.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data74.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... . 241 patterns found. (out of a total of 500 sites) . 238 sites without polymorphism (47.60%). . [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) [ -10124.5145] [GTR parameters ] . ( 0 sec) [ -9962.5024] [Alpha ][ 0.500960] . ( 0 sec) [ -9880.1292] [ 1251] [depth= 8] . ( 0 sec) [ -8728.2596] [ 1250] [depth= 13] . ( 0 sec) [ -8357.2042] [ 1246] [depth= 6] . ( 0 sec) [ -8319.6062] [ 1246] [depth= 5] . ( 0 sec) [ -8294.5378] [ 1238] [depth= 6] . ( 0 sec) [ -8283.5882] [ 1238] [depth= 2] . ( 0 sec) [ -8277.1117] [ 1231] [depth= 11] . ( 0 sec) [ -8183.6106] [ 1231] [depth= 1] . ( 0 sec) [ -8080.1742] [ 1197] [depth= 9] . ( 1 sec) [ -7975.2807] [ 1161] [depth= 8] . ( 1 sec) [ -7838.9863] [ 1129] [depth= 3] . ( 1 sec) [ -7701.6140] [ 1104] [depth= 1] . ( 1 sec) [ -7612.2286] [ 1088] [depth= 14] . ( 1 sec) [ -7584.9010] [ 1088] [depth= 9] . ( 1 sec) [ -7545.3885] [ 1088] [depth= 2] . ( 1 sec) [ -7509.1024] [ 1079] [depth= 11] . ( 1 sec) [ -7496.5163] [ 1078] [depth= 2] . ( 1 sec) [ -7402.0415] [ 1059] [depth= 16] . ( 1 sec) [ -7398.5669] [ 1059] [depth= 1] . ( 1 sec) [ -7210.4777] [ 1048] [depth= 3] . ( 1 sec) [ -7000.5566] [ 1041] [depth= 20] . ( 1 sec) [ -6998.9796] [ 1039] [depth= 3] . ( 1 sec) [ -6664.6308] [ 1017] [depth= 4] . ( 1 sec) [ -6571.3616] [ 989] [depth= 13] . ( 1 sec) [ -6519.1198] [ 989] [depth= 4] . ( 1 sec) [ -6354.7692] [ 924] [depth= 17] . ( 1 sec) [ -6246.6964] [ 920] [depth= 4] . ( 1 sec) [ -6123.8123] [ 887] [depth= 3] . ( 1 sec) [ -5743.2333] [ 886] [depth= 8] . ( 1 sec) [ -5726.3787] [ 891] [depth= 1] . ( 1 sec) [ -5603.6300] [ 888] [depth= 10] . ( 1 sec) [ -5593.4091] [ 888] [depth= 1] . ( 1 sec) [ -5558.2444] [ 888] [depth= 2] . ( 1 sec) [ -5464.8601] [ 863] [depth= 13] . ( 1 sec) [ -5206.5572] [ 844] [depth= 10] . ( 1 sec) [ -5184.5793] [ 843] [depth= 1] . ( 1 sec) [ -5124.4979] [ 816] [depth= 8] . ( 1 sec) [ -5066.2521] [ 802] [depth= 1] . ( 1 sec) [ -4843.1810] [ 799] [depth= 4] . ( 1 sec) [ -4790.8386] [ 792] [depth= 1] . ( 1 sec) [ -4770.5381] [ 781] [depth= 9] . ( 1 sec) [ -4751.8213] [ 777] [depth= 1] . ( 1 sec) [ -4620.1247] [ 748] [depth= 5] . ( 1 sec) [ -4580.1916] [ 740] [depth= 2] . ( 1 sec) [ -4382.8749] [ 722] [depth= 7] . ( 2 sec) [ -4373.7165] [ 722] [depth= 1] . ( 2 sec) [ -4351.4240] [ 722] [depth= 15] . ( 2 sec) [ -4341.8910] [ 723] [depth= 6] . ( 2 sec) [ -4341.0938] [ 724] [depth= 1] . ( 2 sec) [ -4340.0527] [ 722] [depth= 2] . ( 2 sec) [ -4317.2707] [ 722] [depth= 9] . ( 2 sec) [ -4313.3322] [ 721] [depth= 1] . ( 2 sec) [ -4141.5210] [ 663] [depth= 5] . ( 2 sec) [ -4134.3820] [ 663] [depth= 2] . ( 2 sec) [ -4072.9926] [ 639] [depth= 5] . ( 2 sec) [ -4067.6265] [ 639] [depth= 2] . ( 2 sec) [ -4050.4411] [ 636] [depth= 1] . ( 2 sec) [ -3959.5223] [ 612] [depth= 1] . ( 2 sec) [ -3957.6349] [ 611] [depth= 2] . ( 2 sec) [ -3927.0530] [ 594] [depth= 4] . ( 2 sec) [ -3850.8269] [ 576] [depth= 4] . ( 2 sec) [ -3813.4568] [ 566] [depth= 3] . ( 2 sec) [ -3812.1391] [ 566] [depth= 4] . ( 2 sec) [ -3807.5523] [ 565] [depth= 2] . ( 2 sec) [ -3752.1251] [ 551] [depth= 3] . ( 2 sec) [ -3747.6856] [ 551] [depth= 1] . ( 2 sec) [ -3664.0470] [ 530] [depth= 1] . ( 2 sec) [ -3663.2082] [ 529] [depth= 3] . ( 2 sec) [ -3661.5664] [ 529] [depth= 1] . ( 2 sec) [ -3637.1451] [ 514] [depth= 2] . ( 2 sec) [ -3612.4566] [ 507] [depth= 3] . ( 2 sec) [ -3604.8844] [ 507] [depth= 2] . ( 3 sec) [ -3578.4456] [ 498] [depth= 1] . ( 3 sec) [ -3577.6497] [ 498] [depth= 1] . ( 3 sec) [ -3576.7853] [ 497] [depth= 1] . ( 3 sec) [ -3573.4138] [ 500] [depth= 2] . ( 3 sec) [ -3532.4692] [Branch lengths ] . ( 3 sec) [ -3530.7651] [GTR parameters ] . ( 3 sec) [ -3518.3188] [Alpha ][ 1.000782] . ( 3 sec) [ -3513.5172] [ 499] [depth= 1] . ( 3 sec) [ -3502.2266] [ 497] [depth= 1] . ( 4 sec) [ -3494.6120] [ 488] [depth= 1] . ( 4 sec) [ -3492.3568] [ 487] [depth= 1] . ( 4 sec) [ -3451.7752] [ 475] [depth= 1] . ( 4 sec) [ -3446.1273] [ 473] [depth= 3] . ( 4 sec) [ -3445.7574] [ 472] [depth= 1] . ( 4 sec) [ -3438.0054] [ 472] [depth= 1] . ( 4 sec) [ -3433.6965] [ 471] [depth= 2] . ( 5 sec) [ -3432.5174] [ 471] [depth= 1] . ( 6 sec) [ -3432.2241] [ 471] [depth= 1] . ( 6 sec) [ -3425.6021] [Branch lengths ] . ( 7 sec) [ -3425.4736] [GTR parameters ] . ( 7 sec) [ -3424.7144] [Alpha ][ 1.249480] . ( 10 sec) [ -3424.6948] [Branch lengths ] . ( 24 sec) [ -3424.6945] [Branch lengths ] . ( 24 sec) [ -3424.6945] [Topology ] . ( 25 sec) [ -3424.6945] [Topology ] . ( 25 sec) [ -3424.6931] [GTR parameters ] . ( 25 sec) [ -3424.6931] [Alpha ][ 1.251662] . ( 25 sec) [ -3424.6931] [Topology ] . ( 25 sec) [ -3424.6931] [Topology ] . ( 25 sec) [ -3424.6931] [GTR parameters ] . ( 25 sec) [ -3424.6931] [Alpha ][ 1.251662] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3424.693074. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -9519.1654] [GTR parameters ] . ( 0 sec) [ -9355.4411] [Alpha ][ 0.500960] . ( 0 sec) [ -9323.6277] [ 1281] [depth= 3] . ( 0 sec) [ -7872.3869] [ 1279] [depth= 10] . ( 0 sec) [ -7849.1455] [ 1271] [depth= 3] . ( 0 sec) [ -7821.3789] [ 1271] [depth= 2] . ( 0 sec) [ -7802.8362] [ 1264] [depth= 3] . ( 0 sec) [ -7783.8746] [ 1264] [depth= 6] . ( 0 sec) [ -7749.9358] [ 1263] [depth= 3] . ( 0 sec) [ -7680.9674] [ 1236] [depth= 1] . ( 1 sec) [ -7644.7527] [ 1236] [depth= 1] . ( 1 sec) [ -7463.0410] [ 1224] [depth= 10] . ( 1 sec) [ -7397.8187] [ 1224] [depth= 3] . ( 1 sec) [ -7149.1924] [ 1183] [depth= 14] . ( 1 sec) [ -7028.1610] [ 1181] [depth= 4] . ( 1 sec) [ -6813.5273] [ 1150] [depth= 17] . ( 1 sec) [ -6729.8441] [ 1116] [depth= 17] . ( 1 sec) [ -6633.0706] [ 1101] [depth= 4] . ( 1 sec) [ -6612.6166] [ 1100] [depth= 3] . ( 1 sec) [ -6599.1094] [ 1096] [depth= 1] . ( 1 sec) [ -6590.6073] [ 1101] [depth= 1] . ( 1 sec) [ -6521.2285] [ 1069] [depth= 2] . ( 1 sec) [ -6367.2829] [ 1032] [depth= 17] . ( 1 sec) [ -6335.1070] [ 1026] [depth= 4] . ( 1 sec) [ -6312.6466] [ 1014] [depth= 2] . ( 1 sec) [ -6240.0184] [ 1005] [depth= 16] . ( 1 sec) [ -6128.1823] [ 961] [depth= 15] . ( 1 sec) [ -5824.9220] [ 940] [depth= 7] . ( 1 sec) [ -5818.0662] [ 918] [depth= 2] . ( 1 sec) [ -5772.5210] [ 906] [depth= 1] . ( 1 sec) [ -5714.1604] [ 893] [depth= 7] . ( 1 sec) [ -5701.1501] [ 886] [depth= 3] . ( 1 sec) [ -5551.9897] [ 886] [depth= 4] . ( 1 sec) [ -5529.1726] [ 885] [depth= 1] . ( 1 sec) [ -5520.7440] [ 885] [depth= 5] . ( 1 sec) [ -5467.1801] [ 884] [depth= 2] . ( 1 sec) [ -5359.2930] [ 851] [depth= 9] . ( 1 sec) [ -5177.7893] [ 850] [depth= 2] . ( 1 sec) [ -5097.5945] [ 834] [depth= 6] . ( 1 sec) [ -5030.7458] [ 820] [depth= 1] . ( 1 sec) [ -5002.4696] [ 807] [depth= 6] . ( 1 sec) [ -4912.4351] [ 783] [depth= 3] . ( 2 sec) [ -4883.0902] [ 775] [depth= 2] . ( 2 sec) [ -4802.6358] [ 766] [depth= 4] . ( 2 sec) [ -4735.5487] [ 752] [depth= 6] . ( 2 sec) [ -4666.7953] [ 729] [depth= 7] . ( 2 sec) [ -4574.7483] [ 718] [depth= 2] . ( 2 sec) [ -4567.3793] [ 718] [depth= 1] . ( 2 sec) [ -4527.9240] [ 717] [depth= 1] . ( 2 sec) [ -4514.5667] [ 717] [depth= 2] . ( 2 sec) [ -4508.6528] [ 718] [depth= 1] . ( 2 sec) [ -4482.4585] [ 719] [depth= 2] . ( 2 sec) [ -4437.9814] [ 707] [depth= 7] . ( 2 sec) [ -4391.7715] [ 695] [depth= 4] . ( 2 sec) [ -4196.5341] [ 633] [depth= 6] . ( 2 sec) [ -4140.4771] [ 617] [depth= 1] . ( 2 sec) [ -4078.1780] [ 603] [depth= 1] . ( 2 sec) [ -4029.9111] [ 585] [depth= 3] . ( 2 sec) [ -4002.5723] [ 583] [depth= 6] . ( 2 sec) [ -3961.1294] [ 573] [depth= 7] . ( 2 sec) [ -3958.6390] [ 573] [depth= 1] . ( 2 sec) [ -3952.9680] [ 574] [depth= 1] . ( 2 sec) [ -3914.2629] [ 565] [depth= 5] . ( 2 sec) [ -3909.4022] [ 565] [depth= 1] . ( 2 sec) [ -3908.8191] [ 565] [depth= 1] . ( 2 sec) [ -3887.9103] [ 566] [depth= 1] . ( 2 sec) [ -3874.3091] [ 562] [depth= 1] . ( 2 sec) [ -3764.7485] [ 539] [depth= 3] . ( 2 sec) [ -3760.3519] [ 536] [depth= 1] . ( 2 sec) [ -3745.1739] [ 536] [depth= 1] . ( 2 sec) [ -3706.7798] [ 522] [depth= 2] . ( 2 sec) [ -3693.3409] [ 523] [depth= 1] . ( 2 sec) [ -3685.5104] [ 522] [depth= 2] . ( 3 sec) [ -3684.7757] [ 522] [depth= 1] . ( 3 sec) [ -3682.6823] [ 522] [depth= 1] . ( 3 sec) [ -3677.4161] [ 521] [depth= 4] . ( 3 sec) [ -3676.4008] [ 521] [depth= 1] . ( 3 sec) [ -3676.2886] [ 521] [depth= 1] . ( 3 sec) [ -3626.6980] [Branch lengths ] . ( 3 sec) [ -3624.9391] [GTR parameters ] . ( 3 sec) [ -3616.2872] [Alpha ][ 0.881939] . ( 4 sec) [ -3536.3811] [ 499] [depth= 7] . ( 4 sec) [ -3517.9733] [ 498] [depth= 2] . ( 4 sec) [ -3504.3945] [ 493] [depth= 1] . ( 4 sec) [ -3499.0791] [ 491] [depth= 1] . ( 4 sec) [ -3494.0485] [ 492] [depth= 1] . ( 4 sec) [ -3493.4532] [ 491] [depth= 1] . ( 4 sec) [ -3476.6038] [ 483] [depth= 1] . ( 4 sec) [ -3473.0054] [ 482] [depth= 1] . ( 4 sec) [ -3469.2625] [ 484] [depth= 2] . ( 4 sec) [ -3460.6966] [ 475] [depth= 1] . ( 4 sec) [ -3458.6635] [ 475] [depth= 1] . ( 4 sec) [ -3458.5613] [ 475] [depth= 1] . ( 4 sec) [ -3454.0176] [ 476] [depth= 2] . ( 4 sec) [ -3453.9896] [ 476] [depth= 1] . ( 4 sec) [ -3449.1440] [ 477] [depth= 1] . ( 4 sec) [ -3448.8922] [ 476] [depth= 1] . ( 5 sec) [ -3442.3467] [ 474] [depth= 2] . ( 5 sec) [ -3441.2113] [ 474] [depth= 2] . ( 5 sec) [ -3437.3679] [ 473] [depth= 3] . ( 5 sec) [ -3431.4758] [ 472] [depth= 2] . ( 6 sec) [ -3431.3345] [ 472] [depth= 1] . ( 6 sec) [ -3427.3068] [Branch lengths ] . ( 7 sec) [ -3427.2569] [GTR parameters ] . ( 7 sec) [ -3425.3782] [Alpha ][ 1.238245] . ( 7 sec) [ -3424.9007] [ 471] [depth= 1] . ( 10 sec) [ -3424.6992] [Branch lengths ] . ( 10 sec) [ -3424.6957] [GTR parameters ] . ( 10 sec) [ -3424.6941] [Alpha ][ 1.251816] . ( 24 sec) [ -3424.6931] [Branch lengths ] . ( 24 sec) [ -3424.6931] [Topology ] . ( 25 sec) [ -3424.6931] [Topology ] . ( 25 sec) [ -3424.6931] [GTR parameters ] . ( 25 sec) [ -3424.6931] [Alpha ][ 1.251816] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3424.693102. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -10202.6565] [GTR parameters ] . ( 1 sec) [ -10024.7599] [Alpha ][ 0.500960] . ( 1 sec) [ -9969.4927] [ 1279] [depth= 8] . ( 1 sec) [ -9893.5578] [ 1278] [depth= 6] . ( 1 sec) [ -9799.1995] [ 1278] [depth= 1] . ( 1 sec) [ -9771.2306] [ 1278] [depth= 2] . ( 1 sec) [ -9708.3487] [ 1245] [depth= 5] . ( 1 sec) [ -9684.8260] [ 1245] [depth= 3] . ( 2 sec) [ -9486.9657] [ 1218] [depth= 8] . ( 2 sec) [ -9463.0134] [ 1218] [depth= 5] . ( 2 sec) [ -9236.2889] [ 1167] [depth= 9] . ( 2 sec) [ -9220.9719] [ 1176] [depth= 10] . ( 2 sec) [ -9059.7980] [ 1144] [depth= 8] . ( 2 sec) [ -8727.4100] [ 1131] [depth= 17] . ( 2 sec) [ -8642.3797] [ 1111] [depth= 7] . ( 2 sec) [ -8609.3729] [ 1110] [depth= 1] . ( 2 sec) [ -8604.8819] [ 1105] [depth= 2] . ( 3 sec) [ -8416.7536] [ 1104] [depth= 10] . ( 3 sec) [ -8366.9118] [ 1104] [depth= 1] . ( 3 sec) [ -8364.7457] [ 1097] [depth= 12] . ( 3 sec) [ -8163.2449] [ 1046] [depth= 13] . ( 3 sec) [ -8150.5932] [ 1046] [depth= 14] . ( 3 sec) [ -8142.0840] [ 1038] [depth= 2] . ( 3 sec) [ -8131.0384] [ 1036] [depth= 2] . ( 3 sec) [ -7789.7438] [ 976] [depth= 10] . ( 3 sec) [ -7783.1279] [ 974] [depth= 1] . ( 3 sec) [ -7710.3714] [ 956] [depth= 3] . ( 4 sec) [ -7663.5768] [ 953] [depth= 1] . ( 4 sec) [ -7559.1824] [ 923] [depth= 2] . ( 4 sec) [ -7468.8953] [ 912] [depth= 12] . ( 4 sec) [ -7349.6919] [ 917] [depth= 10] . ( 4 sec) [ -7289.1589] [ 916] [depth= 7] . ( 4 sec) [ -7249.3517] [ 908] [depth= 8] . ( 4 sec) [ -7099.4820] [ 887] [depth= 2] . ( 4 sec) [ -7048.6284] [ 862] [depth= 3] . ( 5 sec) [ -7039.9401] [ 862] [depth= 1] . ( 5 sec) [ -7008.8000] [ 852] [depth= 1] . ( 5 sec) [ -7001.8438] [ 848] [depth= 1] . ( 5 sec) [ -6882.0464] [ 818] [depth= 6] . ( 5 sec) [ -6753.7878] [ 830] [depth= 3] . ( 5 sec) [ -6753.0845] [ 830] [depth= 1] . ( 5 sec) [ -6555.5088] [ 823] [depth= 7] . ( 5 sec) [ -6468.4589] [ 799] [depth= 7] . ( 5 sec) [ -6462.3296] [ 798] [depth= 3] . ( 6 sec) [ -6460.0283] [ 798] [depth= 1] . ( 6 sec) [ -6458.3840] [ 796] [depth= 3] . ( 6 sec) [ -6424.6724] [ 795] [depth= 1] . ( 6 sec) [ -5269.7097] [ 778] [depth= 5] . ( 6 sec) [ -5163.9964] [ 794] [depth= 1] . ( 6 sec) [ -5159.3339] [ 783] [depth= 2] . ( 6 sec) [ -5057.0820] [ 781] [depth= 1] . ( 6 sec) [ -5029.4298] [ 780] [depth= 1] . ( 6 sec) [ -4989.1614] [ 778] [depth= 2] . ( 6 sec) [ -4967.2215] [ 779] [depth= 1] . ( 6 sec) [ -4961.3619] [ 780] [depth= 1] . ( 6 sec) [ -4946.1815] [ 780] [depth= 3] . ( 6 sec) [ -4848.0840] [ 752] [depth= 7] . ( 6 sec) [ -4848.0333] [ 753] [depth= 1] . ( 6 sec) [ -4847.8182] [ 753] [depth= 1] . ( 6 sec) [ -4806.2978] [ 735] [depth= 8] . ( 6 sec) [ -4806.0595] [ 735] [depth= 1] . ( 6 sec) [ -4705.3914] [ 703] [depth= 6] . ( 6 sec) [ -4572.2598] [ 683] [depth= 4] . ( 6 sec) [ -4447.1497] [ 653] [depth= 2] . ( 6 sec) [ -4438.4945] [ 650] [depth= 5] . ( 6 sec) [ -4438.2408] [ 652] [depth= 1] . ( 6 sec) [ -4415.6709] [ 648] [depth= 9] . ( 6 sec) [ -4411.4033] [ 643] [depth= 3] . ( 6 sec) [ -4407.3633] [ 638] [depth= 1] . ( 6 sec) [ -4162.0968] [ 638] [depth= 1] . ( 6 sec) [ -3999.3311] [ 605] [depth= 1] . ( 6 sec) [ -3913.2009] [ 587] [depth= 4] . ( 6 sec) [ -3881.4115] [ 585] [depth= 1] . ( 7 sec) [ -3880.6031] [ 586] [depth= 1] . ( 7 sec) [ -3880.5835] [ 586] [depth= 2] . ( 7 sec) [ -3880.5472] [ 586] [depth= 1] . ( 7 sec) [ -3872.3794] [ 585] [depth= 2] . ( 7 sec) [ -3816.7961] [ 573] [depth= 2] . ( 7 sec) [ -3815.6340] [ 572] [depth= 1] . ( 7 sec) [ -3815.0318] [ 572] [depth= 1] . ( 7 sec) [ -3810.1849] [ 571] [depth= 2] . ( 7 sec) [ -3809.1308] [ 571] [depth= 1] . ( 7 sec) [ -3804.0887] [ 570] [depth= 2] . ( 7 sec) [ -3726.5060] [ 554] [depth= 5] . ( 7 sec) [ -3676.8108] [Branch lengths ] . ( 7 sec) [ -3675.4402] [GTR parameters ] . ( 7 sec) [ -3670.9556] [Alpha ][ 0.722691] . ( 7 sec) [ -3578.8153] [ 511] [depth= 4] . ( 7 sec) [ -3578.7828] [ 511] [depth= 1] . ( 8 sec) [ -3578.1386] [ 511] [depth= 3] . ( 8 sec) [ -3572.0772] [ 508] [depth= 1] . ( 8 sec) [ -3570.2790] [ 508] [depth= 1] . ( 8 sec) [ -3568.7272] [ 508] [depth= 2] . ( 8 sec) [ -3550.0843] [ 505] [depth= 1] . ( 8 sec) [ -3549.8207] [ 505] [depth= 2] . ( 8 sec) [ -3486.0893] [ 482] [depth= 1] . ( 8 sec) [ -3483.7344] [ 481] [depth= 2] . ( 9 sec) [ -3480.7052] [ 482] [depth= 1] . ( 9 sec) [ -3480.3287] [ 481] [depth= 1] . ( 9 sec) [ -3461.0374] [ 473] [depth= 2] . ( 9 sec) [ -3460.9501] [ 473] [depth= 1] . ( 10 sec) [ -3459.7721] [ 472] [depth= 1] . ( 10 sec) [ -3459.5766] [ 473] [depth= 1] . ( 10 sec) [ -3459.3619] [ 474] [depth= 1] . ( 11 sec) [ -3457.2867] [Branch lengths ] . ( 11 sec) [ -3456.7110] [GTR parameters ] . ( 11 sec) [ -3452.5255] [Alpha ][ 1.158801] . ( 11 sec) [ -3450.6644] [ 473] [depth= 1] . ( 12 sec) [ -3450.6062] [ 472] [depth= 1] . ( 14 sec) [ -3448.9697] [Branch lengths ] . ( 15 sec) [ -3448.9661] [GTR parameters ] . ( 15 sec) [ -3448.9585] [Alpha ][ 1.184793] . ( 18 sec) [ -3445.3361] [Branch lengths ] . ( 32 sec) [ -3438.6111] [Branch lengths ] . ( 32 sec) [ -3438.6111] [Topology ] . ( 32 sec) [ -3438.0377] [Topology ] . ( 33 sec) [ -3437.7553] [Topology ] . ( 33 sec) [ -3436.3371] [Topology ] . ( 34 sec) [ -3431.8412] [Topology ] . ( 34 sec) [ -3425.8707] [Topology ] . ( 35 sec) [ -3424.9182] [Topology ] . ( 35 sec) [ -3424.8146] [Topology ] . ( 36 sec) [ -3424.8045] [Topology ] . ( 36 sec) [ -3424.8034] [Topology ] . ( 37 sec) [ -3424.7360] [GTR parameters ] . ( 37 sec) [ -3424.6938] [Alpha ][ 1.251112] . ( 37 sec) [ -3424.6938] [Topology ] . ( 37 sec) [ -3424.6932] [Topology ] . ( 37 sec) [ -3424.6931] [GTR parameters ] . ( 37 sec) [ -3424.6931] [Alpha ][ 1.252364] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3424.693120. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -8936.6747] [GTR parameters ] . ( 0 sec) [ -8771.6491] [Alpha ][ 0.500960] . ( 0 sec) [ -8609.6480] [ 1243] [depth= 8] . ( 0 sec) [ -8526.2508] [ 1212] [depth= 8] . ( 0 sec) [ -8470.8752] [ 1201] [depth= 8] . ( 0 sec) [ -8447.0203] [ 1192] [depth= 1] . ( 0 sec) [ -8422.3243] [ 1192] [depth= 3] . ( 0 sec) [ -8360.9099] [ 1182] [depth= 2] . ( 0 sec) [ -8297.8484] [ 1181] [depth= 2] . ( 0 sec) [ -8195.5691] [ 1172] [depth= 3] . ( 0 sec) [ -8142.3010] [ 1171] [depth= 5] . ( 0 sec) [ -8113.8499] [ 1170] [depth= 3] . ( 0 sec) [ -8050.3868] [ 1171] [depth= 1] . ( 0 sec) [ -7912.0603] [ 1133] [depth= 2] . ( 1 sec) [ -7825.4534] [ 1109] [depth= 5] . ( 1 sec) [ -7825.0803] [ 1108] [depth= 2] . ( 1 sec) [ -7805.8864] [ 1108] [depth= 1] . ( 1 sec) [ -7759.4274] [ 1088] [depth= 7] . ( 1 sec) [ -7582.2409] [ 1088] [depth= 1] . ( 1 sec) [ -7325.5383] [ 1049] [depth= 2] . ( 1 sec) [ -7216.2397] [ 1033] [depth= 20] . ( 1 sec) [ -7004.4903] [ 1010] [depth= 5] . ( 1 sec) [ -6438.2308] [ 1005] [depth= 1] . ( 1 sec) [ -6385.3558] [ 999] [depth= 3] . ( 1 sec) [ -6373.5151] [ 1003] [depth= 1] . ( 1 sec) [ -6363.4386] [ 1003] [depth= 9] . ( 1 sec) [ -6297.3023] [ 970] [depth= 10] . ( 1 sec) [ -6189.9041] [ 948] [depth= 1] . ( 1 sec) [ -6115.0184] [ 939] [depth= 16] . ( 1 sec) [ -6057.5264] [ 937] [depth= 2] . ( 1 sec) [ -6057.0816] [ 937] [depth= 3] . ( 1 sec) [ -6033.6724] [ 918] [depth= 2] . ( 1 sec) [ -6032.2151] [ 918] [depth= 1] . ( 1 sec) [ -5816.0398] [ 881] [depth= 12] . ( 1 sec) [ -5594.2119] [ 879] [depth= 7] . ( 1 sec) [ -5593.0138] [ 880] [depth= 9] . ( 1 sec) [ -5507.4275] [ 869] [depth= 4] . ( 1 sec) [ -5504.7094] [ 871] [depth= 2] . ( 1 sec) [ -5375.1809] [ 837] [depth= 15] . ( 1 sec) [ -5126.1357] [ 817] [depth= 6] . ( 1 sec) [ -5118.0137] [ 818] [depth= 5] . ( 1 sec) [ -5103.9945] [ 813] [depth= 1] . ( 1 sec) [ -4975.4763] [ 783] [depth= 8] . ( 2 sec) [ -4876.4792] [ 767] [depth= 10] . ( 2 sec) [ -4783.5335] [ 738] [depth= 2] . ( 2 sec) [ -4775.1337] [ 736] [depth= 2] . ( 2 sec) [ -4696.5409] [ 725] [depth= 11] . ( 2 sec) [ -4574.2131] [ 698] [depth= 1] . ( 2 sec) [ -4533.5052] [ 698] [depth= 3] . ( 2 sec) [ -4436.5810] [ 686] [depth= 4] . ( 2 sec) [ -4335.7919] [ 671] [depth= 1] . ( 2 sec) [ -4314.1999] [ 671] [depth= 1] . ( 2 sec) [ -4314.0215] [ 671] [depth= 1] . ( 2 sec) [ -4221.4267] [ 644] [depth= 4] . ( 2 sec) [ -4217.9902] [ 643] [depth= 1] . ( 2 sec) [ -4209.6835] [ 641] [depth= 3] . ( 2 sec) [ -4188.4276] [ 641] [depth= 2] . ( 2 sec) [ -4185.7406] [ 641] [depth= 1] . ( 2 sec) [ -4016.8127] [ 631] [depth= 5] . ( 2 sec) [ -4016.1299] [ 633] [depth= 2] . ( 3 sec) [ -4011.1682] [ 638] [depth= 1] . ( 3 sec) [ -4010.5478] [ 638] [depth= 1] . ( 3 sec) [ -4009.1609] [ 637] [depth= 1] . ( 3 sec) [ -4001.7220] [ 636] [depth= 1] . ( 3 sec) [ -4000.4179] [ 636] [depth= 1] . ( 3 sec) [ -3978.4766] [ 628] [depth= 1] . ( 3 sec) [ -3977.9754] [ 628] [depth= 1] . ( 3 sec) [ -3974.8388] [ 626] [depth= 1] . ( 3 sec) [ -3965.7407] [ 614] [depth= 2] . ( 3 sec) [ -3791.3643] [ 570] [depth= 16] . ( 4 sec) [ -3777.6229] [ 565] [depth= 1] . ( 4 sec) [ -3777.1348] [ 566] [depth= 2] . ( 4 sec) [ -3776.4381] [ 566] [depth= 1] . ( 4 sec) [ -3775.9588] [ 566] [depth= 1] . ( 4 sec) [ -3775.9363] [ 566] [depth= 1] . ( 4 sec) [ -3699.6749] [ 533] [depth= 5] . ( 4 sec) [ -3649.8427] [ 524] [depth= 6] . ( 4 sec) [ -3646.0897] [ 522] [depth= 1] . ( 4 sec) [ -3641.4096] [ 523] [depth= 1] . ( 5 sec) [ -3610.3814] [Branch lengths ] . ( 5 sec) [ -3608.6924] [GTR parameters ] . ( 5 sec) [ -3600.4156] [Alpha ][ 0.869604] . ( 5 sec) [ -3597.1114] [ 522] [depth= 1] . ( 5 sec) [ -3564.0617] [ 511] [depth= 1] . ( 5 sec) [ -3493.2021] [ 487] [depth= 2] . ( 5 sec) [ -3491.3559] [ 488] [depth= 2] . ( 6 sec) [ -3451.8456] [ 476] [depth= 2] . ( 6 sec) [ -3449.2415] [ 475] [depth= 1] . ( 6 sec) [ -3447.1500] [ 474] [depth= 1] . ( 6 sec) [ -3447.0540] [ 474] [depth= 1] . ( 7 sec) [ -3446.2116] [ 473] [depth= 1] . ( 7 sec) [ -3441.2313] [ 471] [depth= 1] . ( 7 sec) [ -3441.1199] [ 472] [depth= 1] . ( 7 sec) [ -3440.6660] [ 471] [depth= 1] . ( 8 sec) [ -3438.9952] [Branch lengths ] . ( 8 sec) [ -3438.8346] [GTR parameters ] . ( 8 sec) [ -3437.1153] [Alpha ][ 1.197223] . ( 12 sec) [ -3437.0668] [Branch lengths ] . ( 26 sec) [ -3437.0639] [Branch lengths ] . ( 26 sec) [ -3437.0639] [Topology ] . ( 26 sec) [ -3437.0593] [Topology ] . ( 26 sec) [ -3437.0246] [Topology ] . ( 27 sec) [ -3436.7655] [Topology ] . ( 27 sec) [ -3435.1713] [Topology ] . ( 28 sec) [ -3429.9558] [Topology ] . ( 28 sec) [ -3425.3142] [Topology ] . ( 28 sec) [ -3425.2902] [GTR parameters ] . ( 28 sec) [ -3425.2605] [Alpha ][ 1.253822] . ( 28 sec) [ -3425.2605] [Topology ] . ( 29 sec) [ -3424.7541] [Topology ] . ( 29 sec) [ -3424.7013] [Topology ] . ( 30 sec) [ -3424.6960] [Topology ] . ( 30 sec) [ -3424.6954] [Topology ] . ( 31 sec) [ -3424.6934] [GTR parameters ] . ( 31 sec) [ -3424.6934] [Alpha ][ 1.251581] . ( 31 sec) [ -3424.6934] [Topology ] . ( 32 sec) [ -3424.6932] [Topology ] . ( 32 sec) [ -3424.6932] [GTR parameters ] . ( 32 sec) [ -3424.6932] [Alpha ][ 1.251581] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3424.693248. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -10340.6121] [GTR parameters ] . ( 0 sec) [ -10182.8802] [Alpha ][ 0.500960] . ( 0 sec) [ -10075.6445] [ 1280] [depth= 6] . ( 0 sec) [ -9995.8304] [ 1272] [depth= 4] . ( 0 sec) [ -9981.4838] [ 1272] [depth= 2] . ( 0 sec) [ -9978.0652] [ 1272] [depth= 2] . ( 1 sec) [ -9929.1822] [ 1272] [depth= 4] . ( 1 sec) [ -9918.2833] [ 1272] [depth= 2] . ( 1 sec) [ -9725.9890] [ 1270] [depth= 5] . ( 1 sec) [ -9557.7420] [ 1239] [depth= 1] . ( 1 sec) [ -8405.8474] [ 1234] [depth= 13] . ( 1 sec) [ -8185.3532] [ 1203] [depth= 10] . ( 1 sec) [ -7998.9851] [ 1194] [depth= 7] . ( 1 sec) [ -7928.2691] [ 1186] [depth= 3] . ( 1 sec) [ -7916.2439] [ 1186] [depth= 3] . ( 1 sec) [ -7732.9182] [ 1162] [depth= 3] . ( 1 sec) [ -7700.7363] [ 1158] [depth= 1] . ( 1 sec) [ -7546.0763] [ 1155] [depth= 3] . ( 1 sec) [ -7498.3870] [ 1134] [depth= 1] . ( 1 sec) [ -7424.1118] [ 1131] [depth= 8] . ( 1 sec) [ -6424.9641] [ 1118] [depth= 5] . ( 1 sec) [ -6347.8683] [ 1094] [depth= 8] . ( 1 sec) [ -6264.8967] [ 1077] [depth= 10] . ( 1 sec) [ -6085.7135] [ 1066] [depth= 3] . ( 1 sec) [ -5930.5899] [ 1007] [depth= 8] . ( 1 sec) [ -5747.5290] [ 965] [depth= 10] . ( 1 sec) [ -5734.3973] [ 965] [depth= 2] . ( 1 sec) [ -5592.0582] [ 942] [depth= 11] . ( 1 sec) [ -5497.5947] [ 925] [depth= 7] . ( 1 sec) [ -5429.4124] [ 910] [depth= 2] . ( 1 sec) [ -5263.1969] [ 868] [depth= 7] . ( 1 sec) [ -5083.0912] [ 838] [depth= 2] . ( 1 sec) [ -5053.4138] [ 833] [depth= 6] . ( 1 sec) [ -4956.2543] [ 819] [depth= 8] . ( 1 sec) [ -4952.5495] [ 819] [depth= 1] . ( 1 sec) [ -4910.3152] [ 814] [depth= 9] . ( 1 sec) [ -4764.1683] [ 783] [depth= 8] . ( 1 sec) [ -4754.2976] [ 771] [depth= 2] . ( 1 sec) [ -4695.1488] [ 768] [depth= 7] . ( 1 sec) [ -4672.5915] [ 770] [depth= 9] . ( 2 sec) [ -4662.9902] [ 768] [depth= 1] . ( 2 sec) [ -4662.2136] [ 769] [depth= 7] . ( 2 sec) [ -4639.1438] [ 747] [depth= 5] . ( 2 sec) [ -4611.8537] [ 753] [depth= 10] . ( 2 sec) [ -4607.5452] [ 753] [depth= 1] . ( 2 sec) [ -4603.9769] [ 751] [depth= 4] . ( 2 sec) [ -4553.8991] [ 750] [depth= 3] . ( 2 sec) [ -4549.6103] [ 750] [depth= 3] . ( 2 sec) [ -4509.6717] [ 738] [depth= 6] . ( 2 sec) [ -4506.9114] [ 738] [depth= 5] . ( 2 sec) [ -4495.8036] [ 741] [depth= 1] . ( 2 sec) [ -4488.6117] [ 738] [depth= 1] . ( 2 sec) [ -4457.6051] [ 733] [depth= 7] . ( 2 sec) [ -4415.3667] [ 706] [depth= 5] . ( 2 sec) [ -4392.6605] [ 705] [depth= 4] . ( 2 sec) [ -4287.9618] [ 683] [depth= 5] . ( 2 sec) [ -4263.1738] [ 682] [depth= 3] . ( 2 sec) [ -4224.2383] [ 674] [depth= 5] . ( 2 sec) [ -4213.8339] [ 668] [depth= 1] . ( 2 sec) [ -4211.1758] [ 672] [depth= 1] . ( 2 sec) [ -4199.3786] [ 663] [depth= 2] . ( 2 sec) [ -4190.5150] [ 663] [depth= 4] . ( 2 sec) [ -4142.5618] [ 662] [depth= 6] . ( 2 sec) [ -4142.4837] [ 639] [depth= 1] . ( 2 sec) [ -4132.0468] [ 639] [depth= 1] . ( 2 sec) [ -4131.8530] [ 639] [depth= 1] . ( 2 sec) [ -4129.4716] [ 612] [depth= 1] . ( 2 sec) [ -4128.9859] [ 611] [depth= 3] . ( 3 sec) [ -4100.0862] [ 608] [depth= 5] . ( 3 sec) [ -4027.8666] [ 588] [depth= 4] . ( 3 sec) [ -3971.4393] [ 559] [depth= 1] . ( 3 sec) [ -3922.0107] [ 555] [depth= 3] . ( 3 sec) [ -3919.4460] [ 554] [depth= 1] . ( 3 sec) [ -3877.0078] [ 554] [depth= 1] . ( 3 sec) [ -3813.8221] [ 529] [depth= 7] . ( 3 sec) [ -3812.8644] [ 530] [depth= 1] . ( 3 sec) [ -3782.8736] [ 523] [depth= 1] . ( 3 sec) [ -3771.0977] [ 533] [depth= 4] . ( 3 sec) [ -3758.1234] [ 525] [depth= 3] . ( 3 sec) [ -3733.2736] [ 525] [depth= 1] . ( 3 sec) [ -3733.2508] [ 525] [depth= 1] . ( 3 sec) [ -3638.7253] [Branch lengths ] . ( 3 sec) [ -3635.7704] [GTR parameters ] . ( 4 sec) [ -3625.5699] [Alpha ][ 0.910408] . ( 4 sec) [ -3623.2955] [ 525] [depth= 1] . ( 4 sec) [ -3622.5106] [ 523] [depth= 2] . ( 4 sec) [ -3619.8540] [ 523] [depth= 1] . ( 4 sec) [ -3619.6531] [ 522] [depth= 1] . ( 4 sec) [ -3619.6244] [ 522] [depth= 1] . ( 4 sec) [ -3612.8662] [ 521] [depth= 4] . ( 5 sec) [ -3610.6656] [ 520] [depth= 2] . ( 5 sec) [ -3609.9741] [ 519] [depth= 1] . ( 5 sec) [ -3562.1710] [ 500] [depth= 1] . ( 5 sec) [ -3527.2453] [ 491] [depth= 2] . ( 5 sec) [ -3520.0866] [ 493] [depth= 1] . ( 5 sec) [ -3498.1115] [ 485] [depth= 1] . ( 5 sec) [ -3491.1296] [ 483] [depth= 2] . ( 6 sec) [ -3484.1181] [ 481] [depth= 1] . ( 6 sec) [ -3483.2669] [ 481] [depth= 1] . ( 6 sec) [ -3439.5120] [ 471] [depth= 1] . ( 6 sec) [ -3433.3032] [ 472] [depth= 1] . ( 7 sec) [ -3430.7730] [Branch lengths ] . ( 7 sec) [ -3430.4090] [GTR parameters ] . ( 7 sec) [ -3428.8777] [Alpha ][ 1.237848] . ( 8 sec) [ -3428.6531] [ 471] [depth= 1] . ( 10 sec) [ -3427.4466] [Branch lengths ] . ( 10 sec) [ -3427.4430] [GTR parameters ] . ( 10 sec) [ -3427.4418] [Alpha ][ 1.249674] . ( 14 sec) [ -3424.9888] [Branch lengths ] . ( 28 sec) [ -3424.6932] [Branch lengths ] . ( 28 sec) [ -3424.6932] [Topology ] . ( 28 sec) [ -3424.6932] [Topology ] . ( 29 sec) [ -3424.6930] [GTR parameters ] . ( 29 sec) [ -3424.6929] [Alpha ][ 1.251627] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3424.692922. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-3431.794665 . ( 0 sec) [ -3430.1324] [GTR parameters ] . ( 0 sec) [ -3429.5047] [Alpha ][ 1.225211] . ( 0 sec) [ -3429.5047] [Topology ] . ( 1 sec) [ -3425.1146] [Topology ] . ( 1 sec) [ -3424.7672] [Topology ] . ( 2 sec) [ -3424.7130] [Topology ] . ( 2 sec) [ -3424.7024] [Topology ] . ( 3 sec) [ -3424.7000] [Topology ] . ( 3 sec) [ -3424.6995] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-3424.699457 . ( 6 sec) [ -3424.6991] [GTR parameters ] . ( 6 sec) [ -3424.6928] [Alpha ][ 1.251356] . ( 6 sec) [ -3424.6928] [Topology ] . ( 7 sec) [ -3424.6926] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-3424.692568 . ( 10 sec) [ -3424.6925] [GTR parameters ] . ( 10 sec) [ -3424.6925] [Alpha ][ 1.251356] . ( 10 sec) [ -3424.6925] [Topology ] . ( 10 sec) [ -3424.6925] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 17 sec) [ -3430.1324] [GTR parameters ] . ( 17 sec) [ -3429.5047] [Alpha ][ 1.225211] . ( 17 sec) [ -3428.5211] [ 472] [depth= 1] . ( 19 sec) [ -3428.4550] [ 472] [depth= 1] . ( 19 sec) [ -3428.4200] [ 472] [depth= 1] . ( 19 sec) [ -3427.0663] [ 471] [depth= 1] . ( 19 sec) [ -3427.0507] [ 471] [depth= 1] . ( 20 sec) [ -3424.7169] [Branch lengths ] . ( 20 sec) [ -3424.7165] [GTR parameters ] . ( 20 sec) [ -3424.7105] [Alpha ][ 1.250612] . ( 23 sec) [ -3424.6925] [Branch lengths ] . ( 37 sec) [ -3424.6924] [Branch lengths ] . ( 37 sec) [ -3424.6924] [Topology ] . ( 37 sec) [ -3424.6924] [Topology ] . ( 38 sec) [ -3424.6924] [GTR parameters ] . ( 38 sec) [ -3424.6924] [Alpha ][ 1.251862] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -3424.692457 . Log likelihood obtained after SPR moves : -3424.692374 . Log likelihood of the current tree: -3424.692374. . Printing the most likely tree in file 'data74.phy_phyml_tree.txt'... . Best log likelihood : -3424.692374 . Time used 0h0m41s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo