 1] . ( 3 sec) [ -6298.7390] [ 968] [depth= 2] . ( 3 sec) [ -6285.0342] [ 970] [depth= 2] . ( 3 sec) [ -6123.3222] [ 944] [depth= 16] . ( 3 sec) [ -5861.0073] [ 924] [depth= 7] . ( 3 sec) [ -5680.1004] [ 871] [depth= 7] . ( 3 sec) [ -5644.6998] [ 869] [depth= 13] . ( 3 sec) [ -5576.4839] [ 877] [depth= 8] . ( 3 sec) [ -5468.2374] [ 863] [depth= 6] . ( 3 sec) [ -5458.2054] [ 863] [depth= 2] . ( 3 sec) [ -5443.8271] [ 862] [depth= 8] . ( 3 sec) [ -5428.9366] [ 861] [depth= 1] . ( 3 sec) [ -5311.4049] [ 850] [depth= 9] . ( 3 sec) [ -5248.2978] [ 835] [depth= 1] . ( 3 sec) [ -5116.4876] [ 828] [depth= 5] . ( 4 sec) [ -5033.2750] [ 812] [depth= 7] . ( 4 sec) [ -5030.6321] [ 811] [depth= 1] . ( 4 sec) [ -4877.8544] [ 795] [depth= 6] . ( 4 sec) [ -4866.2314] [ 794] [depth= 1] . ( 4 sec) [ -4820.5605] [ 768] [depth= 8] . ( 4 sec) [ -4807.5398] [ 769] [depth= 1] . ( 4 sec) [ -4788.0766] [ 767] [depth= 9] . ( 4 sec) [ -4764.6810] [ 764] [depth= 3] . ( 4 sec) [ -4723.0633] [ 763] [depth= 9] . ( 4 sec) [ -4635.0584] [ 731] [depth= 6] . ( 4 sec) [ -4617.7796] [ 723] [depth= 1] . ( 4 sec) [ -4597.3401] [ 721] [depth= 3] . ( 4 sec) [ -4573.2766] [ 718] [depth= 3] . ( 4 sec) [ -4553.4937] [ 718] [depth= 2] . ( 4 sec) [ -4535.1692] [ 714] [depth= 14] . ( 4 sec) [ -4474.0887] [ 691] [depth= 7] . ( 4 sec) [ -4467.1924] [ 687] [depth= 1] . ( 4 sec) [ -4449.7054] [ 683] [depth= 1] . ( 5 sec) [ -4447.9244] [ 678] [depth= 7] . ( 5 sec) [ -4392.8151] [ 671] [depth= 8] . ( 5 sec) [ -4323.2473] [ 658] [depth= 11] . ( 5 sec) [ -4323.0607] [ 659] [depth= 1] . ( 5 sec) [ -4295.8365] [ 657] [depth= 6] . ( 5 sec) [ -4268.3617] [ 642] [depth= 2] . ( 5 sec) [ -4160.7329] [ 619] [depth= 5] . ( 5 sec) [ -4067.9298] [ 607] [depth= 6] . ( 5 sec) [ -3999.1500] [ 589] [depth= 4] . ( 5 sec) [ -3999.1200] [ 589] [depth= 1] . ( 5 sec) [ -3998.2517] [ 589] [depth= 1] . ( 5 sec) [ -3996.6193] [ 588] [depth= 1] . ( 5 sec) [ -3996.0504] [ 588] [depth= 1] . ( 5 sec) [ -3968.6426] [ 588] [depth= 1] . ( 5 sec) [ -3965.4499] [ 588] [depth= 1] . ( 5 sec) [ -3965.1399] [ 589] [depth= 1] . ( 6 sec) [ -3963.1255] [ 581] [depth= 4] . ( 6 sec) [ -3949.5349] [ 576] [depth= 6] . ( 6 sec) [ -3949.1116] [ 576] [depth= 1] . ( 6 sec) [ -3880.4495] [ 558] [depth= 2] . ( 6 sec) [ -3880.2411] [ 558] [depth= 1] . ( 6 sec) [ -3879.9070] [ 559] [depth= 1] . ( 6 sec) [ -3809.8872] [ 552] [depth= 1] . ( 6 sec) [ -3798.4865] [ 550] [depth= 2] . ( 7 sec) [ -3760.8202] [Branch lengths ] . ( 7 sec) [ -3758.8382] [GTR parameters ] . ( 7 sec) [ -3755.2670] [Alpha ][ 0.685425] . ( 7 sec) [ -3652.6308] [ 531] [depth= 1] . ( 7 sec) [ -3650.8966] [ 529] [depth= 1] . ( 7 sec) [ -3638.1649] [ 525] [depth= 2] . ( 7 sec) [ -3637.0770] [ 523] [depth= 1] . ( 8 sec) [ -3632.6607] [ 523] [depth= 1] . ( 8 sec) [ -3602.9922] [ 510] [depth= 2] . ( 8 sec) [ -3602.9686] [ 510] [depth= 1] . ( 9 sec) [ -3602.8257] [ 510] [depth= 1] . ( 9 sec) [ -3593.7126] [ 506] [depth= 2] . ( 10 sec) [ -3593.6846] [ 506] [depth= 1] . ( 10 sec) [ -3593.6346] [ 506] [depth= 1] . ( 10 sec) [ -3593.1736] [ 506] [depth= 1] . ( 10 sec) [ -3582.4228] [ 502] [depth= 2] . ( 10 sec) [ -3582.3927] [ 502] [depth= 2] . ( 11 sec) [ -3582.3681] [ 502] [depth= 1] . ( 11 sec) [ -3581.8095] [ 504] [depth= 1] . ( 11 sec) [ -3523.6181] [ 488] [depth= 1] . ( 11 sec) [ -3522.2909] [ 488] [depth= 1] . ( 12 sec) [ -3516.9400] [ 486] [depth= 1] . ( 12 sec) [ -3516.1514] [ 486] [depth= 1] . ( 12 sec) [ -3494.3156] [Branch lengths ] . ( 13 sec) [ -3493.9686] [GTR parameters ] . ( 13 sec) [ -3489.2126] [Alpha ][ 1.117913] . ( 15 sec) [ -3489.2019] [ 486] [depth= 2] . ( 15 sec) [ -3488.9592] [ 486] [depth= 1] . ( 15 sec) [ -3488.9067] [ 486] [depth= 1] . ( 17 sec) [ -3484.8219] [Branch lengths ] . ( 17 sec) [ -3484.7958] [GTR parameters ] . ( 17 sec) [ -3484.7949] [Alpha ][ 1.126241] . ( 22 sec) [ -3484.7927] [Branch lengths ] . ( 42 sec) [ -3484.7927] [Branch lengths ] . ( 42 sec) [ -3484.7927] [Topology ] . ( 43 sec) [ -3484.7927] [Topology ] . ( 43 sec) [ -3484.7927] [GTR parameters ] . ( 43 sec) [ -3484.7927] [Alpha ][ 1.126241] . Checking for NNIs, optimizing five branches... . ( 47 sec) [ -3484.7924] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3484.792385. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -8538.0671] [GTR parameters ] . ( 1 sec) [ -8371.4605] [Alpha ][ 0.500960] . ( 1 sec) [ -8219.8843] [ 1275] [depth= 1] . ( 1 sec) [ -8097.5447] [ 1247] [depth= 8] . ( 1 sec) [ -8070.1241] [ 1245] [depth= 3] . ( 1 sec) [ -8026.5601] [ 1245] [depth= 2] . ( 1 sec) [ -7912.5026] [ 1231] [depth= 2] . ( 1 sec) [ -7769.8280] [ 1231] [depth= 6] . ( 1 sec) [ -7510.9512] [ 1195] [depth= 15] . ( 1 sec) [ -7495.3284] [ 1195] [depth= 3] . ( 1 sec) [ -7382.9434] [ 1171] [depth= 4] . ( 1 sec) [ -7328.2129] [ 1162] [depth= 8] . ( 1 sec) [ -7179.1474] [ 1135] [depth= 6] . ( 1 sec) [ -7123.2251] [ 1131] [depth= 13] . ( 1 sec) [ -7015.2962] [ 1111] [depth= 12] . ( 1 sec) [ -6826.0599] [ 1111] [depth= 1] . ( 1 sec) [ -6718.6294] [ 1085] [depth= 8] . ( 1 sec) [ -6708.4579] [ 1085] [depth= 3] . ( 1 sec) [ -6578.1331] [ 1070] [depth= 11] . ( 2 sec) [ -6446.7269] [ 1067] [depth= 12] . ( 2 sec) [ -6231.6622] [ 1011] [depth= 6] . ( 2 sec) [ -6189.3242] [ 995] [depth= 1] . ( 2 sec) [ -6047.0890] [ 963] [depth= 9] . ( 2 sec) [ -5866.9444] [ 897] [depth= 13] . ( 2 sec) [ -5861.4462] [ 893] [depth= 5] . ( 2 sec) [ -5860.9027] [ 893] [depth= 1] . ( 2 sec) [ -5815.4223] [ 893] [depth= 9] . ( 2 sec) [ -5804.3601] [ 884] [depth= 2] . ( 2 sec) [ -5653.8963] [ 851] [depth= 6] . ( 2 sec) [ -5456.5329] [ 846] [depth= 8] . ( 2 sec) [ -5293.3743] [ 840] [depth= 7] . ( 2 sec) [ -5272.8614] [ 840] [depth= 4] . ( 3 sec) [ -5132.7858] [ 827] [depth= 5] . ( 3 sec) [ -5090.4402] [ 810] [depth= 5] . ( 3 sec) [ -5089.5953] [ 810] [depth= 1] . ( 3 sec) [ -5037.9433] [ 793] [depth= 8] . ( 3 sec) [ -4992.5691] [ 772] [depth= 5] . ( 3 sec) [ -4924.7117] [ 754] [depth= 2] . ( 3 sec) [ -4852.8067] [ 738] [depth= 8] . ( 3 sec) [ -4848.6495] [ 738] [depth= 1] . ( 3 sec) [ -4842.0759] [ 741] [depth= 1] . ( 3 sec) [ -4812.8550] [ 734] [depth= 5] . ( 3 sec) [ -4810.2411] [ 734] [depth= 1] . ( 3 sec) [ -4807.3452] [ 736] [depth= 3] . ( 3 sec) [ -4709.0767] [ 723] [depth= 4] . ( 3 sec) [ -4691.0205] [ 723] [depth= 1] . ( 3 sec) [ -4679.5114] [ 720] [depth= 3] . ( 3 sec) [ -4672.3311] [ 720] [depth= 3] . ( 3 sec) [ -4632.0623] [ 718] [depth= 8] . ( 3 sec) [ -4583.7236] [ 705] [depth= 3] . ( 3 sec) [ -4583.2952] [ 705] [depth= 1] . ( 4 sec) [ -4577.6213] [ 705] [depth= 1] . ( 4 sec) [ -4577.3609] [ 705] [depth= 1] . ( 4 sec) [ -4566.0396] [ 704] [depth= 3] . ( 4 sec) [ -4471.5721] [ 698] [depth= 3] . ( 4 sec) [ -4349.3800] [ 661] [depth= 9] . ( 4 sec) [ -4331.5690] [ 661] [depth= 3] . ( 4 sec) [ -4316.6527] [ 659] [depth= 5] . ( 4 sec) [ -4209.2075] [ 637] [depth= 3] . ( 4 sec) [ -4209.1772] [ 637] [depth= 1] . ( 4 sec) [ -4205.6096] [ 638] [depth= 1] . ( 4 sec) [ -4050.0990] [ 600] [depth= 4] . ( 4 sec) [ -4035.3966] [ 594] [depth= 2] . ( 4 sec) [ -4032.7267] [ 593] [depth= 3] . ( 4 sec) [ -3983.5154] [ 583] [depth= 1] . ( 4 sec) [ -3936.4337] [ 584] [depth= 1] . ( 4 sec) [ -3925.6760] [ 584] [depth= 1] . ( 5 sec) [ -3878.8926] [ 573] [depth= 1] . ( 5 sec) [ -3851.2831] [ 566] [depth= 2] . ( 5 sec) [ -3845.5915] [ 563] [depth= 2] . ( 5 sec) [ -3820.8366] [ 553] [depth= 4] . ( 5 sec) [ -3779.2692] [ 542] [depth= 3] . ( 5 sec) [ -3777.2812] [ 541] [depth= 1] . ( 5 sec) [ -3707.0501] [ 521] [depth= 5] . ( 5 sec) [ -3701.7703] [ 522] [depth= 1] . ( 5 sec) [ -3701.1898] [ 522] [depth= 1] . ( 5 sec) [ -3700.0669] [ 522] [depth= 1] . ( 5 sec) [ -3691.8323] [ 520] [depth= 2] . ( 5 sec) [ -3683.4823] [ 525] [depth= 1] . ( 6 sec) [ -3682.8405] [ 525] [depth= 1] . ( 6 sec) [ -3629.3019] [Branch lengths ] . ( 6 sec) [ -3626.3649] [GTR parameters ] . ( 6 sec) [ -3617.1332] [Alpha ][ 0.895875] . ( 7 sec) [ -3609.8735] [ 525] [depth= 1] . ( 7 sec) [ -3559.2126] [ 509] [depth= 1] . ( 7 sec) [ -3556.4142] [ 509] [depth= 1] . ( 7 sec) [ -3551.5804] [ 510] [depth= 3] . ( 7 sec) [ -3551.3974] [ 511] [depth= 1] . ( 7 sec) [ -3551.3497] [ 511] [depth= 1] . ( 7 sec) [ -3547.5660] [ 511] [depth= 1] . ( 8 sec) [ -3546.9756] [ 512] [depth= 1] . ( 8 sec) [ -3544.2390] [ 510] [depth= 1] . ( 8 sec) [ -3544.1434] [ 510] [depth= 2] . ( 8 sec) [ -3542.6315] [ 510] [depth= 1] . ( 8 sec) [ -3531.0352] [ 505] [depth= 1] . ( 8 sec) [ -3530.9634] [ 505] [depth= 1] . ( 8 sec) [ -3530.8677] [ 505] [depth= 1] . ( 8 sec) [ -3530.8045] [ 505] [depth= 1] . ( 8 sec) [ -3517.7437] [ 498] [depth= 2] . ( 8 sec) [ -3516.5933] [ 498] [depth= 1] . ( 9 sec) [ -3512.6383] [ 496] [depth= 1] . ( 9 sec) [ -3502.8539] [ 493] [depth= 2] . ( 9 sec) [ -3492.1951] [ 488] [depth= 2] . ( 10 sec) [ -3492.1720] [ 488] [depth= 1] . ( 10 sec) [ -3492.1572] [ 487] [depth= 1] . ( 11 sec) [ -3492.1097] [ 487] [depth= 1] . ( 12 sec) [ -3490.9266] [Branch lengths ] . ( 12 sec) [ -3490.6036] [GTR parameters ] . ( 12 sec) [ -3489.8263] [Alpha ][ 1.103136] . ( 13 sec) [ -3486.9978] [ 486] [depth= 3] . ( 17 sec) [ -3486.0272] [Branch lengths ] . ( 18 sec) [ -3486.0193] [GTR parameters ] . ( 18 sec) [ -3486.0147] [Alpha ][ 1.121438] . ( 23 sec) [ -3484.8055] [Branch lengths ] . ( 47 sec) [ -3484.7682] [Branch lengths ] . ( 47 sec) [ -3484.7682] [Topology ] . ( 48 sec) [ -3484.7680] [Topology ] . ( 48 sec) [ -3484.7665] [GTR parameters ] . ( 48 sec) [ -3484.7662] [Alpha ][ 1.126494] . ( 48 sec) [ -3484.7662] [Topology ] . ( 49 sec) [ -3484.7662] [Topology ] . ( 49 sec) [ -3484.7662] [GTR parameters ] . ( 49 sec) [ -3484.7662] [Alpha ][ 1.126494] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3484.766185. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -8482.9814] [GTR parameters ] . ( 1 sec) [ -8324.0892] [Alpha ][ 0.500960] . ( 1 sec) [ -8210.9129] [ 1232] [depth= 8] . ( 1 sec) [ -8036.1893] [ 1175] [depth= 9] . ( 2 sec) [ -7917.5119] [ 1158] [depth= 2] . ( 2 sec) [ -7912.7770] [ 1154] [depth= 1] . ( 2 sec) [ -7837.5791] [ 1135] [depth= 4] . ( 2 sec) [ -7728.1685] [ 1118] [depth= 2] . ( 2 sec) [ -7685.5569] [ 1117] [depth= 3] . ( 2 sec) [ -7674.3369] [ 1112] [depth= 1] . ( 2 sec) [ -7584.4229] [ 1096] [depth= 5] . ( 2 sec) [ -7583.9246] [ 1096] [depth= 1] . ( 2 sec) [ -7546.7322] [ 1096] [depth= 2] . ( 2 sec) [ -7488.0569] [ 1090] [depth= 3] . ( 2 sec) [ -7017.2950] [ 1072] [depth= 3] . ( 2 sec) [ -6803.2499] [ 1068] [depth= 11] . ( 2 sec) [ -6751.0885] [ 1053] [depth= 7] . ( 2 sec) [ -6587.8530] [ 1052] [depth= 3] . ( 2 sec) [ -6580.4516] [ 1051] [depth= 2] . ( 2 sec) [ -6468.3654] [ 1031] [depth= 2] . ( 2 sec) [ -6367.7397] [ 1013] [depth= 10] . ( 2 sec) [ -6216.7745] [ 978] [depth= 12] . ( 2 sec) [ -6037.0654] [ 988] [depth= 12] . ( 2 sec) [ -6021.8517] [ 984] [depth= 2] . ( 3 sec) [ -6007.4369] [ 985] [depth= 1] . ( 3 sec) [ -5962.0471] [ 976] [depth= 16] . ( 3 sec) [ -5849.1112] [ 950] [depth= 7] . ( 3 sec) [ -5848.2725] [ 950] [depth= 1] . ( 3 sec) [ -5814.5272] [ 951] [depth= 22] . ( 3 sec) [ -5814.3396] [ 951] [depth= 2] . ( 3 sec) [ -5792.2655] [ 951] [depth= 2] . ( 3 sec) [ -5651.9311] [ 935] [depth= 11] . ( 3 sec) [ -5595.0484] [ 922] [depth= 3] . ( 3 sec) [ -5594.6111] [ 922] [depth= 1] . ( 3 sec) [ -5340.6507] [ 864] [depth= 19] . ( 3 sec) [ -5338.9509] [ 864] [depth= 1] . ( 3 sec) [ -5336.0930] [ 862] [depth= 17] . ( 3 sec) [ -5335.4338] [ 862] [depth= 1] . ( 3 sec) [ -5309.8348] [ 853] [depth= 1] . ( 3 sec) [ -5272.8678] [ 843] [depth= 4] . ( 3 sec) [ -5251.1303] [ 829] [depth= 3] . ( 4 sec) [ -4961.7180] [ 821] [depth= 12] . ( 4 sec) [ -4906.5920] [ 803] [depth= 1] . ( 4 sec) [ -4875.1687] [ 801] [depth= 5] . ( 4 sec) [ -4870.1850] [ 801] [depth= 7] . ( 4 sec) [ -4803.8412] [ 789] [depth= 1] . ( 4 sec) [ -4767.4524] [ 791] [depth= 1] . ( 4 sec) [ -4757.2166] [ 791] [depth= 10] . ( 4 sec) [ -4722.4402] [ 771] [depth= 9] . ( 4 sec) [ -4704.0952] [ 764] [depth= 1] . ( 4 sec) [ -4698.0267] [ 751] [depth= 1] . ( 4 sec) [ -4664.8781] [ 750] [depth= 1] . ( 4 sec) [ -4600.1888] [ 742] [depth= 3] . ( 4 sec) [ -4533.6971] [ 725] [depth= 12] . ( 4 sec) [ -4522.7466] [ 727] [depth= 2] . ( 4 sec) [ -4489.6514] [ 718] [depth= 5] . ( 4 sec) [ -4398.6429] [ 682] [depth= 5] . ( 4 sec) [ -4385.9662] [ 683] [depth= 2] . ( 5 sec) [ -4252.5626] [ 677] [depth= 1] . ( 5 sec) [ -4241.2383] [ 676] [depth= 1] . ( 5 sec) [ -4091.1134] [ 630] [depth= 6] . ( 5 sec) [ -4048.9345] [ 622] [depth= 6] . ( 5 sec) [ -4043.7124] [ 621] [depth= 3] . ( 5 sec) [ -4043.6706] [ 621] [depth= 1] . ( 5 sec) [ -3978.5317] [ 606] [depth= 4] . ( 5 sec) [ -3978.4998] [ 606] [depth= 1] . ( 5 sec) [ -3978.2987] [ 608] [depth= 1] . ( 6 sec) [ -3975.2507] [ 610] [depth= 1] . ( 6 sec) [ -3862.5871] [ 581] [depth= 2] . ( 6 sec) [ -3803.3016] [ 566] [depth= 1] . ( 6 sec) [ -3789.6179] [ 572] [depth= 1] . ( 6 sec) [ -3772.1014] [ 571] [depth= 1] . ( 6 sec) [ -3772.0688] [ 571] [depth= 1] . ( 6 sec) [ -3769.8668] [ 571] [depth= 2] . ( 6 sec) [ -3767.4385] [ 569] [depth= 1] . ( 6 sec) [ -3749.0368] [ 560] [depth= 1] . ( 7 sec) [ -3742.2836] [ 559] [depth= 1] . ( 7 sec) [ -3742.2562] [ 559] [depth= 1] . ( 7 sec) [ -3713.6999] [Branch lengths ] . ( 8 sec) [ -3712.0653] [GTR parameters ] . ( 8 sec) [ -3707.2469] [Alpha ][ 0.746295] . ( 8 sec) [ -3706.7660] [ 559] [depth= 1] . ( 8 sec) [ -3706.7515] [ 559] [depth= 2] . ( 8 sec) [ -3706.7287] [ 559] [depth= 3] . ( 9 sec) [ -3706.6330] [ 559] [depth= 1] . ( 9 sec) [ -3659.6270] [ 546] [depth= 1] . ( 9 sec) [ -3641.9698] [ 542] [depth= 3] . ( 9 sec) [ -3604.0693] [ 519] [depth= 1] . ( 9 sec) [ -3594.5494] [ 519] [depth= 1] . ( 9 sec) [ -3591.4984] [ 519] [depth= 1] . ( 9 sec) [ -3550.5601] [ 508] [depth= 1] . ( 9 sec) [ -3536.6478] [ 505] [depth= 1] . ( 9 sec) [ -3527.8486] [ 499] [depth= 1] . ( 9 sec) [ -3527.8350] [ 499] [depth= 1] . ( 10 sec) [ -3511.9700] [ 495] [depth= 5] . ( 10 sec) [ -3511.9514] [ 495] [depth= 1] . ( 10 sec) [ -3511.9407] [ 495] [depth= 1] . ( 10 sec) [ -3509.0492] [ 494] [depth= 1] . ( 10 sec) [ -3508.6836] [ 494] [depth= 1] . ( 10 sec) [ -3505.1092] [ 492] [depth= 1] . ( 11 sec) [ -3494.3838] [ 488] [depth= 1] . ( 11 sec) [ -3494.0847] [ 488] [depth= 1] . ( 11 sec) [ -3493.4977] [ 488] [depth= 1] . ( 11 sec) [ -3493.4351] [ 488] [depth= 1] . ( 11 sec) [ -3489.8918] [ 486] [depth= 1] . ( 12 sec) [ -3488.6280] [Branch lengths ] . ( 13 sec) [ -3487.9386] [GTR parameters ] . ( 13 sec) [ -3484.9176] [Alpha ][ 1.114205] . ( 13 sec) [ -3484.9071] [ 486] [depth= 2] . ( 17 sec) [ -3484.8133] [Branch lengths ] . ( 18 sec) [ -3484.7994] [GTR parameters ] . ( 18 sec) [ -3484.7980] [Alpha ][ 1.124824] . ( 40 sec) [ -3484.7928] [Branch lengths ] . ( 40 sec) [ -3484.7928] [Topology ] . ( 41 sec) [ -3484.7927] [Topology ] . ( 41 sec) [ -3484.7927] [GTR parameters ] . ( 41 sec) [ -3484.7927] [Alpha ][ 1.126068] . Checking for NNIs, optimizing five branches... . ( 44 sec) [ -3484.7924] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3484.792402. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -9265.3008] [GTR parameters ] . ( 1 sec) [ -9096.3981] [Alpha ][ 0.500960] . ( 1 sec) [ -8898.4786] [ 1290] [depth= 6] . ( 1 sec) [ -8744.3271] [ 1257] [depth= 11] . ( 1 sec) [ -8631.8208] [ 1252] [depth= 3] . ( 1 sec) [ -8594.9933] [ 1252] [depth= 1] . ( 1 sec) [ -8498.0917] [ 1228] [depth= 7] . ( 1 sec) [ -8444.3562] [ 1228] [depth= 4] . ( 1 sec) [ -8433.3284] [ 1226] [depth= 12] . ( 1 sec) [ -8399.6126] [ 1226] [depth= 1] . ( 1 sec) [ -8305.7518] [ 1197] [depth= 9] . ( 1 sec) [ -8206.4740] [ 1185] [depth= 8] . ( 1 sec) [ -8121.7360] [ 1171] [depth= 11] . ( 1 sec) [ -8032.1259] [ 1162] [depth= 1] . ( 2 sec) [ -7952.9511] [ 1136] [depth= 9] . ( 2 sec) [ -7911.3673] [ 1135] [depth= 1] . ( 2 sec) [ -7880.2870] [ 1133] [depth= 3] . ( 2 sec) [ -7829.4985] [ 1133] [depth= 7] . ( 2 sec) [ -7769.5560] [ 1133] [depth= 2] . ( 2 sec) [ -7695.3639] [ 1113] [depth= 2] . ( 2 sec) [ -7654.4159] [ 1118] [depth= 6] . ( 2 sec) [ -7615.7756] [ 1113] [depth= 1] . ( 2 sec) [ -7607.0079] [ 1113] [depth= 6] . ( 2 sec) [ -6949.1506] [ 1093] [depth= 12] . ( 2 sec) [ -6842.0566] [ 1077] [depth= 1] . ( 2 sec) [ -6733.6706] [ 1046] [depth= 10] . ( 2 sec) [ -6731.2178] [ 1046] [depth= 2] . ( 2 sec) [ -6663.9748] [ 1041] [depth= 14] . ( 2 sec) [ -6583.2222] [ 1026] [depth= 9] . ( 2 sec) [ -6511.6802] [ 1000] [depth= 13] . ( 2 sec) [ -6455.5790] [ 978] [depth= 13] . ( 2 sec) [ -6417.1928] [ 970] [depth= 11] . ( 2 sec) [ -6401.4532] [ 964] [depth= 1] . ( 2 sec) [ -6354.2477] [ 944] [depth= 2] . ( 2 sec) [ -6121.0942] [ 942] [depth= 11] . ( 2 sec) [ -6050.2584] [ 923] [depth= 8] . ( 3 sec) [ -5706.5168] [ 905] [depth= 7] . ( 3 sec) [ -5661.9371] [ 907] [depth= 5] . ( 3 sec) [ -5479.4982] [ 871] [depth= 7] . ( 3 sec) [ -5439.0496] [ 855] [depth= 10] . ( 3 sec) [ -5438.3161] [ 855] [depth= 1] . ( 3 sec) [ -5365.7974] [ 842] [depth= 5] . ( 3 sec) [ -5187.6044] [ 829] [depth= 11] . ( 3 sec) [ -5167.0808] [ 834] [depth= 1] . ( 3 sec) [ -5112.8140] [ 829] [depth= 1] . ( 3 sec) [ -5081.3530] [ 811] [depth= 1] . ( 3 sec) [ -5065.7518] [ 805] [depth= 2] . ( 3 sec) [ -5048.2401] [ 806] [depth= 1] . ( 3 sec) [ -4937.6489] [ 781] [depth= 5] . ( 3 sec) [ -4921.4310] [ 778] [depth= 12] . ( 3 sec) [ -4810.0456] [ 763] [depth= 5] . ( 3 sec) [ -4792.0244] [ 763] [depth= 1] . ( 3 sec) [ -4791.4168] [ 763] [depth= 1] . ( 3 sec) [ -4667.3480] [ 736] [depth= 13] . ( 3 sec) [ -4663.2378] [ 736] [depth= 1] . ( 3 sec) [ -4539.6748] [ 688] [depth= 10] . ( 3 sec) [ -4539.1628] [ 689] [depth= 1] . ( 4 sec) [ -4535.6118] [ 688] [depth= 1] . ( 4 sec) [ -4456.2237] [ 693] [depth= 2] . ( 4 sec) [ -4450.2433] [ 696] [depth= 4] . ( 4 sec) [ -4443.9587] [ 694] [depth= 3] . ( 4 sec) [ -4381.8467] [ 695] [depth= 4] . ( 4 sec) [ -4379.1095] [ 694] [depth= 1] . ( 4 sec) [ -4310.2870] [ 668] [depth= 4] . ( 4 sec) [ -4294.2007] [ 665] [depth= 2] . ( 4 sec) [ -4287.9540] [ 667] [depth= 6] . ( 4 sec) [ -4259.2509] [ 666] [depth= 4] . ( 4 sec) [ -4240.7686] [ 656] [depth= 1] . ( 4 sec) [ -4237.8778] [ 655] [depth= 1] . ( 4 sec) [ -4204.4898] [ 639] [depth= 5] . ( 4 sec) [ -4085.4006] [ 617] [depth= 7] . ( 5 sec) [ -4083.4053] [ 614] [depth= 2] . ( 5 sec) [ -4080.4144] [ 613] [depth= 6] . ( 5 sec) [ -4037.5594] [ 610] [depth= 1] . ( 5 sec) [ -4036.8165] [ 610] [depth= 1] . ( 5 sec) [ -4035.0669] [ 611] [depth= 2] . ( 5 sec) [ -3996.4961] [ 609] [depth= 2] . ( 5 sec) [ -3996.2135] [ 610] [depth= 2] . ( 5 sec) [ -3962.6739] [ 596] [depth= 1] . ( 5 sec) [ -3870.5959] [ 576] [depth= 5] . ( 5 sec) [ -3862.1390] [ 576] [depth= 6] . ( 5 sec) [ -3862.0297] [ 576] [depth= 1] . ( 5 sec) [ -3778.9047] [ 556] [depth= 5] . ( 5 sec) [ -3778.5771] [ 556] [depth= 1] . ( 5 sec) [ -3777.9162] [ 556] [depth= 1] . ( 6 sec) [ -3734.9490] [Branch lengths ] . ( 6 sec) [ -3730.8634] [GTR parameters ] . ( 6 sec) [ -3725.8758] [Alpha ][ 0.746309] . ( 6 sec) [ -3690.1138] [ 540] [depth= 3] . ( 7 sec) [ -3683.5599] [ 538] [depth= 3] . ( 7 sec) [ -3682.4247] [ 537] [depth= 2] . ( 7 sec) [ -3681.5385] [ 537] [depth= 2] . ( 7 sec) [ -3622.1550] [ 520] [depth= 4] . ( 7 sec) [ -3577.8581] [ 510] [depth= 2] . ( 7 sec) [ -3576.1538] [ 510] [depth= 1] . ( 7 sec) [ -3576.1360] [ 510] [depth= 1] . ( 7 sec) [ -3574.5582] [ 509] [depth= 1] . ( 7 sec) [ -3574.5482] [ 508] [depth= 1] . ( 7 sec) [ -3571.2915] [ 508] [depth= 3] . ( 7 sec) [ -3571.2650] [ 508] [depth= 1] . ( 8 sec) [ -3570.2673] [ 508] [depth= 1] . ( 8 sec) [ -3570.2533] [ 508] [depth= 2] . ( 8 sec) [ -3558.7380] [ 504] [depth= 1] . ( 8 sec) [ -3504.1636] [ 488] [depth= 1] . ( 8 sec) [ -3499.3936] [ 486] [depth= 1] . ( 8 sec) [ -3499.3237] [ 486] [depth= 1] . ( 8 sec) [ -3499.2326] [ 486] [depth= 1] . ( 9 sec) [ -3496.1415] [ 486] [depth= 1] . ( 10 sec) [ -3496.1103] [ 486] [depth= 1] . ( 10 sec) [ -3495.7714] [ 486] [depth= 1] . ( 10 sec) [ -3495.7490] [ 486] [depth= 1] . ( 11 sec) [ -3495.7380] [ 486] [depth= 1] . ( 11 sec) [ -3492.5878] [Branch lengths ] . ( 11 sec) [ -3492.2877] [GTR parameters ] . ( 11 sec) [ -3489.4282] [Alpha ][ 1.097127] . ( 13 sec) [ -3489.4143] [ 486] [depth= 2] . ( 17 sec) [ -3487.8233] [Branch lengths ] . ( 18 sec) [ -3487.7958] [GTR parameters ] . ( 18 sec) [ -3487.7905] [Alpha ][ 1.116770] . ( 25 sec) [ -3485.0641] [Branch lengths ] . ( 50 sec) [ -3484.8009] [Branch lengths ] . ( 50 sec) [ -3484.8009] [Topology ] . ( 50 sec) [ -3484.8002] [Topology ] . ( 51 sec) [ -3484.7940] [GTR parameters ] . ( 51 sec) [ -3484.7927] [Alpha ][ 1.126720] . ( 51 sec) [ -3484.7927] [Topology ] . ( 51 sec) [ -3484.7927] [Topology ] . ( 51 sec) [ -3484.7927] [GTR parameters ] . ( 51 sec) [ -3484.7927] [Alpha ][ 1.126720] . Checking for NNIs, optimizing five branches... . ( 56 sec) [ -3484.7922] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3484.792229. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-3491.381768 . ( 0 sec) [ -3490.8884] [GTR parameters ] . ( 1 sec) [ -3490.7282] [Alpha ][ 1.104161] . ( 1 sec) [ -3490.7282] [Topology ] . ( 1 sec) [ -3485.5616] [Topology ] . ( 2 sec) [ -3485.0246] [Topology ] . ( 3 sec) [ -3484.9129] [Topology ] . ( 4 sec) [ -3484.8770] [Topology ] . Moving backward . ( 4 sec) [ -3484.8327] [Topology ] . ( 5 sec) [ -3484.8068] [Topology ] . ( 6 sec) [ -3484.8045] [Topology ] . ( 6 sec) [ -3484.8042] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-3484.804156 . ( 11 sec) [ -3484.7990] [GTR parameters ] . ( 11 sec) [ -3484.7928] [Alpha ][ 1.125754] . ( 11 sec) [ -3484.7928] [Topology ] . ( 12 sec) [ -3484.7926] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-3484.792586 . ( 17 sec) [ -3484.7926] [GTR parameters ] . ( 17 sec) [ -3484.7926] [Alpha ][ 1.126879] . ( 17 sec) [ -3484.7926] [Topology ] . ( 18 sec) [ -3484.7925] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 28 sec) [ -3490.8884] [GTR parameters ] . ( 28 sec) [ -3490.7282] [Alpha ][ 1.104161] . ( 28 sec) [ -3490.5952] [ 486] [depth= 1] . ( 28 sec) [ -3490.5730] [ 486] [depth= 1] . ( 30 sec) [ -3490.4514] [ 486] [depth= 1] . ( 30 sec) [ -3489.2123] [ 486] [depth= 1] . ( 30 sec) [ -3488.8578] [ 486] [depth= 1] . ( 31 sec) [ -3488.4670] [ 486] [depth= 1] . ( 31 sec) [ -3488.4157] [ 486] [depth= 1] . ( 32 sec) [ -3487.4073] [ 486] [depth= 2] . ( 33 sec) [ -3487.3836] [ 486] [depth= 2] . ( 33 sec) [ -3487.3454] [ 486] [depth= 2] . ( 33 sec) [ -3487.2853] [ 486] [depth= 2] . ( 33 sec) [ -3487.2702] [ 486] [depth= 2] . ( 33 sec) [ -3487.2406] [ 486] [depth= 1] . ( 33 sec) [ -3484.8259] [Branch lengths ] . ( 33 sec) [ -3484.8205] [GTR parameters ] . ( 34 sec) [ -3484.8154] [Alpha ][ 1.123752] . ( 39 sec) [ -3484.7929] [Branch lengths ] . ( 62 sec) [ -3484.7926] [Branch lengths ] . ( 62 sec) [ -3484.7926] [Topology ] . ( 63 sec) [ -3484.7926] [Topology ] . ( 63 sec) [ -3484.7926] [GTR parameters ] . ( 63 sec) [ -3484.7925] [Alpha ][ 1.126219] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -3484.792537 . Log likelihood obtained after SPR moves : -3484.792506 . Log likelihood of the current tree: -3484.792506. . Printing the most likely tree in file 'data49.phy_phyml_tree.txt'... . Best log likelihood : -3484.766185 . Time used 0h1m7s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo