.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data22.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... . 237 patterns found. (out of a total of 500 sites) . 249 sites without polymorphism (49.80%). . [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)... . ( 0 sec) [ -6966.1634] [GTR parameters ] . ( 0 sec) [ -6863.7221] [Alpha ][ 0.500960] . ( 0 sec) [ -6656.0947] [ 976] [depth= 8] . ( 0 sec) [ -6412.1424] [ 976] [depth= 4] . ( 1 sec) [ -6347.3496] [ 970] [depth= 1] . ( 1 sec) [ -6334.6913] [ 970] [depth= 7] . ( 1 sec) [ -6276.7396] [ 958] [depth= 5] . ( 1 sec) [ -6267.9119] [ 958] [depth= 4] . ( 1 sec) [ -6236.3888] [ 955] [depth= 6] . ( 1 sec) [ -6218.1624] [ 955] [depth= 1] . ( 1 sec) [ -6124.3280] [ 927] [depth= 11] . ( 1 sec) [ -6067.6156] [ 917] [depth= 3] . ( 1 sec) [ -6022.8134] [ 906] [depth= 1] . ( 1 sec) [ -5985.2693] [ 903] [depth= 12] . ( 1 sec) [ -5878.3458] [ 889] [depth= 11] . ( 1 sec) [ -5842.5804] [ 888] [depth= 2] . ( 1 sec) [ -5821.8893] [ 888] [depth= 2] . ( 1 sec) [ -5750.4389] [ 877] [depth= 5] . ( 1 sec) [ -5659.6419] [ 875] [depth= 2] . ( 1 sec) [ -5638.2546] [ 876] [depth= 3] . ( 1 sec) [ -5563.0486] [ 875] [depth= 1] . ( 1 sec) [ -5512.5578] [ 862] [depth= 11] . ( 1 sec) [ -5437.5782] [ 859] [depth= 12] . ( 1 sec) [ -5424.5891] [ 859] [depth= 13] . ( 1 sec) [ -5304.4126] [ 821] [depth= 3] . ( 1 sec) [ -5280.2898] [ 820] [depth= 5] . ( 1 sec) [ -5185.4803] [ 810] [depth= 5] . ( 1 sec) [ -5124.7363] [ 798] [depth= 16] . ( 1 sec) [ -4977.0495] [ 787] [depth= 2] . ( 1 sec) [ -4937.0801] [ 778] [depth= 3] . ( 1 sec) [ -4924.9720] [ 779] [depth= 1] . ( 1 sec) [ -4874.1404] [ 776] [depth= 10] . ( 1 sec) [ -4844.8611] [ 759] [depth= 1] . ( 1 sec) [ -4746.8210] [ 735] [depth= 6] . ( 1 sec) [ -4641.8290] [ 719] [depth= 10] . ( 1 sec) [ -4513.8807] [ 709] [depth= 11] . ( 1 sec) [ -4503.3551] [ 710] [depth= 5] . ( 2 sec) [ -4502.6958] [ 710] [depth= 1] . ( 2 sec) [ -4383.1538] [ 670] [depth= 6] . ( 2 sec) [ -4222.4871] [ 668] [depth= 1] . ( 2 sec) [ -4220.1586] [ 664] [depth= 1] . ( 2 sec) [ -4195.1893] [ 654] [depth= 2] . ( 2 sec) [ -4195.0509] [ 654] [depth= 1] . ( 2 sec) [ -4191.1999] [ 654] [depth= 6] . ( 2 sec) [ -4035.7511] [ 598] [depth= 8] . ( 2 sec) [ -4020.2186] [ 600] [depth= 1] . ( 2 sec) [ -3945.5835] [ 578] [depth= 10] . ( 2 sec) [ -3912.1784] [ 573] [depth= 3] . ( 2 sec) [ -3849.1318] [ 565] [depth= 5] . ( 2 sec) [ -3838.3748] [ 565] [depth= 1] . ( 2 sec) [ -3836.6919] [ 565] [depth= 3] . ( 2 sec) [ -3826.1684] [ 562] [depth= 2] . ( 2 sec) [ -3820.1852] [ 562] [depth= 1] . ( 2 sec) [ -3808.6698] [ 553] [depth= 8] . ( 2 sec) [ -3800.6646] [ 551] [depth= 2] . ( 2 sec) [ -3782.7464] [ 546] [depth= 3] . ( 2 sec) [ -3779.5772] [ 544] [depth= 1] . ( 2 sec) [ -3748.9653] [ 544] [depth= 3] . ( 2 sec) [ -3675.6126] [ 544] [depth= 2] . ( 2 sec) [ -3656.3303] [ 523] [depth= 3] . ( 2 sec) [ -3598.8947] [ 507] [depth= 6] . ( 3 sec) [ -3583.9922] [ 507] [depth= 2] . ( 3 sec) [ -3572.5870] [ 505] [depth= 1] . ( 3 sec) [ -3513.1663] [ 483] [depth= 2] . ( 3 sec) [ -3506.4718] [ 479] [depth= 1] . ( 3 sec) [ -3473.2051] [ 474] [depth= 2] . ( 3 sec) [ -3473.1717] [ 474] [depth= 1] . ( 3 sec) [ -3470.2121] [ 474] [depth= 1] . ( 3 sec) [ -3467.7351] [ 478] [depth= 1] . ( 3 sec) [ -3466.3806] [ 478] [depth= 2] . ( 3 sec) [ -3465.7192] [ 478] [depth= 2] . ( 3 sec) [ -3465.4882] [ 477] [depth= 3] . ( 3 sec) [ -3462.6796] [ 477] [depth= 1] . ( 3 sec) [ -3459.7402] [ 476] [depth= 2] . ( 3 sec) [ -3459.7139] [ 476] [depth= 1] . ( 3 sec) [ -3454.7366] [ 472] [depth= 1] . ( 4 sec) [ -3454.7105] [ 472] [depth= 1] . ( 4 sec) [ -3442.1277] [Branch lengths ] . ( 4 sec) [ -3441.1471] [GTR parameters ] . ( 4 sec) [ -3431.9021] [Alpha ][ 0.935236] . ( 4 sec) [ -3424.4789] [ 471] [depth= 3] . ( 5 sec) [ -3424.0642] [ 471] [depth= 1] . ( 6 sec) [ -3423.5716] [ 470] [depth= 1] . ( 7 sec) [ -3384.1206] [ 459] [depth= 2] . ( 7 sec) [ -3384.1028] [ 459] [depth= 1] . ( 8 sec) [ -3384.0921] [ 459] [depth= 1] . ( 9 sec) [ -3384.0722] [ 459] [depth= 1] . ( 10 sec) [ -3383.4639] [Branch lengths ] . ( 10 sec) [ -3383.2344] [GTR parameters ] . ( 10 sec) [ -3383.0828] [Alpha ][ 1.027533] . ( 16 sec) [ -3383.0747] [Branch lengths ] . ( 33 sec) [ -3383.0744] [Branch lengths ] . ( 33 sec) [ -3383.0744] [Topology ] . ( 33 sec) [ -3383.0744] [Topology ] . ( 33 sec) [ -3383.0732] [GTR parameters ] . ( 33 sec) [ -3383.0731] [Alpha ][ 1.029211] . ( 33 sec) [ -3383.0731] [Topology ] . ( 34 sec) [ -3383.0731] [Topology ] . ( 34 sec) [ -3383.0731] [GTR parameters ] . ( 34 sec) [ -3383.0731] [Alpha ][ 1.029211] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3383.073101. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -7472.6411] [GTR parameters ] . ( 0 sec) [ -7369.2276] [Alpha ][ 0.500960] . ( 0 sec) [ -7324.5967] [ 967] [depth= 3] . ( 0 sec) [ -7232.8990] [ 959] [depth= 10] . ( 0 sec) [ -7098.7566] [ 947] [depth= 4] . ( 0 sec) [ -7090.0789] [ 946] [depth= 3] . ( 0 sec) [ -7047.9976] [ 933] [depth= 1] . ( 1 sec) [ -6974.5654] [ 932] [depth= 4] . ( 1 sec) [ -6974.3333] [ 931] [depth= 1] . ( 1 sec) [ -6956.1856] [ 931] [depth= 2] . ( 1 sec) [ -6953.0517] [ 930] [depth= 1] . ( 1 sec) [ -6132.1897] [ 930] [depth= 1] . ( 1 sec) [ -6069.8599] [ 915] [depth= 3] . ( 1 sec) [ -6018.3470] [ 914] [depth= 2] . ( 1 sec) [ -5982.6544] [ 909] [depth= 15] . ( 1 sec) [ -5921.7360] [ 909] [depth= 1] . ( 1 sec) [ -5539.1492] [ 864] [depth= 8] . ( 1 sec) [ -5504.9088] [ 857] [depth= 7] . ( 1 sec) [ -5373.8572] [ 828] [depth= 3] . ( 1 sec) [ -5317.1124] [ 811] [depth= 14] . ( 1 sec) [ -5316.4588] [ 811] [depth= 3] . ( 1 sec) [ -5238.4843] [ 811] [depth= 2] . ( 1 sec) [ -5209.0883] [ 806] [depth= 2] . ( 1 sec) [ -5121.5445] [ 792] [depth= 12] . ( 1 sec) [ -5093.3991] [ 789] [depth= 6] . ( 1 sec) [ -4967.7125] [ 768] [depth= 3] . ( 1 sec) [ -4936.7908] [ 767] [depth= 15] . ( 1 sec) [ -4865.0998] [ 768] [depth= 2] . ( 1 sec) [ -4798.0245] [ 750] [depth= 3] . ( 1 sec) [ -4781.4919] [ 741] [depth= 9] . ( 1 sec) [ -4745.7428] [ 729] [depth= 7] . ( 1 sec) [ -4657.0904] [ 710] [depth= 16] . ( 1 sec) [ -4634.9349] [ 709] [depth= 1] . ( 1 sec) [ -4631.5578] [ 708] [depth= 1] . ( 1 sec) [ -4558.6508] [ 684] [depth= 16] . ( 1 sec) [ -4518.2429] [ 684] [depth= 3] . ( 1 sec) [ -4498.0257] [ 684] [depth= 1] . ( 1 sec) [ -4426.9216] [ 683] [depth= 2] . ( 1 sec) [ -4387.2773] [ 681] [depth= 9] . ( 1 sec) [ -4385.0753] [ 681] [depth= 3] . ( 1 sec) [ -4370.5949] [ 671] [depth= 2] . ( 2 sec) [ -4347.0798] [ 664] [depth= 12] . ( 2 sec) [ -4328.4980] [ 648] [depth= 8] . ( 2 sec) [ -4323.8984] [ 646] [depth= 11] . ( 2 sec) [ -4318.3158] [ 644] [depth= 3] . ( 2 sec) [ -4318.1127] [ 644] [depth= 1] . ( 2 sec) [ -4242.7408] [ 630] [depth= 4] . ( 2 sec) [ -4226.2846] [ 627] [depth= 3] . ( 2 sec) [ -4109.7299] [ 599] [depth= 5] . ( 2 sec) [ -4030.3410] [ 573] [depth= 1] . ( 2 sec) [ -4023.6892] [ 572] [depth= 1] . ( 2 sec) [ -4016.6802] [ 572] [depth= 1] . ( 2 sec) [ -4000.2124] [ 568] [depth= 8] . ( 2 sec) [ -3975.9640] [ 565] [depth= 3] . ( 2 sec) [ -3951.7174] [ 565] [depth= 1] . ( 2 sec) [ -3951.6297] [ 565] [depth= 1] . ( 2 sec) [ -3922.5274] [ 567] [depth= 6] . ( 2 sec) [ -3913.6275] [ 565] [depth= 6] . ( 2 sec) [ -3913.3992] [ 565] [depth= 2] . ( 2 sec) [ -3910.7248] [ 561] [depth= 1] . ( 2 sec) [ -3907.3457] [ 561] [depth= 3] . ( 2 sec) [ -3887.0829] [ 557] [depth= 1] . ( 2 sec) [ -3835.2370] [ 558] [depth= 3] . ( 2 sec) [ -3831.6286] [ 558] [depth= 2] . ( 2 sec) [ -3813.7550] [ 557] [depth= 1] . ( 2 sec) [ -3772.7350] [ 549] [depth= 2] . ( 2 sec) [ -3772.5528] [ 549] [depth= 1] . ( 2 sec) [ -3710.6947] [ 530] [depth= 1] . ( 2 sec) [ -3657.2365] [ 518] [depth= 6] . ( 2 sec) [ -3657.2103] [ 518] [depth= 1] . ( 2 sec) [ -3655.3017] [ 517] [depth= 2] . ( 2 sec) [ -3655.2459] [ 518] [depth= 1] . ( 3 sec) [ -3624.9585] [ 513] [depth= 1] . ( 3 sec) [ -3612.3638] [ 509] [depth= 5] . ( 3 sec) [ -3612.3274] [ 509] [depth= 2] . ( 3 sec) [ -3609.8682] [ 509] [depth= 1] . ( 3 sec) [ -3531.7607] [ 492] [depth= 5] . ( 3 sec) [ -3483.6263] [ 479] [depth= 1] . ( 3 sec) [ -3482.0170] [ 479] [depth= 2] . ( 3 sec) [ -3481.2829] [ 479] [depth= 1] . ( 3 sec) [ -3459.6812] [Branch lengths ] . ( 3 sec) [ -3457.2852] [GTR parameters ] . ( 3 sec) [ -3448.6649] [Alpha ][ 0.913240] . ( 4 sec) [ -3438.9519] [ 477] [depth= 1] . ( 4 sec) [ -3435.1311] [ 473] [depth= 1] . ( 4 sec) [ -3429.3675] [ 471] [depth= 1] . ( 4 sec) [ -3429.1042] [ 471] [depth= 1] . ( 4 sec) [ -3419.4520] [ 468] [depth= 2] . ( 5 sec) [ -3412.9086] [ 466] [depth= 1] . ( 5 sec) [ -3384.5541] [ 459] [depth= 6] . ( 5 sec) [ -3384.5409] [ 459] [depth= 1] . ( 6 sec) [ -3384.5234] [ 459] [depth= 1] . ( 7 sec) [ -3384.4543] [ 459] [depth= 1] . ( 8 sec) [ -3384.3884] [ 459] [depth= 1] . ( 9 sec) [ -3383.5015] [Branch lengths ] . ( 9 sec) [ -3383.3261] [GTR parameters ] . ( 9 sec) [ -3383.0867] [Alpha ][ 1.027098] . ( 15 sec) [ -3383.0753] [Branch lengths ] . ( 31 sec) [ -3383.0750] [Branch lengths ] . ( 31 sec) [ -3383.0750] [Topology ] . ( 31 sec) [ -3383.0750] [Topology ] . ( 32 sec) [ -3383.0730] [GTR parameters ] . ( 32 sec) [ -3383.0729] [Alpha ][ 1.029239] . ( 32 sec) [ -3383.0729] [Topology ] . ( 32 sec) [ -3383.0729] [Topology ] . ( 32 sec) [ -3383.0729] [GTR parameters ] . ( 32 sec) [ -3383.0729] [Alpha ][ 1.029239] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3383.072937. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -7163.8219] [GTR parameters ] . ( 1 sec) [ -7051.8246] [Alpha ][ 0.500960] . ( 1 sec) [ -7004.2624] [ 1012] [depth= 8] . ( 1 sec) [ -6910.8414] [ 1004] [depth= 6] . ( 1 sec) [ -6910.5027] [ 1002] [depth= 3] . ( 1 sec) [ -6886.4963] [ 1002] [depth= 3] . ( 1 sec) [ -6816.5352] [ 992] [depth= 2] . ( 1 sec) [ -6815.4562] [ 992] [depth= 1] . ( 1 sec) [ -6604.3457] [ 966] [depth= 6] . ( 1 sec) [ -6056.9021] [ 953] [depth= 8] . ( 1 sec) [ -5950.5208] [ 947] [depth= 2] . ( 1 sec) [ -5906.2092] [ 945] [depth= 13] . ( 1 sec) [ -5845.3884] [ 930] [depth= 8] . ( 1 sec) [ -5787.6112] [ 915] [depth= 11] . ( 1 sec) [ -5780.0754] [ 913] [depth= 1] . ( 1 sec) [ -5742.8295] [ 913] [depth= 1] . ( 1 sec) [ -5730.5434] [ 906] [depth= 1] . ( 1 sec) [ -5725.7307] [ 906] [depth= 1] . ( 1 sec) [ -5686.2976] [ 898] [depth= 11] . ( 1 sec) [ -5648.1146] [ 898] [depth= 1] . ( 1 sec) [ -5595.5485] [ 895] [depth= 6] . ( 1 sec) [ -5477.0781] [ 871] [depth= 3] . ( 1 sec) [ -5297.0389] [ 842] [depth= 7] . ( 1 sec) [ -5165.0902] [ 808] [depth= 1] . ( 1 sec) [ -5148.7551] [ 807] [depth= 6] . ( 1 sec) [ -5099.0072] [ 810] [depth= 4] . ( 1 sec) [ -5047.9396] [ 806] [depth= 6] . ( 1 sec) [ -4980.3233] [ 789] [depth= 18] . ( 1 sec) [ -4975.1996] [ 791] [depth= 2] . ( 1 sec) [ -4968.4410] [ 789] [depth= 1] . ( 1 sec) [ -4962.8067] [ 789] [depth= 12] . ( 1 sec) [ -4903.9536] [ 773] [depth= 12] . ( 1 sec) [ -4866.8071] [ 761] [depth= 5] . ( 1 sec) [ -4864.4954] [ 761] [depth= 1] . ( 1 sec) [ -4794.5755] [ 753] [depth= 2] . ( 2 sec) [ -4783.6351] [ 741] [depth= 5] . ( 2 sec) [ -4772.3267] [ 740] [depth= 1] . ( 2 sec) [ -4769.2081] [ 739] [depth= 1] . ( 2 sec) [ -4679.0030] [ 724] [depth= 6] . ( 2 sec) [ -4660.4398] [ 718] [depth= 1] . ( 2 sec) [ -4648.5864] [ 721] [depth= 7] . ( 2 sec) [ -4600.4661] [ 720] [depth= 1] . ( 2 sec) [ -4588.4190] [ 717] [depth= 6] . ( 2 sec) [ -4540.6748] [ 713] [depth= 7] . ( 2 sec) [ -4484.7260] [ 702] [depth= 6] . ( 2 sec) [ -4453.4067] [ 699] [depth= 2] . ( 2 sec) [ -4441.2049] [ 699] [depth= 1] . ( 2 sec) [ -4411.6473] [ 687] [depth= 6] . ( 2 sec) [ -4326.8547] [ 688] [depth= 2] . ( 2 sec) [ -4307.5981] [ 690] [depth= 4] . ( 2 sec) [ -4301.7032] [ 688] [depth= 9] . ( 2 sec) [ -4284.5868] [ 678] [depth= 2] . ( 2 sec) [ -4168.0075] [ 645] [depth= 6] . ( 2 sec) [ -4107.3116] [ 618] [depth= 11] . ( 2 sec) [ -4077.9406] [ 609] [depth= 1] . ( 2 sec) [ -4064.3685] [ 609] [depth= 1] . ( 2 sec) [ -4016.1939] [ 608] [depth= 1] . ( 2 sec) [ -3871.6600] [ 567] [depth= 10] . ( 2 sec) [ -3869.6116] [ 565] [depth= 1] . ( 2 sec) [ -3852.5655] [ 568] [depth= 2] . ( 2 sec) [ -3849.7731] [ 568] [depth= 2] . ( 2 sec) [ -3849.5249] [ 568] [depth= 1] . ( 2 sec) [ -3840.9658] [ 565] [depth= 4] . ( 2 sec) [ -3839.3759] [ 563] [depth= 1] . ( 2 sec) [ -3782.9925] [ 556] [depth= 8] . ( 2 sec) [ -3776.1515] [ 560] [depth= 1] . ( 2 sec) [ -3773.2761] [ 559] [depth= 1] . ( 2 sec) [ -3766.7137] [ 554] [depth= 2] . ( 3 sec) [ -3736.8455] [ 549] [depth= 4] . ( 3 sec) [ -3734.3661] [ 549] [depth= 1] . ( 3 sec) [ -3692.4070] [ 538] [depth= 2] . ( 3 sec) [ -3609.7753] [ 513] [depth= 6] . ( 3 sec) [ -3609.7537] [ 513] [depth= 1] . ( 3 sec) [ -3585.3944] [ 513] [depth= 1] . ( 3 sec) [ -3554.3407] [ 510] [depth= 1] . ( 3 sec) [ -3522.7716] [ 497] [depth= 3] . ( 3 sec) [ -3520.9595] [ 497] [depth= 1] . ( 3 sec) [ -3486.5590] [ 487] [depth= 1] . ( 3 sec) [ -3461.4709] [ 476] [depth= 2] . ( 3 sec) [ -3459.6687] [ 475] [depth= 1] . ( 3 sec) [ -3448.8081] [ 473] [depth= 1] . ( 3 sec) [ -3446.3548] [ 470] [depth= 1] . ( 3 sec) [ -3445.5176] [ 470] [depth= 1] . ( 4 sec) [ -3425.3937] [Branch lengths ] . ( 4 sec) [ -3422.8273] [GTR parameters ] . ( 4 sec) [ -3412.9702] [Alpha ][ 0.955450] . ( 4 sec) [ -3395.8833] [ 463] [depth= 3] . ( 4 sec) [ -3392.7106] [ 461] [depth= 1] . ( 4 sec) [ -3392.3842] [ 461] [depth= 2] . ( 4 sec) [ -3385.1790] [ 459] [depth= 1] . ( 5 sec) [ -3385.1672] [ 459] [depth= 1] . ( 5 sec) [ -3384.0947] [ 459] [depth= 1] . ( 5 sec) [ -3383.9966] [ 459] [depth= 1] . ( 8 sec) [ -3383.8618] [ 459] [depth= 1] . ( 9 sec) [ -3383.3871] [Branch lengths ] . ( 10 sec) [ -3383.1689] [GTR parameters ] . ( 10 sec) [ -3383.0767] [Alpha ][ 1.027688] . ( 16 sec) [ -3383.0738] [Branch lengths ] . ( 32 sec) [ -3383.0738] [Branch lengths ] . ( 32 sec) [ -3383.0738] [Topology ] . ( 32 sec) [ -3383.0738] [Topology ] . ( 32 sec) [ -3383.0730] [GTR parameters ] . ( 32 sec) [ -3383.0729] [Alpha ][ 1.029211] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3383.072913. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -7309.6964] [GTR parameters ] . ( 0 sec) [ -7200.6160] [Alpha ][ 0.500960] . ( 0 sec) [ -7164.9491] [ 1001] [depth= 8] . ( 0 sec) [ -6592.3659] [ 988] [depth= 5] . ( 0 sec) [ -6519.7588] [ 979] [depth= 3] . ( 0 sec) [ -6515.9618] [ 977] [depth= 1] . ( 0 sec) [ -6425.3563] [ 965] [depth= 9] . ( 0 sec) [ -6260.8166] [ 950] [depth= 3] . ( 0 sec) [ -6260.0893] [ 950] [depth= 2] . ( 0 sec) [ -6222.2206] [ 938] [depth= 1] . ( 0 sec) [ -6210.2231] [ 938] [depth= 5] . ( 0 sec) [ -6197.4421] [ 938] [depth= 7] . ( 0 sec) [ -6189.8921] [ 938] [depth= 1] . ( 0 sec) [ -6132.3128] [ 921] [depth= 11] . ( 0 sec) [ -5981.5733] [ 915] [depth= 14] . ( 0 sec) [ -5970.7058] [ 915] [depth= 9] . ( 0 sec) [ -5966.8640] [ 915] [depth= 2] . ( 0 sec) [ -5926.0842] [ 904] [depth= 1] . ( 0 sec) [ -5895.1134] [ 904] [depth= 1] . ( 0 sec) [ -5846.8557] [ 891] [depth= 1] . ( 1 sec) [ -5681.2807] [ 877] [depth= 14] . ( 1 sec) [ -5550.7123] [ 849] [depth= 1] . ( 1 sec) [ -5528.8321] [ 847] [depth= 5] . ( 1 sec) [ -5456.5215] [ 836] [depth= 6] . ( 1 sec) [ -5372.5522] [ 814] [depth= 11] . ( 1 sec) [ -5364.7797] [ 813] [depth= 4] . ( 1 sec) [ -5329.9956] [ 812] [depth= 11] . ( 1 sec) [ -5317.7030] [ 808] [depth= 6] . ( 1 sec) [ -5294.1200] [ 808] [depth= 1] . ( 1 sec) [ -5241.4437] [ 794] [depth= 2] . ( 1 sec) [ -5225.0334] [ 792] [depth= 1] . ( 1 sec) [ -5163.9039] [ 785] [depth= 11] . ( 1 sec) [ -5119.2350] [ 787] [depth= 1] . ( 1 sec) [ -5098.5165] [ 786] [depth= 7] . ( 1 sec) [ -5022.3014] [ 782] [depth= 5] . ( 1 sec) [ -4990.9719] [ 763] [depth= 1] . ( 1 sec) [ -4908.5800] [ 743] [depth= 12] . ( 1 sec) [ -4855.6737] [ 741] [depth= 17] . ( 1 sec) [ -4846.3526] [ 737] [depth= 1] . ( 1 sec) [ -4816.1487] [ 729] [depth= 7] . ( 1 sec) [ -4787.0487] [ 715] [depth= 4] . ( 1 sec) [ -4717.7577] [ 714] [depth= 1] . ( 1 sec) [ -4717.0466] [ 714] [depth= 3] . ( 1 sec) [ -4707.2287] [ 717] [depth= 9] . ( 1 sec) [ -4651.2837] [ 722] [depth= 1] . ( 1 sec) [ -4591.0050] [ 701] [depth= 11] . ( 1 sec) [ -4568.3495] [ 703] [depth= 2] . ( 1 sec) [ -4554.4176] [ 700] [depth= 1] . ( 1 sec) [ -4541.3845] [ 700] [depth= 1] . ( 1 sec) [ -4509.9419] [ 700] [depth= 3] . ( 1 sec) [ -4498.1546] [ 696] [depth= 7] . ( 2 sec) [ -4490.4435] [ 696] [depth= 1] . ( 2 sec) [ -4490.1141] [ 696] [depth= 1] . ( 2 sec) [ -4333.5547] [ 674] [depth= 5] . ( 2 sec) [ -4333.1990] [ 674] [depth= 1] . ( 2 sec) [ -4168.7634] [ 645] [depth= 5] . ( 2 sec) [ -4115.4833] [ 639] [depth= 2] . ( 2 sec) [ -4038.1562] [ 618] [depth= 2] . ( 2 sec) [ -3990.4590] [ 610] [depth= 4] . ( 2 sec) [ -3972.6118] [ 610] [depth= 1] . ( 2 sec) [ -3844.1963] [ 565] [depth= 9] . ( 2 sec) [ -3840.6882] [ 566] [depth= 1] . ( 2 sec) [ -3749.0288] [ 545] [depth= 3] . ( 2 sec) [ -3684.3547] [ 530] [depth= 4] . ( 2 sec) [ -3666.4029] [ 521] [depth= 1] . ( 2 sec) [ -3636.3002] [ 514] [depth= 2] . ( 2 sec) [ -3528.2559] [ 488] [depth= 2] . ( 2 sec) [ -3524.9285] [ 487] [depth= 2] . ( 2 sec) [ -3511.5130] [ 484] [depth= 3] . ( 2 sec) [ -3509.8751] [ 485] [depth= 1] . ( 2 sec) [ -3507.5111] [ 485] [depth= 1] . ( 3 sec) [ -3491.1078] [ 485] [depth= 1] . ( 3 sec) [ -3490.4876] [ 484] [depth= 1] . ( 3 sec) [ -3480.3657] [ 481] [depth= 1] . ( 3 sec) [ -3472.5478] [ 479] [depth= 1] . ( 3 sec) [ -3470.2111] [ 481] [depth= 1] . ( 3 sec) [ -3469.9024] [ 480] [depth= 1] . ( 3 sec) [ -3454.3704] [ 477] [depth= 4] . ( 3 sec) [ -3452.3289] [ 477] [depth= 1] . ( 3 sec) [ -3443.6821] [Branch lengths ] . ( 4 sec) [ -3440.0769] [GTR parameters ] . ( 4 sec) [ -3431.5988] [Alpha ][ 0.911553] . ( 4 sec) [ -3426.5946] [ 475] [depth= 2] . ( 4 sec) [ -3421.2810] [ 472] [depth= 2] . ( 4 sec) [ -3403.9716] [ 462] [depth= 2] . ( 4 sec) [ -3403.9561] [ 462] [depth= 1] . ( 5 sec) [ -3403.9436] [ 462] [depth= 1] . ( 5 sec) [ -3401.0804] [ 461] [depth= 2] . ( 6 sec) [ -3401.0424] [ 461] [depth= 1] . ( 7 sec) [ -3401.0281] [ 461] [depth= 1] . ( 7 sec) [ -3391.1880] [ 459] [depth= 3] . ( 8 sec) [ -3391.1760] [ 459] [depth= 1] . ( 8 sec) [ -3391.0575] [ 459] [depth= 1] . ( 8 sec) [ -3390.5269] [ 463] [depth= 1] . ( 9 sec) [ -3390.3374] [ 463] [depth= 1] . ( 9 sec) [ -3388.6375] [Branch lengths ] . ( 9 sec) [ -3388.4485] [GTR parameters ] . ( 9 sec) [ -3388.2921] [Alpha ][ 1.001376] . ( 10 sec) [ -3383.6619] [ 459] [depth= 1] . ( 15 sec) [ -3383.1042] [Branch lengths ] . ( 15 sec) [ -3383.0912] [GTR parameters ] . ( 15 sec) [ -3383.0792] [Alpha ][ 1.028478] . ( 21 sec) [ -3383.0730] [Branch lengths ] . ( 38 sec) [ -3383.0730] [Branch lengths ] . ( 38 sec) [ -3383.0730] [Topology ] . ( 38 sec) [ -3383.0730] [Topology ] . ( 38 sec) [ -3383.0729] [GTR parameters ] . ( 38 sec) [ -3383.0729] [Alpha ][ 1.029507] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3383.072875. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -7562.5858] [GTR parameters ] . ( 1 sec) [ -7453.5613] [Alpha ][ 0.500960] . ( 1 sec) [ -7403.6955] [ 1008] [depth= 6] . ( 1 sec) [ -7273.7048] [ 998] [depth= 4] . ( 1 sec) [ -7267.4308] [ 996] [depth= 3] . ( 1 sec) [ -7253.0330] [ 996] [depth= 4] . ( 1 sec) [ -7234.4026] [ 992] [depth= 8] . ( 1 sec) [ -7230.0204] [ 992] [depth= 1] . ( 1 sec) [ -7190.4889] [ 986] [depth= 13] . ( 1 sec) [ -7081.6065] [ 986] [depth= 1] . ( 1 sec) [ -6851.9058] [ 947] [depth= 18] . ( 1 sec) [ -6786.4988] [ 932] [depth= 16] . ( 1 sec) [ -6677.6030] [ 920] [depth= 12] . ( 1 sec) [ -6625.8632] [ 915] [depth= 10] . ( 1 sec) [ -6517.7516] [ 903] [depth= 11] . ( 1 sec) [ -6481.1778] [ 903] [depth= 1] . ( 1 sec) [ -6463.2391] [ 903] [depth= 4] . ( 1 sec) [ -6454.0146] [ 902] [depth= 2] . ( 1 sec) [ -6431.4737] [ 901] [depth= 7] . ( 1 sec) [ -6422.7272] [ 901] [depth= 1] . ( 1 sec) [ -6411.6451] [ 901] [depth= 1] . ( 1 sec) [ -6406.6612] [ 900] [depth= 1] . ( 1 sec) [ -6392.7730] [ 899] [depth= 3] . ( 1 sec) [ -6185.3432] [ 853] [depth= 14] . ( 1 sec) [ -6176.2516] [ 850] [depth= 6] . ( 1 sec) [ -6163.9498] [ 845] [depth= 5] . ( 1 sec) [ -6116.7258] [ 840] [depth= 11] . ( 1 sec) [ -6116.3594] [ 840] [depth= 6] . ( 1 sec) [ -6025.6358] [ 816] [depth= 7] . ( 2 sec) [ -6019.8460] [ 814] [depth= 2] . ( 2 sec) [ -6009.6962] [ 813] [depth= 3] . ( 2 sec) [ -5965.0929] [ 807] [depth= 8] . ( 2 sec) [ -5904.6123] [ 804] [depth= 4] . ( 2 sec) [ -5899.9188] [ 807] [depth= 4] . ( 2 sec) [ -5854.7451] [ 791] [depth= 9] . ( 2 sec) [ -5811.4742] [ 790] [depth= 9] . ( 2 sec) [ -5652.0765] [ 752] [depth= 10] . ( 2 sec) [ -5589.5170] [ 738] [depth= 7] . ( 2 sec) [ -5582.9502] [ 736] [depth= 2] . ( 2 sec) [ -5551.4706] [ 727] [depth= 1] . ( 2 sec) [ -5532.6089] [ 723] [depth= 2] . ( 2 sec) [ -5472.4120] [ 721] [depth= 6] . ( 2 sec) [ -5312.8975] [ 691] [depth= 1] . ( 2 sec) [ -5238.7939] [ 680] [depth= 4] . ( 2 sec) [ -5237.6765] [ 680] [depth= 1] . ( 2 sec) [ -5214.4984] [ 672] [depth= 2] . ( 2 sec) [ -5187.9061] [ 653] [depth= 7] . ( 2 sec) [ -4441.1513] [ 655] [depth= 8] . ( 2 sec) [ -4414.1711] [ 650] [depth= 9] . ( 2 sec) [ -4343.3423] [ 630] [depth= 11] . ( 2 sec) [ -4332.0522] [ 627] [depth= 4] . ( 2 sec) [ -4325.0382] [ 615] [depth= 3] . ( 2 sec) [ -4323.4591] [ 615] [depth= 2] . ( 3 sec) [ -4309.9123] [ 615] [depth= 1] . ( 3 sec) [ -4227.4387] [ 615] [depth= 2] . ( 3 sec) [ -4055.7899] [ 586] [depth= 5] . ( 3 sec) [ -4049.2803] [ 589] [depth= 3] . ( 3 sec) [ -4022.3796] [ 586] [depth= 6] . ( 3 sec) [ -4005.9899] [ 585] [depth= 2] . ( 3 sec) [ -4005.9494] [ 585] [depth= 3] . ( 3 sec) [ -3997.8546] [ 585] [depth= 2] . ( 3 sec) [ -3994.3134] [ 584] [depth= 1] . ( 3 sec) [ -3971.2038] [ 574] [depth= 3] . ( 3 sec) [ -3909.8286] [ 556] [depth= 5] . ( 3 sec) [ -3894.2302] [ 555] [depth= 2] . ( 3 sec) [ -3889.8302] [ 552] [depth= 2] . ( 3 sec) [ -3839.0092] [ 540] [depth= 1] . ( 3 sec) [ -3834.7317] [ 541] [depth= 3] . ( 3 sec) [ -3794.5599] [ 539] [depth= 2] . ( 4 sec) [ -3651.6424] [ 516] [depth= 1] . ( 4 sec) [ -3632.6159] [ 511] [depth= 3] . ( 4 sec) [ -3626.4200] [ 509] [depth= 1] . ( 4 sec) [ -3606.6762] [ 505] [depth= 1] . ( 4 sec) [ -3563.2305] [ 493] [depth= 9] . ( 4 sec) [ -3561.8192] [ 493] [depth= 1] . ( 4 sec) [ -3559.9290] [ 493] [depth= 1] . ( 4 sec) [ -3512.1925] [Branch lengths ] . ( 5 sec) [ -3503.9109] [GTR parameters ] . ( 5 sec) [ -3497.0197] [Alpha ][ 0.835054] . ( 5 sec) [ -3495.1958] [ 493] [depth= 3] . ( 5 sec) [ -3488.9031] [ 490] [depth= 2] . ( 5 sec) [ -3452.2872] [ 479] [depth= 7] . ( 5 sec) [ -3442.6018] [ 476] [depth= 1] . ( 6 sec) [ -3438.1695] [ 477] [depth= 1] . ( 6 sec) [ -3436.0746] [ 477] [depth= 1] . ( 6 sec) [ -3436.0591] [ 477] [depth= 1] . ( 6 sec) [ -3428.8440] [ 472] [depth= 1] . ( 6 sec) [ -3427.4651] [ 471] [depth= 1] . ( 6 sec) [ -3419.3837] [ 468] [depth= 1] . ( 7 sec) [ -3419.3434] [ 468] [depth= 1] . ( 7 sec) [ -3418.1827] [ 467] [depth= 1] . ( 8 sec) [ -3385.4844] [ 459] [depth= 6] . ( 8 sec) [ -3385.4618] [ 459] [depth= 1] . ( 8 sec) [ -3385.4505] [ 459] [depth= 1] . ( 9 sec) [ -3385.4385] [ 459] [depth= 1] . ( 10 sec) [ -3384.2017] [Branch lengths ] . ( 10 sec) [ -3383.8610] [GTR parameters ] . ( 10 sec) [ -3383.0879] [Alpha ][ 1.025998] . ( 16 sec) [ -3383.0802] [Branch lengths ] . ( 32 sec) [ -3383.0799] [Branch lengths ] . ( 32 sec) [ -3383.0799] [Topology ] . ( 33 sec) [ -3383.0799] [Topology ] . ( 33 sec) [ -3383.0731] [GTR parameters ] . ( 33 sec) [ -3383.0730] [Alpha ][ 1.029312] . ( 33 sec) [ -3383.0730] [Topology ] . ( 33 sec) [ -3383.0729] [Topology ] . ( 33 sec) [ -3383.0729] [GTR parameters ] . ( 33 sec) [ -3383.0729] [Alpha ][ 1.029312] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3383.072941. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-3389.217077 . ( 0 sec) [ -3388.1055] [GTR parameters ] . ( 0 sec) [ -3388.1023] [Alpha ][ 1.014501] . ( 0 sec) [ -3388.1023] [Topology ] . ( 0 sec) [ -3383.8115] [Topology ] . ( 1 sec) [ -3383.2249] [Topology ] . ( 1 sec) [ -3383.1115] [Topology ] . ( 2 sec) [ -3383.0856] [Topology ] . ( 2 sec) [ -3383.0793] [Topology ] . ( 3 sec) [ -3383.0777] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-3383.077747 . ( 6 sec) [ -3383.0772] [GTR parameters ] . ( 6 sec) [ -3383.0738] [Alpha ][ 1.029469] . ( 6 sec) [ -3383.0738] [Topology ] . ( 6 sec) [ -3383.0731] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-3383.073108 . ( 9 sec) [ -3383.0731] [GTR parameters ] . ( 9 sec) [ -3383.0731] [Alpha ][ 1.029469] . ( 9 sec) [ -3383.0731] [Topology ] . ( 9 sec) [ -3383.0730] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 15 sec) [ -3388.1055] [GTR parameters ] . ( 15 sec) [ -3388.1023] [Alpha ][ 1.014501] . ( 16 sec) [ -3388.0399] [ 459] [depth= 1] . ( 16 sec) [ -3388.0145] [ 459] [depth= 1] . ( 16 sec) [ -3387.9654] [ 459] [depth= 1] . ( 17 sec) [ -3387.4861] [ 459] [depth= 1] . ( 17 sec) [ -3387.4233] [ 459] [depth= 1] . ( 17 sec) [ -3387.2541] [ 459] [depth= 1] . ( 18 sec) [ -3387.1683] [ 459] [depth= 1] . ( 18 sec) [ -3387.1491] [ 459] [depth= 1] . ( 18 sec) [ -3387.0827] [ 459] [depth= 1] . ( 18 sec) [ -3387.0697] [ 459] [depth= 1] . ( 18 sec) [ -3387.0574] [ 459] [depth= 1] . ( 19 sec) [ -3386.6385] [ 459] [depth= 1] . ( 19 sec) [ -3386.5808] [ 459] [depth= 1] . ( 19 sec) [ -3386.3717] [ 459] [depth= 1] . ( 19 sec) [ -3386.2253] [ 459] [depth= 1] . ( 19 sec) [ -3385.9159] [ 459] [depth= 1] . ( 20 sec) [ -3383.0919] [Branch lengths ] . ( 20 sec) [ -3383.0915] [GTR parameters ] . ( 20 sec) [ -3383.0887] [Alpha ][ 1.028080] . ( 26 sec) [ -3383.0731] [Branch lengths ] . ( 42 sec) [ -3383.0729] [Branch lengths ] . ( 42 sec) [ -3383.0729] [Topology ] . ( 43 sec) [ -3383.0729] [Topology ] . ( 43 sec) [ -3383.0729] [GTR parameters ] . ( 43 sec) [ -3383.0728] [Alpha ][ 1.029174] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -3383.072958 . Log likelihood obtained after SPR moves : -3383.072831 . Log likelihood of the current tree: -3383.072831. . Printing the most likely tree in file 'data22.phy_phyml_tree.txt'... . Best log likelihood : -3383.072831 . Time used 0h0m46s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo