.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2946_110x1003_2006.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 . 6 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 614 patterns found. (out of a total of 1003 sites) . 462 sites without polymorphism (46.06%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 36Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 13 sec) [ -37657.5107] [GTR parameters ] . ( 14 sec) [ -36647.8866] [Alpha ][ 0.500960] . ( 14 sec) [ -36427.9518] [ 7117] [depth= 5] . ( 14 sec) [ -36220.1492] [ 7082] [depth= 7] . ( 14 sec) [ -36206.5902] [ 7079] [depth= 3] . ( 15 sec) [ -36203.7173] [ 7078] [depth= 1] . ( 15 sec) [ -36154.8684] [ 7073] [depth= 2] . ( 15 sec) [ -36089.7993] [ 7072] [depth= 4] . ( 15 sec) [ -36045.9718] [ 7066] [depth= 2] . ( 15 sec) [ -36033.9062] [ 7066] [depth= 3] . ( 15 sec) [ -35962.7090] [ 7045] [depth= 6] . ( 15 sec) [ -35955.3350] [ 7042] [depth= 11] . ( 16 sec) [ -35915.1717] [ 7039] [depth= 1] . ( 16 sec) [ -35898.2668] [ 7037] [depth= 2] . ( 16 sec) [ -35779.5781] [ 7016] [depth= 12] . ( 16 sec) [ -35636.0868] [ 6977] [depth= 11] . ( 16 sec) [ -35500.5125] [ 6943] [depth= 1] . ( 17 sec) [ -35168.5758] [ 6879] [depth= 9] . ( 17 sec) [ -35021.2682] [ 6838] [depth= 9] . ( 17 sec) [ -34893.9316] [ 6839] [depth= 6] . ( 17 sec) [ -34860.4134] [ 6835] [depth= 13] . ( 17 sec) [ -34847.2240] [ 6839] [depth= 1] . ( 17 sec) [ -34805.4316] [ 6832] [depth= 27] . ( 17 sec) [ -34778.2142] [ 6821] [depth= 1] . ( 18 sec) [ -34752.5731] [ 6810] [depth= 14] . ( 18 sec) [ -34611.2551] [ 6764] [depth= 13] . ( 18 sec) [ -34049.0436] [ 6697] [depth= 20] . ( 18 sec) [ -33848.2291] [ 6645] [depth= 18] . ( 18 sec) [ -33823.6033] [ 6638] [depth= 26] . ( 19 sec) [ -33556.2625] [ 6572] [depth= 15] . ( 19 sec) [ -33510.2870] [ 6553] [depth= 5] . ( 19 sec) [ -33477.6424] [ 6550] [depth= 16] . ( 19 sec) [ -33448.1368] [ 6551] [depth= 8] . ( 19 sec) [ -33416.2411] [ 6567] [depth= 1] . ( 19 sec) [ -33136.7090] [ 6493] [depth= 14] . ( 19 sec) [ -33042.7695] [ 6474] [depth= 3] . ( 20 sec) [ -32760.1284] [ 6467] [depth= 1] . ( 20 sec) [ -32749.6546] [ 6465] [depth= 1] . ( 20 sec) [ -32580.2526] [ 6429] [depth= 15] . ( 20 sec) [ -32449.4656] [ 6402] [depth= 14] . ( 20 sec) [ -32387.3805] [ 6398] [depth= 1] . ( 20 sec) [ -32267.7177] [ 6391] [depth= 6] . ( 21 sec) [ -32220.2530] [ 6388] [depth= 9] . ( 21 sec) [ -32106.9158] [ 6375] [depth= 5] . ( 21 sec) [ -32040.7165] [ 6373] [depth= 6] . ( 21 sec) [ -31607.4234] [ 6360] [depth= 12] . ( 21 sec) [ -31490.5751] [ 6354] [depth= 2] . ( 21 sec) [ -31380.1116] [ 6306] [depth= 13] . ( 22 sec) [ -31215.8702] [ 6234] [depth= 1] . ( 22 sec) [ -31013.8201] [ 6173] [depth= 17] . ( 22 sec) [ -30803.0414] [ 6141] [depth= 8] . ( 22 sec) [ -30757.6776] [ 6124] [depth= 1] . ( 22 sec) [ -30743.9910] [ 6126] [depth= 12] . ( 22 sec) [ -30624.0372] [ 6083] [depth= 4] . ( 22 sec) [ -30556.4729] [ 6080] [depth= 17] . ( 23 sec) [ -30347.8491] [ 6013] [depth= 8] . ( 23 sec) [ -30316.0675] [ 6008] [depth= 1] . ( 23 sec) [ -30185.0913] [ 5992] [depth= 2] . ( 23 sec) [ -30067.0569] [ 5958] [depth= 2] . ( 23 sec) [ -29925.3478] [ 5939] [depth= 16] . ( 23 sec) [ -29919.3441] [ 5944] [depth= 1] . ( 24 sec) [ -29653.0857] [ 5891] [depth= 12] . ( 24 sec) [ -29526.0605] [ 5848] [depth= 5] . ( 24 sec) [ -29460.0023] [ 5843] [depth= 3] . ( 24 sec) [ -29284.7750] [ 5823] [depth= 12] . ( 24 sec) [ -29276.2987] [ 5826] [depth= 2] . ( 24 sec) [ -29210.1512] [ 5801] [depth= 8] . ( 25 sec) [ -29138.0469] [ 5800] [depth= 20] . ( 25 sec) [ -29082.2674] [ 5765] [depth= 7] . ( 25 sec) [ -28981.1433] [ 5735] [depth= 20] . ( 25 sec) [ -28712.4620] [ 5719] [depth= 14] . ( 25 sec) [ -28710.2098] [ 5723] [depth= 1] . ( 25 sec) [ -28629.0379] [ 5721] [depth= 2] . ( 26 sec) [ -28591.5103] [ 5709] [depth= 10] . ( 26 sec) [ -28528.1330] [ 5697] [depth= 1] . ( 26 sec) [ -28457.0006] [ 5678] [depth= 25] . ( 26 sec) [ -28350.3935] [ 5662] [depth= 9] . ( 26 sec) [ -28118.8625] [ 5643] [depth= 1] . ( 26 sec) [ -27914.4089] [ 5609] [depth= 5] . ( 27 sec) [ -27795.2724] [ 5561] [depth= 17] . ( 27 sec) [ -27792.9353] [ 5564] [depth= 20] . ( 27 sec) [ -27752.2444] [ 5562] [depth= 1] . ( 27 sec) [ -27721.4477] [ 5550] [depth= 13] . ( 28 sec) [ -27700.6652] [ 5537] [depth= 8] . ( 28 sec) [ -27472.7068] [ 5529] [depth= 2] . ( 28 sec) [ -27376.1016] [ 5510] [depth= 8] . ( 28 sec) [ -27176.5583] [ 5457] [depth= 8] . ( 28 sec) [ -27014.0448] [ 5440] [depth= 9] . ( 28 sec) [ -27004.1796] [ 5444] [depth= 1] . ( 28 sec) [ -26894.6702] [ 5411] [depth= 15] . ( 29 sec) [ -26777.0592] [ 5385] [depth= 8] . ( 29 sec) [ -26656.9574] [ 5332] [depth= 6] . ( 29 sec) [ -26629.4943] [ 5326] [depth= 1] . ( 29 sec) [ -26540.1604] [ 5295] [depth= 2] . ( 29 sec) [ -26504.3936] [ 5292] [depth= 3] . ( 29 sec) [ -26468.7543] [ 5285] [depth= 1] . ( 30 sec) [ -26443.5033] [ 5284] [depth= 1] . ( 30 sec) [ -26364.6587] [ 5259] [depth= 9] . ( 30 sec) [ -26291.3382] [ 5259] [depth= 1] . ( 30 sec) [ -26240.1947] [ 5254] [depth= 8] . ( 30 sec) [ -26194.9596] [ 5259] [depth= 14] . ( 30 sec) [ -26123.7280] [ 5210] [depth= 11] . ( 31 sec) [ -25690.8374] [ 5173] [depth= 3] . ( 31 sec) [ -25491.1190] [ 5149] [depth= 2] . ( 31 sec) [ -25342.5602] [ 5113] [depth= 19] . ( 31 sec) [ -25117.4182] [ 5077] [depth= 22] . ( 31 sec) [ -24917.8202] [ 5033] [depth= 8] . ( 31 sec) [ -24650.6434] [ 5003] [depth= 9] . ( 32 sec) [ -24635.5851] [ 5009] [depth= 1] . ( 32 sec) [ -24437.4140] [ 4986] [depth= 6] . ( 32 sec) [ -24408.2694] [ 4974] [depth= 1] . ( 32 sec) [ -24379.7514] [ 4967] [depth= 10] . ( 32 sec) [ -24219.4371] [ 4917] [depth= 13] . ( 32 sec) [ -23661.8166] [ 4900] [depth= 2] . ( 33 sec) [ -23439.0818] [ 4850] [depth= 12] . ( 33 sec) [ -23422.4117] [ 4847] [depth= 1] . ( 33 sec) [ -23411.9540] [ 4844] [depth= 9] . ( 33 sec) [ -23388.5435] [ 4837] [depth= 9] . ( 33 sec) [ -23367.7455] [ 4843] [depth= 1] . ( 33 sec) [ -23288.7361] [ 4832] [depth= 5] . ( 34 sec) [ -23224.7656] [ 4819] [depth= 6] . ( 34 sec) [ -23207.0439] [ 4819] [depth= 1] . ( 34 sec) [ -23204.6557] [ 4819] [depth= 1] . ( 34 sec) [ -23183.6529] [ 4799] [depth= 10] . ( 34 sec) [ -22881.4838] [ 4796] [depth= 1] . ( 34 sec) [ -22684.8239] [ 4790] [depth= 2] . ( 35 sec) [ -22563.2247] [ 4717] [depth= 16] . ( 35 sec) [ -22555.7734] [ 4727] [depth= 1] . ( 35 sec) [ -22377.9428] [ 4688] [depth= 7] . ( 35 sec) [ -22359.7038] [ 4688] [depth= 1] . ( 35 sec) [ -22250.1676] [ 4670] [depth= 8] . ( 35 sec) [ -22107.2056] [ 4657] [depth= 19] . ( 36 sec) [ -21872.3242] [ 4586] [depth= 20] . ( 36 sec) [ -21818.1751] [ 4597] [depth= 14] . ( 36 sec) [ -21729.2986] [ 4573] [depth= 13] . ( 36 sec) [ -21723.5577] [ 4574] [depth= 1] . ( 36 sec) [ -21721.0205] [ 4572] [depth= 2] . ( 36 sec) [ -21575.8382] [ 4542] [depth= 9] . ( 36 sec) [ -21526.2468] [ 4533] [depth= 6] . ( 37 sec) [ -21522.6326] [ 4526] [depth= 4] . ( 37 sec) [ -21522.5772] [ 4525] [depth= 1] . ( 37 sec) [ -21519.9290] [ 4526] [depth= 2] . ( 37 sec) [ -21473.3866] [ 4518] [depth= 6] . ( 37 sec) [ -21448.3647] [ 4513] [depth= 5] . ( 37 sec) [ -21408.8589] [ 4497] [depth= 18] . ( 38 sec) [ -21395.8962] [ 4496] [depth= 1] . ( 38 sec) [ -21379.3067] [ 4490] [depth= 2] . ( 38 sec) [ -21361.0008] [ 4482] [depth= 19] . ( 38 sec) [ -21328.5638] [ 4460] [depth= 11] . ( 38 sec) [ -21304.2214] [ 4455] [depth= 1] . ( 38 sec) [ -21294.9542] [ 4450] [depth= 4] . ( 38 sec) [ -21274.1762] [ 4426] [depth= 6] . ( 39 sec) [ -21272.6352] [ 4429] [depth= 16] . ( 39 sec) [ -21267.7551] [ 4431] [depth= 1] . ( 39 sec) [ -21259.9186] [ 4428] [depth= 2] . ( 39 sec) [ -21099.3153] [ 4376] [depth= 8] . ( 39 sec) [ -20988.6368] [ 4355] [depth= 13] . ( 40 sec) [ -20980.0587] [ 4357] [depth= 2] . ( 40 sec) [ -20979.3334] [ 4357] [depth= 1] . ( 40 sec) [ -20875.4212] [ 4318] [depth= 10] . ( 40 sec) [ -20867.0329] [ 4319] [depth= 1] . ( 40 sec) [ -20781.7076] [ 4298] [depth= 8] . ( 40 sec) [ -20775.4325] [ 4292] [depth= 6] . ( 41 sec) [ -20658.2720] [ 4231] [depth= 13] . ( 41 sec) [ -20651.8863] [ 4231] [depth= 1] . ( 41 sec) [ -20619.4912] [ 4214] [depth= 7] . ( 41 sec) [ -20569.8868] [ 4205] [depth= 6] . ( 41 sec) [ -20556.7802] [ 4195] [depth= 9] . ( 42 sec) [ -20510.2046] [ 4191] [depth= 9] . ( 42 sec) [ -20440.3687] [ 4173] [depth= 12] . ( 42 sec) [ -20415.9975] [ 4174] [depth= 1] . ( 42 sec) [ -20226.6429] [ 4142] [depth= 11] . ( 42 sec) [ -20196.4215] [ 4134] [depth= 2] . ( 42 sec) [ -20184.0304] [ 4128] [depth= 3] . ( 43 sec) [ -20182.1912] [ 4128] [depth= 1] . ( 43 sec) [ -20176.8152] [ 4118] [depth= 2] . ( 43 sec) [ -20151.9642] [ 4109] [depth= 1] . ( 43 sec) [ -20142.4957] [ 4107] [depth= 1] . ( 44 sec) [ -20097.1516] [ 4095] [depth= 1] . ( 44 sec) [ -20083.3742] [ 4086] [depth= 16] . ( 44 sec) [ -20043.8555] [ 4085] [depth= 1] . ( 44 sec) [ -19966.2369] [ 4070] [depth= 4] . ( 45 sec) [ -19965.1432] [ 4072] [depth= 1] . ( 45 sec) [ -19963.2556] [ 4075] [depth= 1] . ( 45 sec) [ -19943.8836] [ 4085] [depth= 1] . ( 45 sec) [ -19941.2633] [ 4083] [depth= 1] . ( 45 sec) [ -19939.7455] [ 4086] [depth= 1] . ( 46 sec) [ -19939.2020] [ 4091] [depth= 1] . ( 46 sec) [ -19890.6907] [ 4081] [depth= 7] . ( 46 sec) [ -19861.5888] [ 4066] [depth= 2] . ( 46 sec) [ -19834.2326] [ 4065] [depth= 2] . ( 46 sec) [ -19669.4021] [ 4031] [depth= 10] . ( 46 sec) [ -19641.1525] [ 4017] [depth= 5] . ( 47 sec) [ -19478.0289] [ 3957] [depth= 12] . ( 47 sec) [ -19234.7888] [ 3889] [depth= 8] . ( 47 sec) [ -19227.9515] [ 3891] [depth= 1] . ( 47 sec) [ -19180.1726] [ 3887] [depth= 2] . ( 47 sec) [ -19160.7465] [ 3888] [depth= 8] . ( 48 sec) [ -19154.8041] [ 3888] [depth= 2] . ( 48 sec) [ -19103.2788] [ 3865] [depth= 7] . ( 48 sec) [ -19097.3860] [ 3866] [depth= 2] . ( 48 sec) [ -19084.9079] [ 3866] [depth= 2] . ( 49 sec) [ -19079.7243] [ 3868] [depth= 2] . ( 49 sec) [ -19025.7567] [ 3841] [depth= 9] . ( 49 sec) [ -18998.6059] [ 3829] [depth= 1] . ( 49 sec) [ -18994.0265] [ 3829] [depth= 1] . ( 49 sec) [ -18991.4265] [ 3827] [depth= 1] . ( 50 sec) [ -18922.0265] [ 3807] [depth= 6] . ( 50 sec) [ -18917.7409] [ 3806] [depth= 1] . ( 50 sec) [ -18916.6311] [ 3804] [depth= 2] . ( 50 sec) [ -18898.4725] [ 3807] [depth= 1] . ( 51 sec) [ -18896.4022] [ 3800] [depth= 6] . ( 51 sec) [ -18889.2538] [ 3799] [depth= 1] . ( 51 sec) [ -18876.6735] [ 3793] [depth= 4] . ( 51 sec) [ -18867.9872] [ 3791] [depth= 3] . ( 52 sec) [ -18840.3798] [ 3779] [depth= 5] . ( 52 sec) [ -18836.7844] [ 3779] [depth= 1] . ( 52 sec) [ -18813.1852] [ 3778] [depth= 4] . ( 52 sec) [ -18790.8799] [ 3766] [depth= 9] . ( 52 sec) [ -18744.9493] [ 3760] [depth= 19] . ( 52 sec) [ -18730.6773] [ 3760] [depth= 1] . ( 53 sec) [ -18691.6851] [ 3749] [depth= 1] . ( 53 sec) [ -18671.7766] [ 3740] [depth= 5] . ( 53 sec) [ -18668.4477] [ 3739] [depth= 2] . ( 53 sec) [ -18645.2495] [ 3733] [depth= 6] . ( 54 sec) [ -18634.6659] [ 3734] [depth= 1] . ( 54 sec) [ -18537.9375] [ 3716] [depth= 3] . ( 54 sec) [ -18531.8905] [ 3712] [depth= 1] . ( 54 sec) [ -18524.6031] [ 3702] [depth= 3] . ( 55 sec) [ -18463.6838] [ 3688] [depth= 8] . ( 55 sec) [ -18452.3044] [ 3685] [depth= 1] . ( 55 sec) [ -18119.9331] [ 3697] [depth= 1] . ( 56 sec) [ -18078.8142] [ 3662] [depth= 2] . ( 56 sec) [ -18066.6330] [ 3669] [depth= 1] . ( 56 sec) [ -17997.2594] [ 3647] [depth= 8] . ( 56 sec) [ -17985.9729] [ 3644] [depth= 1] . ( 56 sec) [ -17978.4374] [ 3644] [depth= 1] . ( 58 sec) [ -17664.1658] [Branch lengths ] . ( 61 sec) [ -17627.7546] [GTR parameters ] . ( 62 sec) [ -17591.3445] [Alpha ][ 0.356299] . ( 62 sec) [ -17569.5440] [ 3633] [depth= 1] . ( 63 sec) [ -17562.6608] [ 3629] [depth= 1] . ( 63 sec) [ -17556.7037] [ 3625] [depth= 4] . ( 63 sec) [ -17552.3791] [ 3620] [depth= 1] . ( 64 sec) [ -17551.6277] [ 3619] [depth= 1] . ( 64 sec) [ -17547.7357] [ 3620] [depth= 1] . ( 64 sec) [ -17546.6379] [ 3619] [depth= 1] . ( 64 sec) [ -17541.3833] [ 3615] [depth= 1] . ( 65 sec) [ -17541.3235] [ 3616] [depth= 1] . ( 66 sec) [ -17541.0405] [ 3619] [depth= 1] . ( 67 sec) [ -17540.1894] [ 3619] [depth= 1] . ( 67 sec) [ -17535.4475] [ 3616] [depth= 1] . ( 68 sec) [ -17533.3463] [ 3615] [depth= 1] . ( 69 sec) [ -17532.0882] [ 3614] [depth= 1] . ( 69 sec) [ -17468.3953] [ 3595] [depth= 19] . ( 70 sec) [ -17445.1929] [ 3586] [depth= 2] . ( 70 sec) [ -17443.7441] [ 3578] [depth= 3] . ( 71 sec) [ -17411.7671] [ 3580] [depth= 1] . ( 71 sec) [ -17406.8944] [ 3585] [depth= 3] . ( 71 sec) [ -17405.0727] [ 3586] [depth= 1] . ( 71 sec) [ -17403.6217] [ 3583] [depth= 1] . ( 72 sec) [ -17397.8343] [ 3583] [depth= 1] . ( 72 sec) [ -17376.5137] [ 3569] [depth= 1] . ( 73 sec) [ -17376.3057] [ 3565] [depth= 6] . ( 73 sec) [ -17365.5311] [ 3557] [depth= 3] . ( 73 sec) [ -17360.8888] [ 3556] [depth= 1] . ( 74 sec) [ -17360.2670] [ 3555] [depth= 1] . ( 74 sec) [ -17347.2478] [ 3554] [depth= 1] . ( 74 sec) [ -17335.5858] [ 3544] [depth= 8] . ( 74 sec) [ -17315.8384] [ 3541] [depth= 1] . ( 76 sec) [ -17315.1121] [ 3542] [depth= 3] . ( 76 sec) [ -17216.1327] [ 3502] [depth= 3] . ( 77 sec) [ -17196.5733] [ 3495] [depth= 2] . ( 78 sec) [ -17191.3228] [ 3498] [depth= 1] . ( 78 sec) [ -17190.0921] [ 3497] [depth= 1] . ( 78 sec) [ -17185.6174] [ 3496] [depth= 2] . ( 79 sec) [ -17182.8512] [ 3494] [depth= 1] . ( 79 sec) [ -17181.9991] [ 3494] [depth= 1] . ( 80 sec) [ -17179.8464] [ 3493] [depth= 2] . ( 80 sec) [ -17179.4926] [ 3495] [depth= 1] . ( 80 sec) [ -17178.5586] [ 3496] [depth= 2] . ( 81 sec) [ -17163.5485] [ 3495] [depth= 1] . ( 81 sec) [ -17158.3627] [ 3494] [depth= 2] . ( 82 sec) [ -17156.4548] [ 3495] [depth= 1] . ( 82 sec) [ -17156.1881] [ 3496] [depth= 1] . ( 83 sec) [ -17156.1612] [ 3496] [depth= 1] . ( 84 sec) [ -17148.6211] [ 3494] [depth= 1] . ( 84 sec) [ -17147.5814] [ 3496] [depth= 1] . ( 85 sec) [ -17147.0292] [ 3500] [depth= 1] . ( 86 sec) [ -17146.8224] [ 3498] [depth= 1] . ( 86 sec) [ -17145.2230] [ 3496] [depth= 4] . ( 87 sec) [ -17144.5379] [ 3498] [depth= 1] . ( 87 sec) [ -17143.9290] [ 3500] [depth= 4] . ( 88 sec) [ -17139.5898] [ 3495] [depth= 2] . ( 88 sec) [ -17137.6394] [ 3493] [depth= 1] . ( 88 sec) [ -17121.3783] [ 3487] [depth= 1] . ( 89 sec) [ -17120.9833] [ 3485] [depth= 1] . ( 89 sec) [ -17120.0118] [ 3483] [depth= 1] . ( 91 sec) [ -17119.6069] [ 3485] [depth= 1] . ( 93 sec) [ -17115.6413] [ 3483] [depth= 1] . ( 93 sec) [ -17114.9174] [ 3483] [depth= 1] . ( 93 sec) [ -17114.7098] [ 3485] [depth= 1] . ( 94 sec) [ -17111.4527] [ 3485] [depth= 1] . ( 95 sec) [ -17111.1838] [ 3483] [depth= 1] . ( 96 sec) [ -17109.5937] [ 3484] [depth= 1] . ( 97 sec) [ -17107.9007] [ 3484] [depth= 1] . ( 97 sec) [ -17107.3831] [ 3484] [depth= 1] . ( 98 sec) [ -17103.7692] [ 3483] [depth= 1] . ( 98 sec) [ -17098.2354] [ 3489] [depth= 1] . ( 98 sec) [ -17096.0856] [ 3489] [depth= 2] . ( 100 sec) [ -17040.5235] [Branch lengths ] . ( 103 sec) [ -17037.6175] [GTR parameters ] . ( 104 sec) [ -17037.6087] [Alpha ][ 0.354310] . ( 106 sec) [ -17037.5961] [ 3489] [depth= 1] . ( 114 sec) [ -17037.2169] [ 3490] [depth= 2] . ( 118 sec) [ -17035.3708] [ 3486] [depth= 8] . ( 122 sec) [ -17033.8839] [ 3485] [depth= 1] . ( 126 sec) [ -17031.2030] [ 3488] [depth= 1] . ( 129 sec) [ -17027.9155] [ 3489] [depth= 1] . ( 141 sec) [ -17027.8317] [ 3488] [depth= 1] . ( 143 sec) [ -17021.6747] [Branch lengths ] . ( 145 sec) [ -17021.6058] [GTR parameters ] . ( 146 sec) [ -17021.5600] [Alpha ][ 0.358583] . ( 187 sec) [ -17017.4793] [Branch lengths ] . ( 252 sec) [ -17017.3942] [ 3487] [depth= 1] . ( 331 sec) [ -17012.0891] [Branch lengths ] . ( 334 sec) [ -17012.0591] [GTR parameters ] . ( 334 sec) [ -17012.0400] [Alpha ][ 0.361334] . ( 440 sec) [ -17012.0036] [ 3488] [depth= 1] . ( 473 sec) [ -17010.1891] [Branch lengths ] . ( 475 sec) [ -17010.1784] [GTR parameters ] . ( 475 sec) [ -17010.1777] [Alpha ][ 0.361828] . ( 620 sec) [ -17009.5897] [Branch lengths ] . ( 620 sec) [ -17009.5897] [Topology ] . ( 623 sec) [ -17007.2924] [Topology ] . ( 626 sec) [ -17000.9746] [Topology ] . ( 629 sec) [ -16994.8698] [Topology ] . ( 632 sec) [ -16993.5629] [Topology ] . ( 635 sec) [ -16993.3589] [Topology ] . ( 638 sec) [ -16993.3295] [Topology ] . ( 640 sec) [ -16993.3271] [GTR parameters ] . ( 640 sec) [ -16993.3267] [Alpha ][ 0.362190] . ( 640 sec) [ -16993.3267] [Topology ] . ( 643 sec) [ -16993.3223] [Topology ] . ( 646 sec) [ -16993.3214] [Topology ] . ( 647 sec) [ -16993.3214] [GTR parameters ] . ( 647 sec) [ -16993.3214] [Alpha ][ 0.362190] . ( 647 sec) [ -16993.3214] [Topology ] . ( 650 sec) [ -16993.3211] [Topology ] . ( 651 sec) [ -16993.3211] [GTR parameters ] . ( 651 sec) [ -16993.3211] [Alpha ][ 0.362190] . Checking for NNIs, optimizing five branches... . ( 675 sec) [ -16993.1594] [Topology ] . Checking for NNIs, optimizing five branches... . ( 699 sec) [ -16993.0461] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -16993.046114. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -41002.1443] [GTR parameters ] . ( 3 sec) [ -40000.8832] [Alpha ][ 0.500960] . ( 3 sec) [ -39875.9823] [ 7073] [depth= 14] . ( 3 sec) [ -39685.7614] [ 7023] [depth= 12] . ( 3 sec) [ -39461.5623] [ 6978] [depth= 10] . ( 4 sec) [ -39399.9442] [ 6955] [depth= 1] . ( 4 sec) [ -38696.7275] [ 6928] [depth= 10] . ( 4 sec) [ -38516.8216] [ 6911] [depth= 1] . ( 4 sec) [ -38493.2683] [ 6912] [depth= 9] . ( 4 sec) [ -38417.6167] [ 6899] [depth= 2] . ( 4 sec) [ -38339.6463] [ 6895] [depth= 5] . ( 4 sec) [ -38134.0342] [ 6890] [depth= 3] . ( 5 sec) [ -37992.3218] [ 6881] [depth= 9] . ( 5 sec) [ -37565.8294] [ 6838] [depth= 8] . ( 5 sec) [ -37508.9224] [ 6837] [depth= 10] . ( 5 sec) [ -37503.6160] [ 6831] [depth= 3] . ( 5 sec) [ -37431.5876] [ 6829] [depth= 8] . ( 5 sec) [ -37403.2825] [ 6817] [depth= 12] . ( 6 sec) [ -37352.5779] [ 6820] [depth= 1] . ( 6 sec) [ -37228.6868] [ 6785] [depth= 8] . ( 6 sec) [ -37011.9420] [ 6762] [depth= 3] . ( 6 sec) [ -36753.2652] [ 6744] [depth= 23] . ( 6 sec) [ -36552.4202] [ 6704] [depth= 20] . ( 6 sec) [ -36355.6424] [ 6731] [depth= 15] . ( 7 sec) [ -36227.6113] [ 6688] [depth= 18] . ( 7 sec) [ -36083.3988] [ 6657] [depth= 1] . ( 7 sec) [ -35759.2357] [ 6638] [depth= 11] . ( 7 sec) [ -35668.8856] [ 6624] [depth= 4] . ( 7 sec) [ -35618.9242] [ 6616] [depth= 7] . ( 7 sec) [ -35552.2983] [ 6608] [depth= 6] . ( 8 sec) [ -35539.3567] [ 6608] [depth= 3] . ( 8 sec) [ -35480.5380] [ 6597] [depth= 5] . ( 8 sec) [ -35395.4959] [ 6594] [depth= 8] . ( 8 sec) [ -35157.3664] [ 6570] [depth= 5] . ( 8 sec) [ -34981.3080] [ 6571] [depth= 1] . ( 8 sec) [ -34889.0313] [ 6535] [depth= 1] . ( 8 sec) [ -34741.2501] [ 6474] [depth= 7] . ( 9 sec) [ -34626.1169] [ 6462] [depth= 10] . ( 9 sec) [ -34433.3761] [ 6486] [depth= 13] . ( 9 sec) [ -34382.3822] [ 6471] [depth= 23] . ( 9 sec) [ -34279.9815] [ 6451] [depth= 1] . ( 9 sec) [ -34177.0889] [ 6439] [depth= 18] . ( 9 sec) [ -33983.6761] [ 6430] [depth= 19] . ( 10 sec) [ -33962.8712] [ 6428] [depth= 1] . ( 10 sec) [ -33850.6824] [ 6399] [depth= 7] . ( 10 sec) [ -33791.3281] [ 6388] [depth= 16] . ( 10 sec) [ -33698.8798] [ 6373] [depth= 1] . ( 10 sec) [ -33663.8556] [ 6359] [depth= 14] . ( 10 sec) [ -33644.2817] [ 6356] [depth= 1] . ( 11 sec) [ -33613.5749] [ 6341] [depth= 8] . ( 11 sec) [ -33588.2724] [ 6340] [depth= 1] . ( 11 sec) [ -33545.8234] [ 6335] [depth= 15] . ( 11 sec) [ -33274.4930] [ 6334] [depth= 1] . ( 11 sec) [ -33039.9364] [ 6247] [depth= 1] . ( 11 sec) [ -32932.4626] [ 6226] [depth= 18] . ( 12 sec) [ -32574.0266] [ 6146] [depth= 12] . ( 12 sec) [ -32550.6854] [ 6134] [depth= 17] . ( 12 sec) [ -32249.8643] [ 6121] [depth= 6] . ( 12 sec) [ -32189.2079] [ 6121] [depth= 2] . ( 12 sec) [ -32119.1807] [ 6118] [depth= 15] . ( 13 sec) [ -31995.8732] [ 6086] [depth= 9] . ( 13 sec) [ -31912.1692] [ 6082] [depth= 1] . ( 13 sec) [ -31868.2771] [ 6070] [depth= 8] . ( 13 sec) [ -31806.4400] [ 6070] [depth= 2] . ( 14 sec) [ -31599.4965] [ 6012] [depth= 13] . ( 14 sec) [ -31565.6637] [ 6003] [depth= 4] . ( 14 sec) [ -31549.3302] [ 5999] [depth= 1] . ( 14 sec) [ -31535.3784] [ 6002] [depth= 9] . ( 14 sec) [ -31510.1676] [ 6002] [depth= 1] . ( 14 sec) [ -31447.7372] [ 5986] [depth= 10] . ( 15 sec) [ -31407.7183] [ 5983] [depth= 4] . ( 15 sec) [ -31140.0109] [ 5949] [depth= 14] . ( 15 sec) [ -30894.3327] [ 5898] [depth= 1] . ( 15 sec) [ -30877.9006] [ 5907] [depth= 12] . ( 15 sec) [ -30786.7114] [ 5901] [depth= 10] . ( 16 sec) [ -30718.5678] [ 5886] [depth= 1] . ( 16 sec) [ -30616.8853] [ 5861] [depth= 7] . ( 16 sec) [ -30602.2348] [ 5861] [depth= 1] . ( 16 sec) [ -30592.4804] [ 5862] [depth= 13] . ( 16 sec) [ -30451.9686] [ 5825] [depth= 7] . ( 17 sec) [ -30367.5598] [ 5799] [depth= 5] . ( 17 sec) [ -30343.1037] [ 5795] [depth= 6] . ( 17 sec) [ -30321.3509] [ 5800] [depth= 1] . ( 17 sec) [ -30301.2516] [ 5797] [depth= 11] . ( 17 sec) [ -30232.6919] [ 5797] [depth= 1] . ( 17 sec) [ -30181.5222] [ 5773] [depth= 11] . ( 17 sec) [ -30130.7140] [ 5788] [depth= 15] . ( 18 sec) [ -30122.9000] [ 5783] [depth= 1] . ( 18 sec) [ -30086.9016] [ 5759] [depth= 9] . ( 18 sec) [ -29530.5603] [ 5698] [depth= 13] . ( 18 sec) [ -29495.6914] [ 5690] [depth= 1] . ( 18 sec) [ -29475.2415] [ 5671] [depth= 10] . ( 18 sec) [ -29390.7630] [ 5677] [depth= 1] . ( 19 sec) [ -29280.9757] [ 5633] [depth= 11] . ( 19 sec) [ -29189.0178] [ 5630] [depth= 14] . ( 19 sec) [ -29188.0789] [ 5630] [depth= 1] . ( 19 sec) [ -29086.8797] [ 5619] [depth= 6] . ( 19 sec) [ -29034.6348] [ 5611] [depth= 1] . ( 19 sec) [ -29004.1875] [ 5602] [depth= 10] . ( 20 sec) [ -28999.7998] [ 5601] [depth= 1] . ( 20 sec) [ -28899.4671] [ 5587] [depth= 1] . ( 20 sec) [ -28756.8521] [ 5536] [depth= 10] . ( 20 sec) [ -28739.4990] [ 5534] [depth= 1] . ( 20 sec) [ -28655.0865] [ 5488] [depth= 3] . ( 20 sec) [ -28641.3948] [ 5480] [depth= 7] . ( 21 sec) [ -28579.0429] [ 5470] [depth= 8] . ( 21 sec) [ -28474.4143] [ 5459] [depth= 4] . ( 21 sec) [ -28389.7907] [ 5443] [depth= 13] . ( 21 sec) [ -28358.2683] [ 5436] [depth= 2] . ( 21 sec) [ -28312.6800] [ 5422] [depth= 3] . ( 22 sec) [ -28211.6364] [ 5394] [depth= 1] . ( 22 sec) [ -28203.8884] [ 5394] [depth= 1] . ( 22 sec) [ -28203.5661] [ 5390] [depth= 5] . ( 22 sec) [ -28179.7154] [ 5381] [depth= 4] . ( 22 sec) [ -28176.6435] [ 5380] [depth= 4] . ( 22 sec) [ -28103.2059] [ 5371] [depth= 3] . ( 23 sec) [ -28065.3896] [ 5373] [depth= 12] . ( 23 sec) [ -27990.5929] [ 5336] [depth= 4] . ( 23 sec) [ -27958.6112] [ 5331] [depth= 6] . ( 23 sec) [ -27925.9653] [ 5333] [depth= 18] . ( 23 sec) [ -27922.7508] [ 5334] [depth= 1] . ( 23 sec) [ -27867.1212] [ 5316] [depth= 14] . ( 23 sec) [ -27865.4095] [ 5315] [depth= 1] . ( 24 sec) [ -27684.9823] [ 5273] [depth= 11] . ( 24 sec) [ -27602.1940] [ 5229] [depth= 7] . ( 24 sec) [ -27589.6634] [ 5223] [depth= 2] . ( 24 sec) [ -27546.0812] [ 5203] [depth= 10] . ( 25 sec) [ -27542.7018] [ 5202] [depth= 1] . ( 25 sec) [ -27468.7281] [ 5171] [depth= 1] . ( 25 sec) [ -27401.9538] [ 5166] [depth= 4] . ( 25 sec) [ -27322.0367] [ 5141] [depth= 15] . ( 25 sec) [ -25463.5130] [ 5139] [depth= 19] . ( 26 sec) [ -25462.7487] [ 5142] [depth= 1] . ( 26 sec) [ -25460.6013] [ 5132] [depth= 1] . ( 26 sec) [ -25377.0361] [ 5129] [depth= 1] . ( 26 sec) [ -25297.4015] [ 5119] [depth= 12] . ( 26 sec) [ -25197.2968] [ 5092] [depth= 8] . ( 26 sec) [ -25079.5383] [ 5073] [depth= 13] . ( 27 sec) [ -25030.6330] [ 5067] [depth= 1] . ( 27 sec) [ -24575.8597] [ 5032] [depth= 3] . ( 27 sec) [ -24494.1041] [ 5000] [depth= 9] . ( 27 sec) [ -24283.2577] [ 4963] [depth= 4] . ( 27 sec) [ -24144.9208] [ 4899] [depth= 15] . ( 28 sec) [ -23962.3507] [ 4879] [depth= 15] . ( 28 sec) [ -23861.0656] [ 4855] [depth= 8] . ( 28 sec) [ -23815.6607] [ 4843] [depth= 2] . ( 28 sec) [ -23770.8062] [ 4817] [depth= 2] . ( 28 sec) [ -23740.9648] [ 4806] [depth= 1] . ( 28 sec) [ -23670.0614] [ 4803] [depth= 2] . ( 29 sec) [ -23622.4213] [ 4791] [depth= 21] . ( 29 sec) [ -23532.1451] [ 4772] [depth= 25] . ( 29 sec) [ -23372.7061] [ 4779] [depth= 1] . ( 29 sec) [ -22613.5113] [ 4727] [depth= 15] . ( 29 sec) [ -22571.3915] [ 4726] [depth= 1] . ( 29 sec) [ -22354.3451] [ 4683] [depth= 10] . ( 30 sec) [ -22348.0876] [ 4677] [depth= 33] . ( 30 sec) [ -22167.1175] [ 4604] [depth= 34] . ( 30 sec) [ -22114.8192] [ 4587] [depth= 10] . ( 30 sec) [ -22032.0725] [ 4609] [depth= 1] . ( 30 sec) [ -22018.0776] [ 4587] [depth= 2] . ( 31 sec) [ -21994.6350] [ 4564] [depth= 1] . ( 31 sec) [ -21910.2257] [ 4550] [depth= 4] . ( 31 sec) [ -21762.0730] [ 4526] [depth= 8] . ( 31 sec) [ -21634.8677] [ 4498] [depth= 20] . ( 31 sec) [ -21634.0847] [ 4497] [depth= 1] . ( 32 sec) [ -21389.6290] [ 4484] [depth= 9] . ( 32 sec) [ -21331.7154] [ 4468] [depth= 4] . ( 32 sec) [ -21328.8050] [ 4472] [depth= 4] . ( 32 sec) [ -21328.1766] [ 4471] [depth= 10] . ( 33 sec) [ -21319.9941] [ 4463] [depth= 3] . ( 33 sec) [ -21309.1122] [ 4464] [depth= 1] . ( 33 sec) [ -21251.5840] [ 4429] [depth= 11] . ( 33 sec) [ -21090.5206] [ 4417] [depth= 13] . ( 33 sec) [ -20982.3422] [ 4408] [depth= 13] . ( 33 sec) [ -20920.1945] [ 4373] [depth= 1] . ( 33 sec) [ -20911.6208] [ 4377] [depth= 1] . ( 34 sec) [ -20820.3078] [ 4361] [depth= 5] . ( 34 sec) [ -20810.2045] [ 4354] [depth= 1] . ( 34 sec) [ -20772.0841] [ 4332] [depth= 12] . ( 34 sec) [ -20756.0110] [ 4330] [depth= 1] . ( 34 sec) [ -20720.8891] [ 4320] [depth= 10] . ( 35 sec) [ -20674.7778] [ 4304] [depth= 1] . ( 35 sec) [ -20666.0939] [ 4297] [depth= 7] . ( 35 sec) [ -20563.6597] [ 4275] [depth= 15] . ( 35 sec) [ -20322.7197] [ 4227] [depth= 22] . ( 35 sec) [ -20304.0034] [ 4230] [depth= 1] . ( 36 sec) [ -20287.9051] [ 4223] [depth= 10] . ( 36 sec) [ -20233.2589] [ 4211] [depth= 2] . ( 36 sec) [ -20145.8400] [ 4186] [depth= 11] . ( 36 sec) [ -20072.8305] [ 4176] [depth= 1] . ( 36 sec) [ -19913.3302] [ 4143] [depth= 3] . ( 37 sec) [ -19911.1776] [ 4145] [depth= 1] . ( 37 sec) [ -19910.8423] [ 4147] [depth= 1] . ( 37 sec) [ -19908.8581] [ 4144] [depth= 1] . ( 37 sec) [ -19847.8203] [ 4119] [depth= 14] . ( 37 sec) [ -19760.0208] [ 4104] [depth= 1] . ( 38 sec) [ -19757.4257] [ 4104] [depth= 1] . ( 38 sec) [ -19750.4140] [ 4093] [depth= 11] . ( 38 sec) [ -19747.8701] [ 4093] [depth= 1] . ( 38 sec) [ -19741.7920] [ 4090] [depth= 1] . ( 38 sec) [ -19741.7432] [ 4088] [depth= 4] . ( 39 sec) [ -19727.2667] [ 4088] [depth= 1] . ( 39 sec) [ -19600.4203] [ 4065] [depth= 4] . ( 39 sec) [ -19600.0632] [ 4065] [depth= 1] . ( 39 sec) [ -19564.6223] [ 4061] [depth= 7] . ( 39 sec) [ -19539.5451] [ 4037] [depth= 3] . ( 40 sec) [ -19496.0282] [ 4033] [depth= 1] . ( 40 sec) [ -19488.4902] [ 4033] [depth= 1] . ( 40 sec) [ -19464.7871] [ 4021] [depth= 1] . ( 40 sec) [ -19427.0346] [ 4019] [depth= 1] . ( 40 sec) [ -19381.6355] [ 4007] [depth= 8] . ( 41 sec) [ -19362.4611] [ 4002] [depth= 13] . ( 41 sec) [ -19357.0766] [ 4001] [depth= 2] . ( 41 sec) [ -19347.3925] [ 4002] [depth= 1] . ( 41 sec) [ -19343.3790] [ 4001] [depth= 1] . ( 41 sec) [ -19321.7474] [ 3990] [depth= 6] . ( 41 sec) [ -19290.8498] [ 3975] [depth= 10] . ( 42 sec) [ -19281.3222] [ 3968] [depth= 2] . ( 42 sec) [ -19277.3817] [ 3969] [depth= 1] . ( 42 sec) [ -19272.5147] [ 3967] [depth= 1] . ( 42 sec) [ -19259.3601] [ 3980] [depth= 1] . ( 43 sec) [ -19250.1183] [ 3979] [depth= 2] . ( 43 sec) [ -19234.7429] [ 3972] [depth= 6] . ( 43 sec) [ -19209.1045] [ 3973] [depth= 3] . ( 43 sec) [ -19180.9918] [ 3966] [depth= 1] . ( 43 sec) [ -19136.6891] [ 3952] [depth= 1] . ( 44 sec) [ -19099.7538] [ 3940] [depth= 1] . ( 44 sec) [ -19020.5994] [ 3916] [depth= 6] . ( 44 sec) [ -19014.1757] [ 3917] [depth= 1] . ( 44 sec) [ -18959.8411] [ 3903] [depth= 1] . ( 44 sec) [ -18934.6278] [ 3891] [depth= 6] . ( 45 sec) [ -18878.2010] [ 3891] [depth= 3] . ( 45 sec) [ -18855.0401] [ 3887] [depth= 3] . ( 45 sec) [ -18847.3944] [ 3882] [depth= 2] . ( 45 sec) [ -18696.9172] [ 3806] [depth= 7] . ( 45 sec) [ -18688.7556] [ 3805] [depth= 1] . ( 45 sec) [ -18678.1374] [ 3806] [depth= 5] . ( 46 sec) [ -18676.5849] [ 3802] [depth= 3] . ( 46 sec) [ -18676.1648] [ 3807] [depth= 1] . ( 46 sec) [ -18674.3501] [ 3807] [depth= 2] . ( 46 sec) [ -18627.7968] [ 3799] [depth= 4] . ( 47 sec) [ -18627.6134] [ 3800] [depth= 1] . ( 47 sec) [ -18616.9594] [ 3798] [depth= 7] . ( 48 sec) [ -18177.9190] [Branch lengths ] . ( 54 sec) [ -17932.6341] [GTR parameters ] . ( 54 sec) [ -17891.5329] [Alpha ][ 0.360628] . ( 55 sec) [ -17891.2309] [ 3795] [depth= 1] . ( 55 sec) [ -17864.4397] [ 3785] [depth= 8] . ( 56 sec) [ -17862.3057] [ 3781] [depth= 4] . ( 56 sec) [ -17842.8783] [ 3771] [depth= 7] . ( 56 sec) [ -17842.3517] [ 3771] [depth= 2] . ( 57 sec) [ -17842.1259] [ 3772] [depth= 1] . ( 57 sec) [ -17838.6554] [ 3770] [depth= 1] . ( 58 sec) [ -17837.9854] [ 3783] [depth= 1] . ( 58 sec) [ -17766.6297] [ 3749] [depth= 11] . ( 59 sec) [ -17705.5928] [ 3726] [depth= 3] . ( 59 sec) [ -17627.5233] [ 3721] [depth= 3] . ( 59 sec) [ -17594.4219] [ 3656] [depth= 10] . ( 59 sec) [ -17587.7714] [ 3648] [depth= 1] . ( 60 sec) [ -17585.6957] [ 3649] [depth= 1] . ( 60 sec) [ -17522.1628] [ 3629] [depth= 4] . ( 60 sec) [ -17522.0738] [ 3626] [depth= 2] . ( 60 sec) [ -17521.1646] [ 3630] [depth= 1] . ( 60 sec) [ -17519.2250] [ 3629] [depth= 1] . ( 62 sec) [ -17518.9098] [ 3629] [depth= 1] . ( 63 sec) [ -17517.4452] [ 3628] [depth= 1] . ( 63 sec) [ -17514.7349] [ 3625] [depth= 2] . ( 63 sec) [ -17506.5675] [ 3614] [depth= 1] . ( 64 sec) [ -17504.8318] [ 3614] [depth= 1] . ( 64 sec) [ -17504.0771] [ 3617] [depth= 1] . ( 65 sec) [ -17504.0636] [ 3617] [depth= 1] . ( 65 sec) [ -17501.8610] [ 3616] [depth= 1] . ( 66 sec) [ -17499.7921] [ 3615] [depth= 1] . ( 66 sec) [ -17477.2999] [ 3612] [depth= 2] . ( 66 sec) [ -17474.3725] [ 3615] [depth= 2] . ( 67 sec) [ -17432.4933] [ 3608] [depth= 7] . ( 67 sec) [ -17431.3716] [ 3608] [depth= 1] . ( 67 sec) [ -17289.8152] [ 3554] [depth= 8] . ( 68 sec) [ -17288.8105] [ 3557] [depth= 2] . ( 68 sec) [ -17287.8332] [ 3556] [depth= 1] . ( 69 sec) [ -17286.9104] [ 3557] [depth= 1] . ( 69 sec) [ -17283.6563] [ 3551] [depth= 5] . ( 69 sec) [ -17267.3380] [ 3554] [depth= 1] . ( 72 sec) [ -17262.0232] [ 3559] [depth= 1] . ( 72 sec) [ -17259.3020] [ 3554] [depth= 1] . ( 72 sec) [ -17245.9624] [ 3553] [depth= 3] . ( 73 sec) [ -17245.3981] [ 3555] [depth= 1] . ( 73 sec) [ -17242.4903] [ 3554] [depth= 2] . ( 74 sec) [ -17230.6335] [ 3548] [depth= 3] . ( 74 sec) [ -17227.4873] [ 3546] [depth= 2] . ( 74 sec) [ -17226.9039] [ 3548] [depth= 1] . ( 75 sec) [ -17226.6000] [ 3544] [depth= 3] . ( 75 sec) [ -17223.0356] [ 3546] [depth= 2] . ( 78 sec) [ -17222.9040] [ 3546] [depth= 1] . ( 79 sec) [ -17222.5995] [ 3548] [depth= 1] . ( 79 sec) [ -17221.0065] [ 3548] [depth= 1] . ( 80 sec) [ -17213.7590] [ 3545] [depth= 5] . ( 80 sec) [ -17213.6214] [ 3545] [depth= 1] . ( 80 sec) [ -17212.5686] [ 3546] [depth= 1] . ( 81 sec) [ -17211.6919] [ 3545] [depth= 1] . ( 82 sec) [ -17169.9486] [ 3522] [depth= 9] . ( 82 sec) [ -17169.8394] [ 3522] [depth= 1] . ( 83 sec) [ -17147.5291] [ 3520] [depth= 3] . ( 84 sec) [ -17147.2451] [ 3521] [depth= 1] . ( 85 sec) [ -17144.1769] [ 3524] [depth= 1] . ( 85 sec) [ -17143.7283] [ 3525] [depth= 1] . ( 85 sec) [ -17118.9663] [ 3510] [depth= 1] . ( 88 sec) [ -17117.9783] [ 3514] [depth= 1] . ( 88 sec) [ -17114.5594] [ 3514] [depth= 1] . ( 91 sec) [ -17113.8523] [ 3515] [depth= 1] . ( 92 sec) [ -17111.0078] [ 3516] [depth= 2] . ( 93 sec) [ -17110.0845] [ 3520] [depth= 1] . ( 94 sec) [ -17103.3584] [ 3514] [depth= 2] . ( 94 sec) [ -17098.8664] [ 3514] [depth= 1] . ( 95 sec) [ -17097.9869] [ 3515] [depth= 1] . ( 96 sec) [ -17097.7180] [ 3513] [depth= 1] . ( 96 sec) [ -17091.5303] [ 3505] [depth= 1] . ( 96 sec) [ -17089.1461] [ 3501] [depth= 1] . ( 98 sec) [ -17089.1133] [ 3501] [depth= 1] . ( 98 sec) [ -17089.0973] [ 3499] [depth= 1] . ( 100 sec) [ -17042.2294] [Branch lengths ] . ( 107 sec) [ -17040.3136] [GTR parameters ] . ( 107 sec) [ -17040.2993] [Alpha ][ 0.362969] . ( 110 sec) [ -17039.7220] [ 3499] [depth= 1] . ( 114 sec) [ -17038.4423] [ 3500] [depth= 1] . ( 116 sec) [ -17036.2954] [ 3500] [depth= 1] . ( 116 sec) [ -17034.9258] [ 3491] [depth= 3] . ( 123 sec) [ -17034.8382] [ 3491] [depth= 1] . ( 125 sec) [ -17034.6421] [ 3493] [depth= 1] . ( 126 sec) [ -17034.4079] [ 3491] [depth= 1] . ( 127 sec) [ -17034.1029] [ 3489] [depth= 1] . ( 128 sec) [ -17033.8591] [ 3489] [depth= 3] . ( 134 sec) [ -17027.0661] [ 3492] [depth= 9] . ( 144 sec) [ -17026.7703] [ 3485] [depth= 1] . ( 149 sec) [ -17026.5279] [ 3483] [depth= 2] . ( 151 sec) [ -17009.3176] [Branch lengths ] . ( 155 sec) [ -17009.0598] [GTR parameters ] . ( 156 sec) [ -17009.0506] [Alpha ][ 0.360952] . ( 157 sec) [ -17008.8974] [ 3482] [depth= 1] . ( 157 sec) [ -17008.8663] [ 3486] [depth= 1] . ( 168 sec) [ -17008.8543] [ 3490] [depth= 1] . ( 173 sec) [ -17008.5662] [ 3486] [depth= 1] . ( 173 sec) [ -17008.5378] [ 3488] [depth= 2] . ( 179 sec) [ -17003.3784] [ 3489] [depth= 3] . ( 187 sec) [ -17003.1822] [ 3490] [depth= 1] . ( 195 sec) [ -16997.0463] [Branch lengths ] . ( 199 sec) [ -16997.0308] [GTR parameters ] . ( 199 sec) [ -16997.0302] [Alpha ][ 0.361392] . ( 242 sec) [ -16995.0271] [Branch lengths ] . ( 382 sec) [ -16994.9443] [Branch lengths ] . ( 383 sec) [ -16994.9443] [Topology ] . ( 386 sec) [ -16994.9424] [Topology ] . ( 389 sec) [ -16994.9420] [Topology ] . ( 390 sec) [ -16994.9408] [GTR parameters ] . ( 391 sec) [ -16994.9408] [Alpha ][ 0.361392] . ( 391 sec) [ -16994.9408] [Topology ] . ( 394 sec) [ -16994.9406] [Topology ] . ( 396 sec) [ -16994.9402] [GTR parameters ] . ( 396 sec) [ -16994.9402] [Alpha ][ 0.361392] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -16994.940238. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 5 sec) [ -39321.9721] [GTR parameters ] . ( 6 sec) [ -38324.5128] [Alpha ][ 0.500960] . ( 6 sec) [ -37727.4338] [ 6989] [depth= 15] . ( 6 sec) [ -37493.5807] [ 6946] [depth= 11] . ( 7 sec) [ -37351.0315] [ 6917] [depth= 13] . ( 7 sec) [ -37308.1224] [ 6888] [depth= 1] . ( 7 sec) [ -37204.2532] [ 6866] [depth= 12] . ( 7 sec) [ -37057.6911] [ 6856] [depth= 5] . ( 7 sec) [ -36942.7849] [ 6848] [depth= 9] . ( 7 sec) [ -36830.8798] [ 6809] [depth= 1] . ( 7 sec) [ -36768.3237] [ 6791] [depth= 6] . ( 7 sec) [ -36646.6895] [ 6777] [depth= 5] . ( 8 sec) [ -36357.1869] [ 6767] [depth= 7] . ( 8 sec) [ -36283.9091] [ 6718] [depth= 3] . ( 8 sec) [ -36250.3290] [ 6713] [depth= 11] . ( 8 sec) [ -36103.5831] [ 6704] [depth= 12] . ( 8 sec) [ -35888.4256] [ 6699] [depth= 4] . ( 8 sec) [ -35510.9814] [ 6647] [depth= 7] . ( 8 sec) [ -35212.2340] [ 6627] [depth= 2] . ( 9 sec) [ -35184.1655] [ 6626] [depth= 1] . ( 9 sec) [ -35096.5968] [ 6615] [depth= 4] . ( 9 sec) [ -35076.0682] [ 6606] [depth= 18] . ( 9 sec) [ -34800.7911] [ 6565] [depth= 8] . ( 9 sec) [ -34708.3165] [ 6567] [depth= 6] . ( 9 sec) [ -34588.8217] [ 6550] [depth= 23] . ( 9 sec) [ -34574.3845] [ 6551] [depth= 1] . ( 10 sec) [ -34499.2498] [ 6530] [depth= 1] . ( 10 sec) [ -34405.4487] [ 6529] [depth= 1] . ( 10 sec) [ -34261.3539] [ 6516] [depth= 20] . ( 10 sec) [ -34251.3967] [ 6519] [depth= 2] . ( 10 sec) [ -34194.5930] [ 6497] [depth= 1] . ( 10 sec) [ -34139.9394] [ 6487] [depth= 12] . ( 10 sec) [ -34136.3432] [ 6494] [depth= 1] . ( 11 sec) [ -33980.5974] [ 6446] [depth= 6] . ( 11 sec) [ -33829.1571] [ 6402] [depth= 20] . ( 11 sec) [ -33819.3867] [ 6401] [depth= 1] . ( 11 sec) [ -33724.1527] [ 6370] [depth= 14] . ( 11 sec) [ -33465.4394] [ 6362] [depth= 3] . ( 11 sec) [ -33192.8942] [ 6345] [depth= 1] . ( 12 sec) [ -32658.3174] [ 6307] [depth= 16] . ( 12 sec) [ -32563.5067] [ 6334] [depth= 28] . ( 12 sec) [ -32398.3729] [ 6294] [depth= 1] . ( 12 sec) [ -32384.4630] [ 6295] [depth= 17] . ( 12 sec) [ -32312.0802] [ 6281] [depth= 22] . ( 12 sec) [ -32293.1150] [ 6282] [depth= 1] . ( 13 sec) [ -32272.9315] [ 6271] [depth= 20] . ( 13 sec) [ -32236.5946] [ 6269] [depth= 1] . ( 13 sec) [ -32123.8854] [ 6240] [depth= 14] . ( 13 sec) [ -32062.4078] [ 6224] [depth= 17] . ( 13 sec) [ -31928.1253] [ 6193] [depth= 1] . ( 13 sec) [ -31820.3840] [ 6186] [depth= 20] . ( 14 sec) [ -31751.1150] [ 6180] [depth= 16] . ( 14 sec) [ -31271.3686] [ 6173] [depth= 8] . ( 14 sec) [ -31244.6220] [ 6173] [depth= 1] . ( 14 sec) [ -31223.5200] [ 6165] [depth= 25] . ( 14 sec) [ -31206.8015] [ 6165] [depth= 1] . ( 14 sec) [ -31158.7137] [ 6158] [depth= 17] . ( 14 sec) [ -31150.6098] [ 6157] [depth= 1] . ( 15 sec) [ -31097.7235] [ 6136] [depth= 8] . ( 15 sec) [ -31013.3449] [ 6114] [depth= 22] . ( 15 sec) [ -30909.2979] [ 6090] [depth= 22] . ( 15 sec) [ -30886.4762] [ 6082] [depth= 13] . ( 15 sec) [ -30736.0337] [ 6065] [depth= 8] . ( 15 sec) [ -30664.8473] [ 6049] [depth= 1] . ( 16 sec) [ -30566.0787] [ 6031] [depth= 19] . ( 16 sec) [ -30282.4926] [ 6003] [depth= 1] . ( 16 sec) [ -30169.3565] [ 5992] [depth= 12] . ( 16 sec) [ -29752.7789] [ 5895] [depth= 13] . ( 16 sec) [ -29711.3398] [ 5889] [depth= 13] . ( 16 sec) [ -29485.2334] [ 5860] [depth= 11] . ( 17 sec) [ -29272.0901] [ 5814] [depth= 5] . ( 17 sec) [ -29174.6159] [ 5780] [depth= 18] . ( 17 sec) [ -29172.4831] [ 5783] [depth= 6] . ( 17 sec) [ -28962.1794] [ 5731] [depth= 21] . ( 17 sec) [ -28931.4408] [ 5730] [depth= 2] . ( 17 sec) [ -28778.5634] [ 5686] [depth= 14] . ( 18 sec) [ -28744.2492] [ 5678] [depth= 5] . ( 18 sec) [ -28713.3621] [ 5670] [depth= 2] . ( 18 sec) [ -28666.8279] [ 5643] [depth= 22] . ( 18 sec) [ -28647.8074] [ 5657] [depth= 1] . ( 18 sec) [ -28638.1518] [ 5650] [depth= 1] . ( 18 sec) [ -28401.4761] [ 5637] [depth= 1] . ( 18 sec) [ -28261.2787] [ 5622] [depth= 4] . ( 19 sec) [ -28245.3779] [ 5622] [depth= 9] . ( 19 sec) [ -28070.9468] [ 5561] [depth= 23] . ( 19 sec) [ -28000.4880] [ 5536] [depth= 26] . ( 19 sec) [ -27756.8533] [ 5508] [depth= 1] . ( 19 sec) [ -27677.4463] [ 5479] [depth= 21] . ( 20 sec) [ -27487.4414] [ 5426] [depth= 8] . ( 20 sec) [ -27477.6070] [ 5437] [depth= 1] . ( 20 sec) [ -27361.1480] [ 5403] [depth= 11] . ( 20 sec) [ -27147.0055] [ 5379] [depth= 12] . ( 20 sec) [ -27135.9415] [ 5380] [depth= 1] . ( 20 sec) [ -27132.8388] [ 5383] [depth= 1] . ( 20 sec) [ -27091.7432] [ 5366] [depth= 14] . ( 21 sec) [ -26994.0674] [ 5326] [depth= 12] . ( 21 sec) [ -26935.9677] [ 5303] [depth= 10] . ( 21 sec) [ -26609.0177] [ 5265] [depth= 9] . ( 21 sec) [ -26557.6545] [ 5254] [depth= 20] . ( 21 sec) [ -26399.9890] [ 5219] [depth= 12] . ( 21 sec) [ -26368.6123] [ 5217] [depth= 1] . ( 22 sec) [ -26350.0044] [ 5211] [depth= 2] . ( 22 sec) [ -26339.4991] [ 5205] [depth= 2] . ( 22 sec) [ -26220.7583] [ 5178] [depth= 16] . ( 22 sec) [ -26190.8399] [ 5172] [depth= 1] . ( 22 sec) [ -26151.0621] [ 5161] [depth= 3] . ( 22 sec) [ -26137.9418] [ 5158] [depth= 1] . ( 23 sec) [ -25941.3304] [ 5109] [depth= 16] . ( 23 sec) [ -25928.0428] [ 5105] [depth= 1] . ( 23 sec) [ -25732.1441] [ 5060] [depth= 14] . ( 23 sec) [ -25721.1890] [ 5058] [depth= 1] . ( 23 sec) [ -25711.0051] [ 5062] [depth= 1] . ( 23 sec) [ -25653.3204] [ 5051] [depth= 9] . ( 24 sec) [ -25465.8391] [ 5004] [depth= 8] . ( 24 sec) [ -25445.9490] [ 4987] [depth= 9] . ( 24 sec) [ -25440.0897] [ 4987] [depth= 1] . ( 24 sec) [ -25327.2765] [ 4950] [depth= 1] . ( 24 sec) [ -25242.7290] [ 4920] [depth= 8] . ( 25 sec) [ -25112.1892] [ 4872] [depth= 10] . ( 25 sec) [ -25106.3022] [ 4872] [depth= 1] . ( 25 sec) [ -25062.3898] [ 4874] [depth= 8] . ( 25 sec) [ -24986.8089] [ 4853] [depth= 4] . ( 25 sec) [ -24877.5923] [ 4823] [depth= 3] . ( 25 sec) [ -24863.8249] [ 4822] [depth= 1] . ( 26 sec) [ -24838.7566] [ 4822] [depth= 10] . ( 26 sec) [ -24776.4459] [ 4808] [depth= 14] . ( 26 sec) [ -24720.2378] [ 4804] [depth= 5] . ( 26 sec) [ -24640.3704] [ 4781] [depth= 7] . ( 26 sec) [ -24615.4496] [ 4775] [depth= 3] . ( 26 sec) [ -24499.3205] [ 4731] [depth= 7] . ( 27 sec) [ -24483.7103] [ 4725] [depth= 5] . ( 27 sec) [ -24466.1786] [ 4722] [depth= 2] . ( 27 sec) [ -24400.7102] [ 4702] [depth= 6] . ( 27 sec) [ -24392.9391] [ 4701] [depth= 8] . ( 27 sec) [ -24344.7423] [ 4680] [depth= 7] . ( 27 sec) [ -24338.0255] [ 4678] [depth= 1] . ( 27 sec) [ -24333.5331] [ 4676] [depth= 2] . ( 28 sec) [ -24333.0473] [ 4676] [depth= 1] . ( 28 sec) [ -24328.0835] [ 4674] [depth= 2] . ( 28 sec) [ -24284.6534] [ 4665] [depth= 2] . ( 28 sec) [ -24145.1708] [ 4633] [depth= 10] . ( 28 sec) [ -24093.1130] [ 4627] [depth= 1] . ( 28 sec) [ -23974.6651] [ 4589] [depth= 17] . ( 29 sec) [ -23945.0343] [ 4580] [depth= 1] . ( 29 sec) [ -23930.5853] [ 4589] [depth= 1] . ( 29 sec) [ -23894.1225] [ 4568] [depth= 2] . ( 29 sec) [ -23884.2898] [ 4558] [depth= 3] . ( 29 sec) [ -23830.9939] [ 4555] [depth= 4] . ( 30 sec) [ -23827.2930] [ 4554] [depth= 1] . ( 30 sec) [ -23742.4566] [ 4545] [depth= 1] . ( 30 sec) [ -23714.5156] [ 4545] [depth= 7] . ( 30 sec) [ -23609.5627] [ 4536] [depth= 1] . ( 30 sec) [ -23497.2809] [ 4505] [depth= 11] . ( 30 sec) [ -23478.9919] [ 4506] [depth= 13] . ( 31 sec) [ -23451.1164] [ 4490] [depth= 1] . ( 31 sec) [ -23385.4066] [ 4479] [depth= 9] . ( 31 sec) [ -23120.0527] [ 4455] [depth= 17] . ( 31 sec) [ -23069.5142] [ 4441] [depth= 7] . ( 31 sec) [ -23024.5675] [ 4392] [depth= 16] . ( 31 sec) [ -23024.4789] [ 4396] [depth= 1] . ( 32 sec) [ -22937.5858] [ 4364] [depth= 18] . ( 32 sec) [ -22930.9985] [ 4368] [depth= 1] . ( 32 sec) [ -22921.1129] [ 4367] [depth= 1] . ( 32 sec) [ -22916.0237] [ 4367] [depth= 1] . ( 32 sec) [ -22887.1984] [ 4363] [depth= 11] . ( 32 sec) [ -22780.9166] [ 4315] [depth= 7] . ( 32 sec) [ -22753.6897] [ 4312] [depth= 1] . ( 33 sec) [ -22693.5605] [ 4284] [depth= 5] . ( 33 sec) [ -22595.0444] [ 4278] [depth= 2] . ( 33 sec) [ -22561.7937] [ 4276] [depth= 1] . ( 33 sec) [ -22388.5651] [ 4243] [depth= 7] . ( 33 sec) [ -22364.8779] [ 4247] [depth= 1] . ( 33 sec) [ -22346.6830] [ 4223] [depth= 9] . ( 34 sec) [ -22346.2673] [ 4225] [depth= 1] . ( 34 sec) [ -22332.5731] [ 4221] [depth= 1] . ( 34 sec) [ -22265.3851] [ 4196] [depth= 3] . ( 34 sec) [ -22223.8889] [ 4192] [depth= 1] . ( 34 sec) [ -22111.9941] [ 4171] [depth= 4] . ( 34 sec) [ -22107.6930] [ 4171] [depth= 1] . ( 34 sec) [ -21795.6470] [ 4116] [depth= 11] . ( 35 sec) [ -21764.9729] [ 4113] [depth= 3] . ( 35 sec) [ -21760.4635] [ 4111] [depth= 1] . ( 35 sec) [ -21759.0766] [ 4111] [depth= 3] . ( 35 sec) [ -21754.3488] [ 4111] [depth= 1] . ( 35 sec) [ -21727.4212] [ 4096] [depth= 1] . ( 35 sec) [ -21726.8894] [ 4094] [depth= 1] . ( 36 sec) [ -21726.1610] [ 4096] [depth= 18] . ( 36 sec) [ -21623.5898] [ 4072] [depth= 8] . ( 36 sec) [ -21620.2054] [ 4072] [depth= 2] . ( 36 sec) [ -21601.1266] [ 4070] [depth= 1] . ( 36 sec) [ -21594.3078] [ 4069] [depth= 1] . ( 37 sec) [ -21571.5093] [ 4059] [depth= 2] . ( 37 sec) [ -19986.8491] [ 4046] [depth= 10] . ( 37 sec) [ -19959.6012] [ 4039] [depth= 1] . ( 37 sec) [ -19908.8197] [ 4036] [depth= 3] . ( 37 sec) [ -19843.1801] [ 4019] [depth= 5] . ( 37 sec) [ -19836.3375] [ 4019] [depth= 2] . ( 38 sec) [ -19824.0009] [ 4018] [depth= 5] . ( 38 sec) [ -19805.8829] [ 4021] [depth= 4] . ( 38 sec) [ -19798.9415] [ 4018] [depth= 1] . ( 38 sec) [ -19390.7480] [ 3974] [depth= 2] . ( 38 sec) [ -19374.6108] [ 3977] [depth= 1] . ( 38 sec) [ -19360.6890] [ 3957] [depth= 1] . ( 38 sec) [ -19355.1523] [ 3955] [depth= 1] . ( 39 sec) [ -19354.4602] [ 3955] [depth= 2] . ( 39 sec) [ -19237.1644] [ 3921] [depth= 13] . ( 39 sec) [ -19209.8879] [ 3918] [depth= 11] . ( 39 sec) [ -19204.1816] [ 3916] [depth= 2] . ( 39 sec) [ -19202.5827] [ 3915] [depth= 5] . ( 40 sec) [ -19184.9505] [ 3912] [depth= 1] . ( 40 sec) [ -19151.1772] [ 3907] [depth= 3] . ( 40 sec) [ -19090.3982] [ 3880] [depth= 7] . ( 40 sec) [ -19084.9791] [ 3872] [depth= 4] . ( 40 sec) [ -19059.4054] [ 3861] [depth= 10] . ( 40 sec) [ -19056.2744] [ 3862] [depth= 1] . ( 41 sec) [ -19029.6344] [ 3861] [depth= 1] . ( 41 sec) [ -19022.6484] [ 3854] [depth= 1] . ( 41 sec) [ -19019.7973] [ 3852] [depth= 2] . ( 41 sec) [ -18995.4395] [ 3850] [depth= 1] . ( 41 sec) [ -18928.3166] [ 3848] [depth= 1] . ( 42 sec) [ -18884.7393] [ 3839] [depth= 6] . ( 42 sec) [ -18872.2805] [ 3833] [depth= 1] . ( 42 sec) [ -18830.4518] [ 3823] [depth= 1] . ( 42 sec) [ -18807.1223] [ 3813] [depth= 3] . ( 42 sec) [ -18790.7415] [ 3804] [depth= 5] . ( 42 sec) [ -18770.6178] [ 3803] [depth= 7] . ( 42 sec) [ -18769.3240] [ 3804] [depth= 2] . ( 43 sec) [ -18748.8923] [ 3796] [depth= 3] . ( 43 sec) [ -18724.7540] [ 3799] [depth= 3] . ( 43 sec) [ -18721.4543] [ 3795] [depth= 3] . ( 43 sec) [ -18704.7446] [ 3791] [depth= 1] . ( 43 sec) [ -18696.7372] [ 3791] [depth= 1] . ( 43 sec) [ -18678.1901] [ 3785] [depth= 1] . ( 44 sec) [ -18653.2770] [ 3779] [depth= 2] . ( 44 sec) [ -18648.1875] [ 3775] [depth= 1] . ( 44 sec) [ -18606.0706] [ 3777] [depth= 1] . ( 44 sec) [ -18601.8631] [ 3776] [depth= 1] . ( 44 sec) [ -18600.9625] [ 3776] [depth= 1] . ( 44 sec) [ -18599.8163] [ 3781] [depth= 1] . ( 45 sec) [ -18512.6615] [ 3755] [depth= 2] . ( 45 sec) [ -18435.0826] [ 3742] [depth= 6] . ( 45 sec) [ -18431.7015] [ 3742] [depth= 4] . ( 45 sec) [ -18425.4509] [ 3740] [depth= 2] . ( 45 sec) [ -18393.2506] [ 3743] [depth= 9] . ( 46 sec) [ -18393.2075] [ 3745] [depth= 1] . ( 46 sec) [ -18385.8682] [ 3746] [depth= 3] . ( 46 sec) [ -18378.0741] [ 3735] [depth= 4] . ( 46 sec) [ -18376.2400] [ 3729] [depth= 2] . ( 46 sec) [ -18351.4872] [ 3725] [depth= 3] . ( 47 sec) [ -18344.3418] [ 3724] [depth= 1] . ( 47 sec) [ -18319.9109] [ 3720] [depth= 1] . ( 49 sec) [ -18007.4466] [Branch lengths ] . ( 54 sec) [ -17754.6131] [GTR parameters ] . ( 55 sec) [ -17721.2989] [Alpha ][ 0.363373] . ( 55 sec) [ -17718.7173] [ 3723] [depth= 3] . ( 55 sec) [ -17712.4390] [ 3719] [depth= 2] . ( 56 sec) [ -17706.1883] [ 3712] [depth= 4] . ( 56 sec) [ -17701.7750] [ 3711] [depth= 1] . ( 56 sec) [ -17699.5058] [ 3710] [depth= 1] . ( 56 sec) [ -17687.0464] [ 3705] [depth= 3] . ( 57 sec) [ -17685.9877] [ 3703] [depth= 1] . ( 57 sec) [ -17673.3775] [ 3701] [depth= 1] . ( 57 sec) [ -17662.7748] [ 3698] [depth= 5] . ( 58 sec) [ -17654.7524] [ 3690] [depth= 3] . ( 59 sec) [ -17654.1867] [ 3690] [depth= 3] . ( 59 sec) [ -17654.1032] [ 3689] [depth= 11] . ( 60 sec) [ -17652.7551] [ 3690] [depth= 3] . ( 61 sec) [ -17645.3348] [ 3687] [depth= 2] . ( 61 sec) [ -17642.9020] [ 3683] [depth= 1] . ( 61 sec) [ -17609.2085] [ 3678] [depth= 5] . ( 61 sec) [ -17602.9950] [ 3679] [depth= 1] . ( 61 sec) [ -17539.3774] [ 3654] [depth= 2] . ( 61 sec) [ -17538.9785] [ 3653] [depth= 1] . ( 62 sec) [ -17538.9280] [ 3652] [depth= 1] . ( 62 sec) [ -17535.2546] [ 3652] [depth= 1] . ( 62 sec) [ -17507.3307] [ 3630] [depth= 1] . ( 64 sec) [ -17492.7137] [ 3597] [depth= 5] . ( 64 sec) [ -17483.7642] [ 3596] [depth= 4] . ( 64 sec) [ -17458.2142] [ 3584] [depth= 2] . ( 64 sec) [ -17457.8379] [ 3584] [depth= 2] . ( 65 sec) [ -17428.6371] [ 3559] [depth= 15] . ( 65 sec) [ -17428.1427] [ 3559] [depth= 1] . ( 65 sec) [ -17389.9922] [ 3537] [depth= 2] . ( 65 sec) [ -17386.1091] [ 3536] [depth= 1] . ( 65 sec) [ -17385.6488] [ 3536] [depth= 1] . ( 66 sec) [ -17382.9762] [ 3534] [depth= 7] . ( 66 sec) [ -17382.5851] [ 3532] [depth= 1] . ( 66 sec) [ -17380.5460] [ 3531] [depth= 1] . ( 66 sec) [ -17376.0936] [ 3530] [depth= 2] . ( 67 sec) [ -17372.7564] [ 3533] [depth= 1] . ( 67 sec) [ -17367.9266] [ 3531] [depth= 4] . ( 67 sec) [ -17364.8149] [ 3532] [depth= 3] . ( 68 sec) [ -17348.3583] [ 3538] [depth= 1] . ( 68 sec) [ -17347.7288] [ 3538] [depth= 1] . ( 68 sec) [ -17347.0789] [ 3542] [depth= 1] . ( 68 sec) [ -17341.3955] [ 3540] [depth= 1] . ( 69 sec) [ -17341.3769] [ 3540] [depth= 1] . ( 69 sec) [ -17341.1305] [ 3539] [depth= 1] . ( 70 sec) [ -17340.1551] [ 3539] [depth= 1] . ( 70 sec) [ -17339.8361] [ 3542] [depth= 1] . ( 70 sec) [ -17339.7391] [ 3543] [depth= 1] . ( 71 sec) [ -17339.0736] [ 3543] [depth= 1] . ( 71 sec) [ -17336.1591] [ 3543] [depth= 1] . ( 72 sec) [ -17320.0676] [ 3539] [depth= 2] . ( 72 sec) [ -17313.9247] [ 3535] [depth= 1] . ( 73 sec) [ -17311.2055] [ 3535] [depth= 2] . ( 73 sec) [ -17282.5105] [ 3518] [depth= 5] . ( 74 sec) [ -17251.5416] [ 3508] [depth= 1] . ( 74 sec) [ -17250.4529] [ 3508] [depth= 1] . ( 75 sec) [ -17249.3859] [ 3506] [depth= 1] . ( 75 sec) [ -17242.9620] [ 3506] [depth= 1] . ( 76 sec) [ -17232.5856] [ 3510] [depth= 4] . ( 76 sec) [ -17226.5226] [ 3505] [depth= 4] . ( 78 sec) [ -17222.8726] [ 3501] [depth= 1] . ( 78 sec) [ -17213.5824] [ 3499] [depth= 1] . ( 78 sec) [ -17204.2163] [ 3500] [depth= 1] . ( 79 sec) [ -17203.1280] [ 3499] [depth= 1] . ( 80 sec) [ -17202.9267] [ 3503] [depth= 1] . ( 80 sec) [ -17202.6527] [ 3507] [depth= 1] . ( 81 sec) [ -17196.3674] [ 3504] [depth= 1] . ( 81 sec) [ -17195.1678] [ 3506] [depth= 1] . ( 81 sec) [ -17195.1180] [ 3506] [depth= 2] . ( 83 sec) [ -17193.1233] [ 3509] [depth= 1] . ( 83 sec) [ -17192.2887] [ 3506] [depth= 2] . ( 84 sec) [ -17190.0502] [ 3503] [depth= 1] . ( 85 sec) [ -17189.8048] [ 3505] [depth= 1] . ( 85 sec) [ -17189.6073] [ 3507] [depth= 1] . ( 85 sec) [ -17189.0002] [ 3502] [depth= 2] . ( 87 sec) [ -17188.3673] [ 3504] [depth= 1] . ( 87 sec) [ -17187.6417] [ 3501] [depth= 1] . ( 88 sec) [ -17186.8820] [ 3495] [depth= 1] . ( 88 sec) [ -17184.4364] [ 3496] [depth= 1] . ( 88 sec) [ -17174.3538] [ 3499] [depth= 11] . ( 89 sec) [ -17173.0528] [ 3495] [depth= 1] . ( 89 sec) [ -17162.1959] [ 3497] [depth= 1] . ( 89 sec) [ -17142.1337] [ 3495] [depth= 5] . ( 89 sec) [ -17127.7159] [ 3493] [depth= 1] . ( 90 sec) [ -17123.8316] [ 3487] [depth= 1] . ( 91 sec) [ -17053.5171] [Branch lengths ] . ( 96 sec) [ -17050.2354] [GTR parameters ] . ( 96 sec) [ -17050.0814] [Alpha ][ 0.355486] . ( 97 sec) [ -17048.9431] [ 3489] [depth= 2] . ( 100 sec) [ -17047.8363] [ 3489] [depth= 2] . ( 101 sec) [ -17047.6032] [ 3491] [depth= 1] . ( 105 sec) [ -17045.3111] [ 3485] [depth= 5] . ( 112 sec) [ -17045.1356] [ 3487] [depth= 2] . ( 113 sec) [ -17042.8991] [ 3486] [depth= 2] . ( 114 sec) [ -17042.8763] [ 3486] [depth= 1] . ( 115 sec) [ -17042.5398] [ 3485] [depth= 1] . ( 116 sec) [ -17042.5015] [ 3488] [depth= 1] . ( 118 sec) [ -17039.9667] [ 3487] [depth= 1] . ( 119 sec) [ -17039.8068] [ 3490] [depth= 1] . ( 130 sec) [ -17039.3167] [ 3489] [depth= 1] . ( 130 sec) [ -17039.2021] [ 3489] [depth= 2] . ( 132 sec) [ -17035.0507] [ 3490] [depth= 3] . ( 133 sec) [ -17034.8026] [ 3491] [depth= 1] . ( 136 sec) [ -17012.6327] [Branch lengths ] . ( 139 sec) [ -17012.4448] [GTR parameters ] . ( 139 sec) [ -17012.4358] [Alpha ][ 0.357347] . ( 142 sec) [ -17012.3296] [ 3490] [depth= 1] . ( 146 sec) [ -17012.2503] [ 3489] [depth= 3] . ( 149 sec) [ -17011.7501] [ 3490] [depth= 1] . ( 152 sec) [ -17011.0122] [ 3488] [depth= 1] . ( 156 sec) [ -17010.9302] [ 3488] [depth= 1] . ( 163 sec) [ -17010.4835] [ 3489] [depth= 1] . ( 169 sec) [ -17008.3221] [ 3491] [depth= 3] . ( 171 sec) [ -17005.3443] [ 3494] [depth= 1] . ( 173 sec) [ -17004.0321] [ 3495] [depth= 1] . ( 180 sec) [ -16997.2018] [Branch lengths ] . ( 184 sec) [ -16997.1006] [GTR parameters ] . ( 184 sec) [ -16997.0784] [Alpha ][ 0.360317] . ( 189 sec) [ -16997.0201] [ 3496] [depth= 1] . ( 202 sec) [ -16996.9951] [ 3495] [depth= 1] . ( 216 sec) [ -16996.9152] [ 3493] [depth= 1] . ( 229 sec) [ -16995.5662] [Branch lengths ] . ( 233 sec) [ -16995.5507] [GTR parameters ] . ( 233 sec) [ -16995.5487] [Alpha ][ 0.361165] . ( 280 sec) [ -16995.2310] [Branch lengths ] . ( 347 sec) [ -16995.1826] [ 3492] [depth= 1] . ( 371 sec) [ -16994.7783] [ 3492] [depth= 1] . ( 430 sec) [ -16994.4116] [Branch lengths ] . ( 432 sec) [ -16994.4045] [GTR parameters ] . ( 432 sec) [ -16994.4036] [Alpha ][ 0.361707] . ( 432 sec) [ -16994.4036] [Topology ] . ( 435 sec) [ -16994.2570] [Topology ] . ( 438 sec) [ -16993.7002] [Topology ] . ( 441 sec) [ -16993.3133] [Topology ] . ( 445 sec) [ -16993.1776] [Topology ] . ( 448 sec) [ -16993.1427] [Topology ] . ( 451 sec) [ -16993.1354] [Topology ] . ( 453 sec) [ -16993.1345] [GTR parameters ] . ( 453 sec) [ -16993.1341] [Alpha ][ 0.362068] . ( 453 sec) [ -16993.1341] [Topology ] . ( 456 sec) [ -16993.1326] [Topology ] . ( 460 sec) [ -16993.1322] [Topology ] . ( 460 sec) [ -16993.1322] [GTR parameters ] . ( 461 sec) [ -16993.1322] [Alpha ][ 0.362068] . ( 461 sec) [ -16993.1322] [Topology ] . ( 464 sec) [ -16993.1321] [Topology ] . ( 465 sec) [ -16993.1321] [GTR parameters ] . ( 465 sec) [ -16993.1321] [Alpha ][ 0.362068] . Checking for NNIs, optimizing five branches... . ( 488 sec) [ -16993.0214] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -16993.021380. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 6 sec) [ -39285.9532] [GTR parameters ] . ( 7 sec) [ -38301.6662] [Alpha ][ 0.500960] . ( 7 sec) [ -38143.8251] [ 7059] [depth= 4] . ( 7 sec) [ -38014.5795] [ 7035] [depth= 12] . ( 7 sec) [ -37952.9380] [ 7012] [depth= 2] . ( 7 sec) [ -37857.0084] [ 6984] [depth= 1] . ( 7 sec) [ -37721.2480] [ 6960] [depth= 14] . ( 8 sec) [ -37595.0447] [ 6955] [depth= 1] . ( 8 sec) [ -37558.6011] [ 6941] [depth= 11] . ( 8 sec) [ -37515.8656] [ 6923] [depth= 1] . ( 8 sec) [ -37427.6650] [ 6901] [depth= 10] . ( 8 sec) [ -37419.6447] [ 6901] [depth= 1] . ( 8 sec) [ -37354.7174] [ 6890] [depth= 2] . ( 8 sec) [ -37329.4183] [ 6869] [depth= 5] . ( 9 sec) [ -37270.7785] [ 6858] [depth= 11] . ( 9 sec) [ -37147.4006] [ 6854] [depth= 1] . ( 9 sec) [ -37131.5184] [ 6844] [depth= 4] . ( 9 sec) [ -37055.5148] [ 6827] [depth= 4] . ( 9 sec) [ -36956.3253] [ 6827] [depth= 1] . ( 9 sec) [ -36936.0134] [ 6824] [depth= 3] . ( 9 sec) [ -36929.4146] [ 6823] [depth= 1] . ( 9 sec) [ -36865.3351] [ 6820] [depth= 5] . ( 10 sec) [ -36841.7959] [ 6816] [depth= 3] . ( 10 sec) [ -36694.0805] [ 6792] [depth= 12] . ( 10 sec) [ -36679.0282] [ 6788] [depth= 2] . ( 10 sec) [ -36075.7419] [ 6780] [depth= 1] . ( 10 sec) [ -35928.5644] [ 6770] [depth= 1] . ( 10 sec) [ -35580.0391] [ 6769] [depth= 8] . ( 10 sec) [ -35522.4292] [ 6711] [depth= 2] . ( 11 sec) [ -35476.6458] [ 6702] [depth= 17] . ( 11 sec) [ -35235.4842] [ 6665] [depth= 19] . ( 11 sec) [ -35047.2416] [ 6652] [depth= 12] . ( 11 sec) [ -34722.4387] [ 6637] [depth= 19] . ( 11 sec) [ -34590.8693] [ 6604] [depth= 9] . ( 11 sec) [ -34487.4451] [ 6585] [depth= 3] . ( 12 sec) [ -34429.0132] [ 6575] [depth= 18] . ( 12 sec) [ -34380.0230] [ 6565] [depth= 17] . ( 12 sec) [ -34305.2414] [ 6542] [depth= 15] . ( 12 sec) [ -34192.1905] [ 6510] [depth= 11] . ( 12 sec) [ -34087.6890] [ 6490] [depth= 8] . ( 13 sec) [ -33951.0964] [ 6478] [depth= 18] . ( 13 sec) [ -33568.2084] [ 6484] [depth= 1] . ( 13 sec) [ -33509.3283] [ 6470] [depth= 1] . ( 13 sec) [ -33405.5693] [ 6432] [depth= 15] . ( 13 sec) [ -33242.6208] [ 6371] [depth= 16] . ( 13 sec) [ -33057.9621] [ 6378] [depth= 16] . ( 13 sec) [ -32884.5710] [ 6354] [depth= 15] . ( 14 sec) [ -32820.8653] [ 6332] [depth= 1] . ( 14 sec) [ -32508.5315] [ 6235] [depth= 17] . ( 14 sec) [ -32159.1974] [ 6192] [depth= 11] . ( 14 sec) [ -32080.8646] [ 6171] [depth= 12] . ( 14 sec) [ -31978.6910] [ 6165] [depth= 2] . ( 14 sec) [ -31887.1947] [ 6142] [depth= 16] . ( 15 sec) [ -31868.5935] [ 6131] [depth= 17] . ( 15 sec) [ -31155.7196] [ 6084] [depth= 8] . ( 15 sec) [ -31004.4909] [ 6047] [depth= 16] . ( 15 sec) [ -30909.2326] [ 6002] [depth= 19] . ( 15 sec) [ -28648.4763] [ 5990] [depth= 20] . ( 15 sec) [ -28626.7559] [ 5988] [depth= 2] . ( 16 sec) [ -28548.2451] [ 5977] [depth= 8] . ( 16 sec) [ -28364.1318] [ 5904] [depth= 10] . ( 16 sec) [ -28217.9553] [ 5915] [depth= 12] . ( 16 sec) [ -28150.5010] [ 5899] [depth= 4] . ( 16 sec) [ -28107.2267] [ 5898] [depth= 3] . ( 16 sec) [ -27931.1303] [ 5836] [depth= 16] . ( 17 sec) [ -27914.1741] [ 5834] [depth= 1] . ( 17 sec) [ -27865.0542] [ 5821] [depth= 6] . ( 17 sec) [ -27686.6136] [ 5798] [depth= 6] . ( 17 sec) [ -27559.1901] [ 5773] [depth= 6] . ( 17 sec) [ -27551.2235] [ 5754] [depth= 9] . ( 17 sec) [ -27429.3142] [ 5750] [depth= 1] . ( 18 sec) [ -27294.7977] [ 5698] [depth= 14] . ( 18 sec) [ -27251.0372] [ 5688] [depth= 1] . ( 18 sec) [ -27236.9540] [ 5676] [depth= 7] . ( 18 sec) [ -27140.6101] [ 5655] [depth= 13] . ( 18 sec) [ -27067.8899] [ 5647] [depth= 1] . ( 18 sec) [ -27013.4432] [ 5630] [depth= 7] . ( 19 sec) [ -26846.8892] [ 5604] [depth= 7] . ( 19 sec) [ -26765.3072] [ 5611] [depth= 1] . ( 19 sec) [ -26708.8606] [ 5591] [depth= 2] . ( 19 sec) [ -26622.7769] [ 5561] [depth= 12] . ( 19 sec) [ -26537.9971] [ 5540] [depth= 13] . ( 19 sec) [ -26475.3506] [ 5537] [depth= 11] . ( 19 sec) [ -26447.6000] [ 5525] [depth= 1] . ( 20 sec) [ -26347.6846] [ 5501] [depth= 11] . ( 20 sec) [ -26345.5021] [ 5491] [depth= 2] . ( 20 sec) [ -26155.0145] [ 5499] [depth= 2] . ( 20 sec) [ -26132.5088] [ 5490] [depth= 13] . ( 20 sec) [ -26002.9233] [ 5443] [depth= 15] . ( 20 sec) [ -25996.1680] [ 5442] [depth= 1] . ( 20 sec) [ -25651.6841] [ 5409] [depth= 7] . ( 21 sec) [ -25374.4050] [ 5357] [depth= 6] . ( 21 sec) [ -25263.7450] [ 5320] [depth= 15] . ( 21 sec) [ -25186.2586] [ 5307] [depth= 17] . ( 21 sec) [ -25178.4760] [ 5308] [depth= 1] . ( 21 sec) [ -25125.8930] [ 5307] [depth= 9] . ( 21 sec) [ -25115.4853] [ 5306] [depth= 2] . ( 22 sec) [ -25076.8006] [ 5280] [depth= 7] . ( 22 sec) [ -24941.4604] [ 5246] [depth= 11] . ( 22 sec) [ -24922.5533] [ 5240] [depth= 1] . ( 22 sec) [ -24842.2105] [ 5203] [depth= 3] . ( 22 sec) [ -24678.8084] [ 5181] [depth= 17] . ( 22 sec) [ -24672.7509] [ 5181] [depth= 1] . ( 22 sec) [ -24567.7832] [ 5161] [depth= 15] . ( 23 sec) [ -24563.1775] [ 5160] [depth= 1] . ( 23 sec) [ -24385.5307] [ 5116] [depth= 15] . ( 23 sec) [ -24344.7392] [ 5112] [depth= 1] . ( 23 sec) [ -24302.4815] [ 5108] [depth= 3] . ( 23 sec) [ -24189.4572] [ 5118] [depth= 1] . ( 23 sec) [ -24185.6606] [ 5093] [depth= 5] . ( 24 sec) [ -23868.4799] [ 5022] [depth= 6] . ( 24 sec) [ -23843.5574] [ 5023] [depth= 1] . ( 24 sec) [ -23802.6477] [ 5011] [depth= 1] . ( 24 sec) [ -23759.8637] [ 5006] [depth= 1] . ( 24 sec) [ -23637.2780] [ 4978] [depth= 4] . ( 24 sec) [ -23625.0766] [ 4977] [depth= 1] . ( 25 sec) [ -23560.7770] [ 4942] [depth= 9] . ( 25 sec) [ -23552.5314] [ 4943] [depth= 2] . ( 25 sec) [ -23542.4955] [ 4939] [depth= 1] . ( 25 sec) [ -23532.0277] [ 4940] [depth= 8] . ( 25 sec) [ -23524.9626] [ 4940] [depth= 1] . ( 25 sec) [ -23429.4883] [ 4935] [depth= 19] . ( 26 sec) [ -23375.1342] [ 4921] [depth= 5] . ( 26 sec) [ -23365.7260] [ 4917] [depth= 2] . ( 26 sec) [ -23300.5325] [ 4905] [depth= 1] . ( 26 sec) [ -23295.8416] [ 4905] [depth= 1] . ( 26 sec) [ -22955.5232] [ 4879] [depth= 21] . ( 26 sec) [ -22950.4082] [ 4877] [depth= 1] . ( 27 sec) [ -22930.6732] [ 4873] [depth= 4] . ( 27 sec) [ -22930.5281] [ 4867] [depth= 3] . ( 27 sec) [ -22848.8202] [ 4827] [depth= 5] . ( 27 sec) [ -22836.6787] [ 4824] [depth= 1] . ( 27 sec) [ -22783.9537] [ 4806] [depth= 15] . ( 28 sec) [ -22759.5239] [ 4805] [depth= 1] . ( 28 sec) [ -22726.5192] [ 4775] [depth= 8] . ( 28 sec) [ -22716.6930] [ 4771] [depth= 1] . ( 28 sec) [ -22501.9308] [ 4697] [depth= 13] . ( 28 sec) [ -22495.8382] [ 4698] [depth= 1] . ( 28 sec) [ -22415.1614] [ 4655] [depth= 9] . ( 29 sec) [ -22280.1182] [ 4646] [depth= 1] . ( 29 sec) [ -22277.1858] [ 4646] [depth= 2] . ( 29 sec) [ -22223.5305] [ 4650] [depth= 2] . ( 29 sec) [ -22181.0423] [ 4639] [depth= 5] . ( 29 sec) [ -22162.3134] [ 4623] [depth= 9] . ( 30 sec) [ -22150.9592] [ 4615] [depth= 1] . ( 30 sec) [ -22115.3488] [ 4603] [depth= 7] . ( 30 sec) [ -22024.7316] [ 4591] [depth= 7] . ( 30 sec) [ -22023.2260] [ 4593] [depth= 1] . ( 31 sec) [ -21996.5690] [ 4591] [depth= 5] . ( 31 sec) [ -21966.4425] [ 4596] [depth= 9] . ( 31 sec) [ -21931.3076] [ 4587] [depth= 1] . ( 31 sec) [ -21827.9755] [ 4552] [depth= 13] . ( 31 sec) [ -21796.2555] [ 4545] [depth= 1] . ( 31 sec) [ -21771.4058] [ 4528] [depth= 5] . ( 31 sec) [ -21769.2395] [ 4528] [depth= 2] . ( 32 sec) [ -21707.3974] [ 4510] [depth= 1] . ( 32 sec) [ -21700.6821] [ 4509] [depth= 1] . ( 32 sec) [ -21415.9075] [ 4470] [depth= 6] . ( 32 sec) [ -21112.7255] [ 4451] [depth= 9] . ( 32 sec) [ -21068.8539] [ 4435] [depth= 7] . ( 32 sec) [ -20983.5062] [ 4413] [depth= 22] . ( 33 sec) [ -20956.2544] [ 4410] [depth= 9] . ( 33 sec) [ -20860.7199] [ 4363] [depth= 9] . ( 33 sec) [ -20838.7677] [ 4350] [depth= 2] . ( 33 sec) [ -20766.8236] [ 4344] [depth= 7] . ( 33 sec) [ -20729.1268] [ 4329] [depth= 10] . ( 34 sec) [ -20723.1136] [ 4328] [depth= 1] . ( 34 sec) [ -20598.6223] [ 4283] [depth= 20] . ( 34 sec) [ -20452.9193] [ 4210] [depth= 15] . ( 34 sec) [ -20421.1231] [ 4200] [depth= 4] . ( 34 sec) [ -20370.7163] [ 4184] [depth= 3] . ( 35 sec) [ -20366.5709] [ 4183] [depth= 1] . ( 35 sec) [ -20052.3300] [ 4117] [depth= 12] . ( 35 sec) [ -20001.9334] [ 4090] [depth= 2] . ( 35 sec) [ -19892.0591] [ 4062] [depth= 7] . ( 35 sec) [ -19860.8631] [ 4036] [depth= 4] . ( 35 sec) [ -19764.8261] [ 4026] [depth= 7] . ( 35 sec) [ -19760.7029] [ 4026] [depth= 1] . ( 36 sec) [ -19674.7423] [ 4027] [depth= 1] . ( 36 sec) [ -19666.5069] [ 4030] [depth= 2] . ( 36 sec) [ -19658.1646] [ 4031] [depth= 1] . ( 36 sec) [ -19644.0557] [ 4022] [depth= 2] . ( 36 sec) [ -19642.0508] [ 4022] [depth= 1] . ( 37 sec) [ -19640.4336] [ 4022] [depth= 1] . ( 37 sec) [ -19537.7323] [ 3995] [depth= 5] . ( 37 sec) [ -19534.3044] [ 4000] [depth= 1] . ( 37 sec) [ -19533.3036] [ 3992] [depth= 2] . ( 37 sec) [ -19516.3579] [ 3977] [depth= 4] . ( 37 sec) [ -19405.7970] [ 3958] [depth= 4] . ( 37 sec) [ -19389.3329] [ 3951] [depth= 4] . ( 38 sec) [ -19358.5981] [ 3941] [depth= 3] . ( 38 sec) [ -19317.2512] [ 3934] [depth= 1] . ( 38 sec) [ -19313.5037] [ 3936] [depth= 1] . ( 38 sec) [ -19307.7780] [ 3934] [depth= 1] . ( 38 sec) [ -19282.5591] [ 3930] [depth= 2] . ( 38 sec) [ -19264.6065] [ 3926] [depth= 1] . ( 39 sec) [ -19250.1969] [ 3924] [depth= 1] . ( 39 sec) [ -19232.2037] [ 3923] [depth= 4] . ( 39 sec) [ -19195.7714] [ 3915] [depth= 9] . ( 39 sec) [ -19192.8841] [ 3920] [depth= 3] . ( 39 sec) [ -19184.8558] [ 3914] [depth= 2] . ( 39 sec) [ -19172.2505] [ 3912] [depth= 1] . ( 40 sec) [ -19168.1997] [ 3908] [depth= 2] . ( 40 sec) [ -19166.8927] [ 3908] [depth= 1] . ( 40 sec) [ -19166.0545] [ 3912] [depth= 1] . ( 41 sec) [ -19134.7202] [ 3894] [depth= 5] . ( 41 sec) [ -19126.1300] [ 3897] [depth= 3] . ( 41 sec) [ -19107.5578] [ 3888] [depth= 10] . ( 41 sec) [ -19104.0008] [ 3886] [depth= 2] . ( 42 sec) [ -19094.7775] [ 3886] [depth= 3] . ( 42 sec) [ -19093.7266] [ 3892] [depth= 1] . ( 42 sec) [ -19084.5465] [ 3891] [depth= 7] . ( 42 sec) [ -19072.5831] [ 3876] [depth= 3] . ( 43 sec) [ -18994.8365] [ 3836] [depth= 3] . ( 43 sec) [ -18919.1136] [ 3827] [depth= 1] . ( 43 sec) [ -18877.3992] [ 3827] [depth= 2] . ( 44 sec) [ -18873.8139] [ 3828] [depth= 1] . ( 44 sec) [ -18825.7688] [ 3847] [depth= 7] . ( 45 sec) [ -18653.1485] [ 3783] [depth= 8] . ( 45 sec) [ -18619.7742] [ 3774] [depth= 1] . ( 45 sec) [ -18588.5362] [ 3756] [depth= 4] . ( 46 sec) [ -18582.1301] [ 3752] [depth= 3] . ( 46 sec) [ -18526.7246] [ 3749] [depth= 1] . ( 46 sec) [ -18448.2546] [ 3742] [depth= 4] . ( 47 sec) [ -18408.3434] [ 3737] [depth= 1] . ( 47 sec) [ -18404.1792] [ 3737] [depth= 3] . ( 47 sec) [ -18399.8455] [ 3734] [depth= 1] . ( 48 sec) [ -18384.7890] [ 3729] [depth= 9] . ( 48 sec) [ -18350.8870] [ 3721] [depth= 4] . ( 49 sec) [ -18305.8099] [ 3717] [depth= 1] . ( 49 sec) [ -18305.4054] [ 3720] [depth= 1] . ( 49 sec) [ -18262.0540] [ 3709] [depth= 1] . ( 49 sec) [ -18246.7863] [ 3704] [depth= 2] . ( 50 sec) [ -18197.7915] [ 3696] [depth= 5] . ( 50 sec) [ -18185.2958] [ 3684] [depth= 9] . ( 51 sec) [ -18182.4689] [ 3686] [depth= 1] . ( 51 sec) [ -18115.1733] [ 3668] [depth= 13] . ( 51 sec) [ -18113.2016] [ 3669] [depth= 1] . ( 52 sec) [ -17748.0329] [Branch lengths ] . ( 55 sec) [ -17737.9419] [GTR parameters ] . ( 56 sec) [ -17704.7629] [Alpha ][ 0.363848] . ( 56 sec) [ -17700.1329] [ 3667] [depth= 1] . ( 56 sec) [ -17692.8842] [ 3662] [depth= 6] . ( 57 sec) [ -17691.3875] [ 3661] [depth= 1] . ( 57 sec) [ -17685.2585] [ 3659] [depth= 1] . ( 57 sec) [ -17679.6930] [ 3659] [depth= 1] . ( 57 sec) [ -17662.5592] [ 3662] [depth= 3] . ( 57 sec) [ -17580.6920] [ 3638] [depth= 7] . ( 57 sec) [ -17575.8386] [ 3635] [depth= 1] . ( 58 sec) [ -17573.1661] [ 3631] [depth= 1] . ( 58 sec) [ -17571.7687] [ 3629] [depth= 1] . ( 58 sec) [ -17571.4970] [ 3632] [depth= 1] . ( 59 sec) [ -17541.8891] [ 3622] [depth= 1] . ( 59 sec) [ -17540.7264] [ 3624] [depth= 1] . ( 60 sec) [ -17537.7267] [ 3623] [depth= 1] . ( 60 sec) [ -17537.1196] [ 3624] [depth= 1] . ( 61 sec) [ -17536.1724] [ 3624] [depth= 1] . ( 61 sec) [ -17531.7525] [ 3617] [depth= 1] . ( 61 sec) [ -17526.5836] [ 3613] [depth= 1] . ( 62 sec) [ -17526.0635] [ 3613] [depth= 1] . ( 62 sec) [ -17524.6605] [ 3611] [depth= 1] . ( 62 sec) [ -17515.4740] [ 3606] [depth= 1] . ( 62 sec) [ -17514.1729] [ 3604] [depth= 1] . ( 63 sec) [ -17510.2486] [ 3604] [depth= 1] . ( 63 sec) [ -17508.8701] [ 3609] [depth= 1] . ( 63 sec) [ -17508.3167] [ 3610] [depth= 1] . ( 63 sec) [ -17506.2092] [ 3609] [depth= 1] . ( 64 sec) [ -17470.0058] [ 3596] [depth= 3] . ( 64 sec) [ -17455.1779] [ 3595] [depth= 1] . ( 64 sec) [ -17453.9110] [ 3595] [depth= 5] . ( 64 sec) [ -17442.7060] [ 3594] [depth= 1] . ( 65 sec) [ -17435.5971] [ 3592] [depth= 2] . ( 65 sec) [ -17421.1988] [ 3587] [depth= 1] . ( 65 sec) [ -17413.7725] [ 3586] [depth= 2] . ( 65 sec) [ -17411.8479] [ 3582] [depth= 1] . ( 66 sec) [ -17394.9440] [ 3571] [depth= 2] . ( 66 sec) [ -17389.9851] [ 3576] [depth= 1] . ( 66 sec) [ -17386.5736] [ 3574] [depth= 1] . ( 67 sec) [ -17375.1151] [ 3569] [depth= 3] . ( 67 sec) [ -17352.4917] [ 3559] [depth= 1] . ( 67 sec) [ -17346.3737] [ 3562] [depth= 10] . ( 68 sec) [ -17344.3178] [ 3561] [depth= 1] . ( 69 sec) [ -17320.2469] [ 3550] [depth= 2] . ( 69 sec) [ -17317.6343] [ 3549] [depth= 1] . ( 69 sec) [ -17315.4030] [ 3548] [depth= 1] . ( 69 sec) [ -17303.7743] [ 3541] [depth= 4] . ( 70 sec) [ -17301.6373] [ 3537] [depth= 2] . ( 70 sec) [ -17300.7081] [ 3537] [depth= 1] . ( 70 sec) [ -17300.1462] [ 3536] [depth= 1] . ( 70 sec) [ -17294.5066] [ 3533] [depth= 12] . ( 71 sec) [ -17293.8125] [ 3530] [depth= 1] . ( 71 sec) [ -17289.6391] [ 3529] [depth= 1] . ( 72 sec) [ -17270.5961] [ 3524] [depth= 9] . ( 72 sec) [ -17259.9704] [ 3521] [depth= 2] . ( 72 sec) [ -17257.9581] [ 3520] [depth= 2] . ( 72 sec) [ -17255.7924] [ 3519] [depth= 1] . ( 74 sec) [ -17253.9868] [ 3520] [depth= 1] . ( 75 sec) [ -17243.8994] [ 3519] [depth= 10] . ( 75 sec) [ -17239.2672] [ 3515] [depth= 2] . ( 75 sec) [ -17235.9742] [ 3515] [depth= 1] . ( 75 sec) [ -17208.3793] [ 3510] [depth= 1] . ( 76 sec) [ -17196.9933] [ 3508] [depth= 2] . ( 77 sec) [ -17194.1682] [ 3508] [depth= 1] . ( 77 sec) [ -17182.3581] [ 3505] [depth= 1] . ( 77 sec) [ -17176.7566] [ 3502] [depth= 2] . ( 77 sec) [ -17167.1836] [ 3506] [depth= 2] . ( 78 sec) [ -17166.9824] [ 3511] [depth= 1] . ( 79 sec) [ -17166.3508] [ 3510] [depth= 2] . ( 80 sec) [ -17163.9732] [ 3508] [depth= 1] . ( 80 sec) [ -17154.0657] [ 3502] [depth= 2] . ( 82 sec) [ -17142.7011] [ 3501] [depth= 1] . ( 82 sec) [ -17134.9184] [ 3504] [depth= 9] . ( 83 sec) [ -17134.1564] [ 3506] [depth= 2] . ( 87 sec) [ -17132.0542] [ 3506] [depth= 1] . ( 87 sec) [ -17129.3457] [ 3501] [depth= 2] . ( 87 sec) [ -17129.1334] [ 3499] [depth= 1] . ( 88 sec) [ -17125.0594] [ 3498] [depth= 1] . ( 89 sec) [ -17122.0593] [ 3501] [depth= 1] . ( 90 sec) [ -17120.1479] [ 3503] [depth= 1] . ( 90 sec) [ -17119.1066] [ 3501] [depth= 1] . ( 91 sec) [ -17114.6207] [ 3499] [depth= 1] . ( 93 sec) [ -17114.2389] [ 3504] [depth= 1] . ( 95 sec) [ -17113.5025] [ 3503] [depth= 1] . ( 95 sec) [ -17112.9186] [ 3503] [depth= 1] . ( 95 sec) [ -17112.6245] [ 3499] [depth= 1] . ( 97 sec) [ -17046.8201] [Branch lengths ] . ( 99 sec) [ -17044.2709] [GTR parameters ] . ( 100 sec) [ -17044.2286] [Alpha ][ 0.359904] . ( 101 sec) [ -17041.7164] [ 3496] [depth= 4] . ( 102 sec) [ -17035.3187] [ 3495] [depth= 2] . ( 107 sec) [ -17028.8867] [ 3487] [depth= 1] . ( 111 sec) [ -17027.9242] [ 3488] [depth= 1] . ( 118 sec) [ -17024.3915] [ 3482] [depth= 5] . ( 120 sec) [ -17022.5778] [ 3482] [depth= 1] . ( 122 sec) [ -17021.9565] [ 3481] [depth= 1] . ( 125 sec) [ -17020.8306] [ 3482] [depth= 1] . ( 125 sec) [ -17017.0678] [ 3483] [depth= 1] . ( 126 sec) [ -17012.0947] [ 3485] [depth= 2] . ( 128 sec) [ -17011.7635] [ 3490] [depth= 1] . ( 130 sec) [ -17009.7904] [ 3489] [depth= 1] . ( 136 sec) [ -17007.2372] [ 3491] [depth= 1] . ( 139 sec) [ -16997.8854] [Branch lengths ] . ( 141 sec) [ -16997.7299] [GTR parameters ] . ( 141 sec) [ -16997.7299] [Alpha ][ 0.359904] . ( 154 sec) [ -16997.5952] [ 3491] [depth= 1] . ( 183 sec) [ -16995.9121] [Branch lengths ] . ( 184 sec) [ -16995.9003] [GTR parameters ] . ( 184 sec) [ -16995.8998] [Alpha ][ 0.360294] . ( 200 sec) [ -16995.8578] [ 3492] [depth= 1] . ( 229 sec) [ -16994.8748] [Branch lengths ] . ( 230 sec) [ -16994.8691] [GTR parameters ] . ( 230 sec) [ -16994.8673] [Alpha ][ 0.361081] . ( 272 sec) [ -16994.7539] [Branch lengths ] . ( 369 sec) [ -16994.4124] [ 3492] [depth= 1] . ( 414 sec) [ -16994.1938] [Branch lengths ] . ( 416 sec) [ -16994.1901] [GTR parameters ] . ( 417 sec) [ -16994.1901] [Alpha ][ 0.361081] . ( 417 sec) [ -16994.1901] [Topology ] . ( 420 sec) [ -16993.2212] [Topology ] . ( 423 sec) [ -16993.1503] [Topology ] . ( 426 sec) [ -16993.1419] [Topology ] . ( 429 sec) [ -16993.1399] [Topology ] . ( 432 sec) [ -16993.1393] [Topology ] . ( 433 sec) [ -16993.1362] [GTR parameters ] . ( 433 sec) [ -16993.1339] [Alpha ][ 0.362000] . ( 434 sec) [ -16993.1339] [Topology ] . ( 437 sec) [ -16993.1333] [Topology ] . ( 437 sec) [ -16993.1332] [GTR parameters ] . ( 437 sec) [ -16993.1332] [Alpha ][ 0.362000] . Checking for NNIs, optimizing five branches... . ( 460 sec) [ -16993.0262] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -16993.026181. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -37246.0358] [GTR parameters ] . ( 3 sec) [ -36287.6350] [Alpha ][ 0.500960] . ( 3 sec) [ -36153.3448] [ 6970] [depth= 12] . ( 3 sec) [ -35966.0061] [ 6930] [depth= 14] . ( 4 sec) [ -35920.1293] [ 6928] [depth= 2] . ( 4 sec) [ -35911.9502] [ 6921] [depth= 7] . ( 4 sec) [ -35804.6847] [ 6898] [depth= 6] . ( 4 sec) [ -35778.9509] [ 6897] [depth= 1] . ( 4 sec) [ -35633.9885] [ 6898] [depth= 2] . ( 4 sec) [ -35535.3627] [ 6888] [depth= 9] . ( 4 sec) [ -35418.6063] [ 6877] [depth= 1] . ( 5 sec) [ -35321.3689] [ 6869] [depth= 5] . ( 5 sec) [ -35307.3542] [ 6867] [depth= 3] . ( 5 sec) [ -35265.7711] [ 6864] [depth= 3] . ( 5 sec) [ -35192.3328] [ 6837] [depth= 10] . ( 5 sec) [ -35151.6251] [ 6837] [depth= 1] . ( 5 sec) [ -34958.3964] [ 6827] [depth= 20] . ( 5 sec) [ -34914.7815] [ 6828] [depth= 1] . ( 6 sec) [ -34871.3620] [ 6813] [depth= 10] . ( 6 sec) [ -34169.1868] [ 6744] [depth= 6] . ( 6 sec) [ -33911.7973] [ 6661] [depth= 11] . ( 6 sec) [ -33514.4163] [ 6598] [depth= 16] . ( 6 sec) [ -33491.6417] [ 6594] [depth= 8] . ( 6 sec) [ -33435.0565] [ 6581] [depth= 6] . ( 7 sec) [ -33340.1865] [ 6570] [depth= 21] . ( 7 sec) [ -33270.5510] [ 6575] [depth= 5] . ( 7 sec) [ -32987.7976] [ 6521] [depth= 19] . ( 7 sec) [ -32102.1313] [ 6510] [depth= 1] . ( 7 sec) [ -32030.7920] [ 6499] [depth= 13] . ( 7 sec) [ -31887.2194] [ 6481] [depth= 17] . ( 7 sec) [ -31770.4613] [ 6490] [depth= 1] . ( 8 sec) [ -31628.3057] [ 6456] [depth= 11] . ( 8 sec) [ -31440.2074] [ 6425] [depth= 11] . ( 8 sec) [ -31364.3672] [ 6410] [depth= 11] . ( 8 sec) [ -31301.8842] [ 6394] [depth= 17] . ( 8 sec) [ -31223.4732] [ 6365] [depth= 17] . ( 8 sec) [ -31162.6514] [ 6301] [depth= 15] . ( 9 sec) [ -31136.0435] [ 6299] [depth= 6] . ( 9 sec) [ -31048.3000] [ 6282] [depth= 1] . ( 9 sec) [ -30965.8303] [ 6251] [depth= 1] . ( 9 sec) [ -30888.0773] [ 6226] [depth= 16] . ( 9 sec) [ -30793.7541] [ 6193] [depth= 18] . ( 9 sec) [ -30660.7626] [ 6181] [depth= 3] . ( 10 sec) [ -30353.5310] [ 6127] [depth= 17] . ( 10 sec) [ -30301.9306] [ 6114] [depth= 17] . ( 10 sec) [ -30258.5845] [ 6107] [depth= 3] . ( 10 sec) [ -30132.2601] [ 6084] [depth= 9] . ( 10 sec) [ -30026.1440] [ 6081] [depth= 1] . ( 10 sec) [ -29795.8767] [ 6059] [depth= 15] . ( 10 sec) [ -29717.0175] [ 6101] [depth= 1] . ( 11 sec) [ -29421.0494] [ 6042] [depth= 2] . ( 11 sec) [ -29270.6896] [ 6013] [depth= 16] . ( 11 sec) [ -29021.7419] [ 5975] [depth= 14] . ( 11 sec) [ -28625.2306] [ 5891] [depth= 16] . ( 11 sec) [ -28491.7204] [ 5895] [depth= 13] . ( 11 sec) [ -28442.5508] [ 5876] [depth= 7] . ( 12 sec) [ -28137.0313] [ 5822] [depth= 8] . ( 12 sec) [ -27933.2367] [ 5778] [depth= 8] . ( 12 sec) [ -27781.6919] [ 5731] [depth= 1] . ( 12 sec) [ -27755.0687] [ 5721] [depth= 8] . ( 12 sec) [ -27751.2829] [ 5725] [depth= 13] . ( 12 sec) [ -27702.9781] [ 5724] [depth= 13] . ( 13 sec) [ -27580.6211] [ 5688] [depth= 8] . ( 13 sec) [ -27323.4636] [ 5635] [depth= 1] . ( 13 sec) [ -27123.8217] [ 5586] [depth= 2] . ( 13 sec) [ -27104.2062] [ 5567] [depth= 11] . ( 13 sec) [ -27087.7553] [ 5563] [depth= 2] . ( 13 sec) [ -27016.0620] [ 5539] [depth= 4] . ( 13 sec) [ -26983.9975] [ 5541] [depth= 1] . ( 14 sec) [ -26841.7536] [ 5521] [depth= 19] . ( 14 sec) [ -26830.9900] [ 5523] [depth= 1] . ( 14 sec) [ -26670.4195] [ 5501] [depth= 20] . ( 14 sec) [ -26651.2342] [ 5500] [depth= 9] . ( 14 sec) [ -26647.1588] [ 5499] [depth= 1] . ( 15 sec) [ -26582.6211] [ 5488] [depth= 14] . ( 15 sec) [ -26522.2482] [ 5481] [depth= 1] . ( 15 sec) [ -26503.5809] [ 5463] [depth= 8] . ( 15 sec) [ -26499.7123] [ 5459] [depth= 14] . ( 15 sec) [ -26474.8707] [ 5457] [depth= 1] . ( 15 sec) [ -26355.9785] [ 5448] [depth= 17] . ( 16 sec) [ -26038.8476] [ 5418] [depth= 17] . ( 16 sec) [ -25994.9318] [ 5411] [depth= 14] . ( 16 sec) [ -25977.3903] [ 5407] [depth= 14] . ( 16 sec) [ -25976.4040] [ 5413] [depth= 19] . ( 16 sec) [ -25881.5625] [ 5385] [depth= 6] . ( 16 sec) [ -25846.7550] [ 5351] [depth= 2] . ( 17 sec) [ -25703.9831] [ 5336] [depth= 1] . ( 17 sec) [ -25650.9457] [ 5349] [depth= 1] . ( 17 sec) [ -25384.1812] [ 5278] [depth= 10] . ( 17 sec) [ -25374.4937] [ 5277] [depth= 1] . ( 17 sec) [ -25299.4685] [ 5270] [depth= 3] . ( 17 sec) [ -25240.1106] [ 5289] [depth= 3] . ( 18 sec) [ -25089.3108] [ 5226] [depth= 15] . ( 18 sec) [ -25089.0601] [ 5225] [depth= 1] . ( 18 sec) [ -25075.4110] [ 5223] [depth= 10] . ( 18 sec) [ -25049.2153] [ 5223] [depth= 9] . ( 18 sec) [ -25034.2089] [ 5219] [depth= 13] . ( 18 sec) [ -24969.5671] [ 5198] [depth= 8] . ( 19 sec) [ -24804.8855] [ 5172] [depth= 11] . ( 19 sec) [ -24782.2260] [ 5171] [depth= 1] . ( 19 sec) [ -24779.6187] [ 5170] [depth= 1] . ( 19 sec) [ -24688.2805] [ 5170] [depth= 10] . ( 19 sec) [ -24584.1278] [ 5150] [depth= 5] . ( 19 sec) [ -24395.7412] [ 5146] [depth= 5] . ( 19 sec) [ -24307.3365] [ 5132] [depth= 12] . ( 20 sec) [ -24256.8153] [ 5120] [depth= 16] . ( 20 sec) [ -24244.2771] [ 5116] [depth= 2] . ( 20 sec) [ -24188.6886] [ 5106] [depth= 16] . ( 20 sec) [ -24068.4488] [ 5104] [depth= 9] . ( 20 sec) [ -24018.7748] [ 5088] [depth= 7] . ( 20 sec) [ -23958.0014] [ 5086] [depth= 3] . ( 20 sec) [ -23705.4205] [ 5034] [depth= 17] . ( 21 sec) [ -23648.8996] [ 5022] [depth= 18] . ( 21 sec) [ -23612.5576] [ 5029] [depth= 1] . ( 21 sec) [ -23460.0572] [ 4990] [depth= 13] . ( 21 sec) [ -23425.4152] [ 4986] [depth= 2] . ( 21 sec) [ -23355.8529] [ 4973] [depth= 6] . ( 22 sec) [ -23355.7163] [ 4983] [depth= 1] . ( 22 sec) [ -23208.6732] [ 4966] [depth= 4] . ( 22 sec) [ -23207.6246] [ 4968] [depth= 1] . ( 22 sec) [ -23200.2071] [ 4969] [depth= 4] . ( 23 sec) [ -22976.1749] [ 4940] [depth= 2] . ( 23 sec) [ -22970.9382] [ 4947] [depth= 1] . ( 23 sec) [ -22905.8484] [ 4927] [depth= 18] . ( 23 sec) [ -22777.6693] [ 4884] [depth= 16] . ( 23 sec) [ -22768.9652] [ 4877] [depth= 1] . ( 23 sec) [ -22674.5664] [ 4834] [depth= 15] . ( 24 sec) [ -22621.7602] [ 4827] [depth= 7] . ( 24 sec) [ -22591.7127] [ 4821] [depth= 2] . ( 24 sec) [ -22578.1544] [ 4818] [depth= 20] . ( 24 sec) [ -22575.1685] [ 4822] [depth= 1] . ( 24 sec) [ -22541.1887] [ 4811] [depth= 4] . ( 24 sec) [ -22515.2580] [ 4787] [depth= 4] . ( 24 sec) [ -22471.2837] [ 4770] [depth= 13] . ( 25 sec) [ -22459.6184] [ 4763] [depth= 1] . ( 25 sec) [ -22381.7688] [ 4735] [depth= 10] . ( 25 sec) [ -22380.6366] [ 4737] [depth= 15] . ( 25 sec) [ -22361.8330] [ 4735] [depth= 1] . ( 25 sec) [ -22357.7258] [ 4728] [depth= 4] . ( 26 sec) [ -22357.2313] [ 4727] [depth= 1] . ( 26 sec) [ -22280.8583] [ 4706] [depth= 16] . ( 26 sec) [ -22199.8044] [ 4689] [depth= 9] . ( 26 sec) [ -22172.7721] [ 4674] [depth= 12] . ( 26 sec) [ -22100.7218] [ 4652] [depth= 10] . ( 26 sec) [ -22094.7793] [ 4651] [depth= 1] . ( 27 sec) [ -22085.8762] [ 4652] [depth= 1] . ( 27 sec) [ -22005.4370] [ 4631] [depth= 12] . ( 27 sec) [ -21982.4091] [ 4628] [depth= 3] . ( 27 sec) [ -21906.8853] [ 4616] [depth= 1] . ( 27 sec) [ -21597.6503] [ 4615] [depth= 2] . ( 27 sec) [ -21521.5190] [ 4600] [depth= 13] . ( 28 sec) [ -21381.5169] [ 4577] [depth= 1] . ( 28 sec) [ -21220.7199] [ 4532] [depth= 10] . ( 28 sec) [ -21196.7324] [ 4499] [depth= 14] . ( 28 sec) [ -21152.5667] [ 4484] [depth= 4] . ( 28 sec) [ -21145.2153] [ 4487] [depth= 1] . ( 29 sec) [ -21075.0683] [ 4459] [depth= 6] . ( 29 sec) [ -20985.8176] [ 4430] [depth= 17] . ( 29 sec) [ -20976.9651] [ 4412] [depth= 7] . ( 29 sec) [ -20845.7965] [ 4371] [depth= 20] . ( 29 sec) [ -20838.6939] [ 4375] [depth= 1] . ( 29 sec) [ -20838.1066] [ 4373] [depth= 10] . ( 30 sec) [ -20827.6649] [ 4376] [depth= 24] . ( 30 sec) [ -20817.7326] [ 4375] [depth= 4] . ( 30 sec) [ -20815.9693] [ 4375] [depth= 1] . ( 30 sec) [ -20802.6375] [ 4382] [depth= 2] . ( 30 sec) [ -20563.3689] [ 4342] [depth= 7] . ( 31 sec) [ -20562.5678] [ 4342] [depth= 1] . ( 31 sec) [ -20496.6790] [ 4337] [depth= 6] . ( 31 sec) [ -20483.4017] [ 4326] [depth= 4] . ( 31 sec) [ -20479.7301] [ 4324] [depth= 5] . ( 31 sec) [ -20415.3877] [ 4305] [depth= 2] . ( 31 sec) [ -20394.2698] [ 4305] [depth= 3] . ( 31 sec) [ -20374.9580] [ 4306] [depth= 1] . ( 32 sec) [ -20332.1943] [ 4283] [depth= 10] . ( 32 sec) [ -20288.8925] [ 4301] [depth= 1] . ( 32 sec) [ -20286.6791] [ 4304] [depth= 3] . ( 32 sec) [ -20271.9518] [ 4303] [depth= 1] . ( 32 sec) [ -20246.6214] [ 4291] [depth= 1] . ( 32 sec) [ -20222.7814] [ 4272] [depth= 1] . ( 33 sec) [ -20221.6639] [ 4275] [depth= 5] . ( 33 sec) [ -20161.9367] [ 4289] [depth= 1] . ( 33 sec) [ -20092.1071] [ 4265] [depth= 6] . ( 33 sec) [ -20060.2927] [ 4254] [depth= 6] . ( 33 sec) [ -19957.4364] [ 4211] [depth= 15] . ( 33 sec) [ -19952.3277] [ 4212] [depth= 1] . ( 33 sec) [ -19880.9540] [ 4190] [depth= 11] . ( 34 sec) [ -19870.3475] [ 4190] [depth= 1] . ( 34 sec) [ -19866.4966] [ 4192] [depth= 1] . ( 34 sec) [ -19827.7201] [ 4181] [depth= 3] . ( 34 sec) [ -19806.8554] [ 4181] [depth= 1] . ( 34 sec) [ -19766.9909] [ 4179] [depth= 1] . ( 35 sec) [ -19758.4987] [ 4163] [depth= 2] . ( 35 sec) [ -19735.2613] [ 4148] [depth= 6] . ( 35 sec) [ -19717.4585] [ 4145] [depth= 2] . ( 35 sec) [ -19622.0981] [ 4121] [depth= 7] . ( 35 sec) [ -19591.3115] [ 4114] [depth= 1] . ( 35 sec) [ -19505.5822] [ 4091] [depth= 9] . ( 36 sec) [ -19492.4526] [ 4088] [depth= 5] . ( 36 sec) [ -19453.1726] [ 4073] [depth= 4] . ( 36 sec) [ -19440.8284] [ 4078] [depth= 5] . ( 36 sec) [ -19351.5770] [ 4050] [depth= 3] . ( 37 sec) [ -19338.3448] [ 4047] [depth= 1] . ( 37 sec) [ -19227.0262] [ 4007] [depth= 1] . ( 37 sec) [ -19209.8214] [ 4001] [depth= 1] . ( 37 sec) [ -19153.9143] [ 3995] [depth= 2] . ( 37 sec) [ -19140.0390] [ 3992] [depth= 1] . ( 38 sec) [ -19138.4537] [ 3994] [depth= 1] . ( 38 sec) [ -19107.9240] [ 3993] [depth= 3] . ( 38 sec) [ -19100.9737] [ 3993] [depth= 5] . ( 39 sec) [ -18929.8839] [ 3956] [depth= 7] . ( 39 sec) [ -18836.3273] [ 3940] [depth= 5] . ( 39 sec) [ -18829.3688] [ 3940] [depth= 1] . ( 39 sec) [ -18800.9244] [ 3934] [depth= 5] . ( 39 sec) [ -18755.4750] [ 3914] [depth= 4] . ( 39 sec) [ -18741.8653] [ 3906] [depth= 2] . ( 40 sec) [ -18666.5487] [ 3887] [depth= 5] . ( 40 sec) [ -18648.9383] [ 3885] [depth= 1] . ( 40 sec) [ -18644.3203] [ 3890] [depth= 1] . ( 40 sec) [ -18508.4780] [ 3838] [depth= 14] . ( 40 sec) [ -18496.1941] [ 3835] [depth= 3] . ( 40 sec) [ -18366.7365] [ 3789] [depth= 5] . ( 41 sec) [ -18315.1137] [ 3780] [depth= 1] . ( 41 sec) [ -18313.8620] [ 3783] [depth= 1] . ( 41 sec) [ -18308.1982] [ 3785] [depth= 1] . ( 41 sec) [ -18163.7733] [ 3715] [depth= 9] . ( 42 sec) [ -18157.1034] [ 3713] [depth= 7] . ( 42 sec) [ -18157.0616] [ 3714] [depth= 1] . ( 42 sec) [ -18156.9472] [ 3714] [depth= 1] . ( 42 sec) [ -18153.7957] [ 3713] [depth= 1] . ( 43 sec) [ -18145.8871] [ 3707] [depth= 1] . ( 43 sec) [ -18122.3507] [ 3714] [depth= 1] . ( 43 sec) [ -18105.3615] [ 3714] [depth= 8] . ( 43 sec) [ -18096.9262] [ 3714] [depth= 1] . ( 44 sec) [ -18095.3285] [ 3711] [depth= 1] . ( 44 sec) [ -18094.0493] [ 3716] [depth= 1] . ( 44 sec) [ -18087.0132] [ 3712] [depth= 3] . ( 44 sec) [ -18083.7354] [ 3711] [depth= 1] . ( 45 sec) [ -17788.7894] [Branch lengths ] . ( 48 sec) [ -17777.5085] [GTR parameters ] . ( 49 sec) [ -17743.9300] [Alpha ][ 0.360792] . ( 49 sec) [ -17735.6424] [ 3707] [depth= 3] . ( 50 sec) [ -17730.1726] [ 3701] [depth= 2] . ( 50 sec) [ -17729.1443] [ 3698] [depth= 5] . ( 50 sec) [ -17723.7632] [ 3693] [depth= 1] . ( 51 sec) [ -17701.1730] [ 3676] [depth= 3] . ( 51 sec) [ -17695.1039] [ 3673] [depth= 1] . ( 51 sec) [ -17676.8524] [ 3671] [depth= 6] . ( 51 sec) [ -17669.1723] [ 3672] [depth= 4] . ( 52 sec) [ -17668.1947] [ 3667] [depth= 1] . ( 52 sec) [ -17668.0520] [ 3666] [depth= 1] . ( 53 sec) [ -17639.4601] [ 3654] [depth= 1] . ( 53 sec) [ -17630.3765] [ 3652] [depth= 1] . ( 53 sec) [ -17616.1867] [ 3643] [depth= 4] . ( 54 sec) [ -17614.5598] [ 3644] [depth= 1] . ( 54 sec) [ -17606.0608] [ 3632] [depth= 9] . ( 54 sec) [ -17591.1346] [ 3619] [depth= 14] . ( 54 sec) [ -17588.9912] [ 3621] [depth= 2] . ( 55 sec) [ -17579.7574] [ 3611] [depth= 2] . ( 55 sec) [ -17579.2701] [ 3594] [depth= 15] . ( 55 sec) [ -17482.4994] [ 3597] [depth= 1] . ( 56 sec) [ -17482.1442] [ 3596] [depth= 1] . ( 56 sec) [ -17481.4996] [ 3591] [depth= 1] . ( 57 sec) [ -17474.0313] [ 3593] [depth= 1] . ( 57 sec) [ -17463.1417] [ 3595] [depth= 3] . ( 57 sec) [ -17458.9270] [ 3594] [depth= 2] . ( 57 sec) [ -17456.4257] [ 3592] [depth= 2] . ( 58 sec) [ -17452.3701] [ 3591] [depth= 4] . ( 58 sec) [ -17451.9859] [ 3595] [depth= 1] . ( 58 sec) [ -17419.8778] [ 3576] [depth= 16] . ( 59 sec) [ -17418.4098] [ 3577] [depth= 1] . ( 59 sec) [ -17417.7907] [ 3577] [depth= 1] . ( 59 sec) [ -17417.0995] [ 3574] [depth= 1] . ( 60 sec) [ -17412.3633] [ 3570] [depth= 8] . ( 61 sec) [ -17411.4162] [ 3568] [depth= 7] . ( 61 sec) [ -17405.5930] [ 3564] [depth= 1] . ( 61 sec) [ -17398.2993] [ 3560] [depth= 1] . ( 61 sec) [ -17396.5172] [ 3559] [depth= 2] . ( 62 sec) [ -17394.7922] [ 3561] [depth= 2] . ( 62 sec) [ -17387.7199] [ 3557] [depth= 2] . ( 63 sec) [ -17383.7368] [ 3555] [depth= 1] . ( 63 sec) [ -17376.2946] [ 3552] [depth= 1] . ( 63 sec) [ -17376.2425] [ 3552] [depth= 1] . ( 64 sec) [ -17331.3655] [ 3538] [depth= 1] . ( 64 sec) [ -17302.9506] [ 3524] [depth= 2] . ( 64 sec) [ -17301.2287] [ 3523] [depth= 2] . ( 65 sec) [ -17299.7472] [ 3524] [depth= 1] . ( 66 sec) [ -17298.4003] [ 3522] [depth= 2] . ( 66 sec) [ -17278.4430] [ 3522] [depth= 1] . ( 67 sec) [ -17269.9581] [ 3519] [depth= 1] . ( 67 sec) [ -17257.1077] [ 3517] [depth= 1] . ( 68 sec) [ -17245.2872] [ 3514] [depth= 3] . ( 69 sec) [ -17244.1424] [ 3516] [depth= 1] . ( 69 sec) [ -17244.0785] [ 3516] [depth= 1] . ( 70 sec) [ -17227.0647] [ 3509] [depth= 4] . ( 70 sec) [ -17220.5793] [ 3511] [depth= 1] . ( 71 sec) [ -17219.8458] [ 3512] [depth= 1] . ( 71 sec) [ -17219.3794] [ 3516] [depth= 1] . ( 72 sec) [ -17219.3377] [ 3515] [depth= 1] . ( 72 sec) [ -17219.3002] [ 3515] [depth= 1] . ( 73 sec) [ -17219.2490] [ 3516] [depth= 1] . ( 73 sec) [ -17218.6849] [ 3515] [depth= 1] . ( 74 sec) [ -17190.2132] [ 3516] [depth= 12] . ( 74 sec) [ -17188.9630] [ 3515] [depth= 1] . ( 74 sec) [ -17188.8381] [ 3515] [depth= 1] . ( 74 sec) [ -17182.0423] [ 3511] [depth= 2] . ( 75 sec) [ -17181.3772] [ 3514] [depth= 2] . ( 75 sec) [ -17180.9430] [ 3515] [depth= 1] . ( 76 sec) [ -17169.5993] [ 3507] [depth= 1] . ( 77 sec) [ -17125.7360] [ 3501] [depth= 1] . ( 77 sec) [ -17120.0841] [ 3500] [depth= 3] . ( 77 sec) [ -17118.7984] [ 3498] [depth= 1] . ( 77 sec) [ -17116.8603] [ 3499] [depth= 1] . ( 77 sec) [ -17116.7716] [ 3497] [depth= 1] . ( 78 sec) [ -17113.4517] [ 3500] [depth= 1] . ( 79 sec) [ -17113.1844] [ 3500] [depth= 1] . ( 79 sec) [ -17111.8043] [ 3502] [depth= 1] . ( 80 sec) [ -17109.9732] [ 3502] [depth= 2] . ( 80 sec) [ -17109.1663] [ 3502] [depth= 1] . ( 83 sec) [ -17107.3275] [ 3503] [depth= 1] . ( 84 sec) [ -17106.1623] [ 3502] [depth= 1] . ( 85 sec) [ -17100.9907] [ 3503] [depth= 1] . ( 86 sec) [ -17059.2095] [Branch lengths ] . ( 89 sec) [ -17055.4208] [GTR parameters ] . ( 90 sec) [ -17055.4032] [Alpha ][ 0.357996] . ( 93 sec) [ -17055.3211] [ 3504] [depth= 1] . ( 96 sec) [ -17054.9966] [ 3504] [depth= 1] . ( 101 sec) [ -17054.9391] [ 3505] [depth= 1] . ( 102 sec) [ -17053.4876] [ 3503] [depth= 3] . ( 103 sec) [ -17047.9895] [ 3502] [depth= 3] . ( 107 sec) [ -17047.9422] [ 3501] [depth= 1] . ( 111 sec) [ -17047.9189] [ 3503] [depth= 1] . ( 116 sec) [ -17044.5597] [ 3494] [depth= 2] . ( 118 sec) [ -17044.5284] [ 3494] [depth= 1] . ( 118 sec) [ -17042.9052] [ 3493] [depth= 1] . ( 122 sec) [ -17042.4370] [ 3494] [depth= 1] . ( 126 sec) [ -17042.3456] [ 3494] [depth= 1] . ( 132 sec) [ -17032.5173] [Branch lengths ] . ( 134 sec) [ -17032.4205] [GTR parameters ] . ( 134 sec) [ -17032.4070] [Alpha ][ 0.360303] . ( 143 sec) [ -17032.1373] [ 3492] [depth= 1] . ( 177 sec) [ -17018.7938] [Branch lengths ] . ( 178 sec) [ -17018.7816] [GTR parameters ] . ( 178 sec) [ -17018.7759] [Alpha ][ 0.361778] . ( 192 sec) [ -17018.5280] [ 3490] [depth= 2] . ( 194 sec) [ -17018.5032] [ 3491] [depth= 1] . ( 218 sec) [ -17004.3765] [Branch lengths ] . ( 220 sec) [ -17004.3672] [GTR parameters ] . ( 220 sec) [ -17004.3669] [Alpha ][ 0.362140] . ( 235 sec) [ -17004.2177] [ 3496] [depth= 3] . ( 241 sec) [ -17002.1101] [ 3493] [depth= 1] . ( 246 sec) [ -17002.0248] [ 3493] [depth= 1] . ( 247 sec) [ -17001.7672] [ 3493] [depth= 1] . ( 251 sec) [ -16998.7935] [ 3494] [depth= 1] . ( 262 sec) [ -16993.5876] [Branch lengths ] . ( 264 sec) [ -16993.5606] [GTR parameters ] . ( 264 sec) [ -16993.5602] [Alpha ][ 0.361671] . ( 278 sec) [ -16993.3860] [ 3493] [depth= 1] . ( 304 sec) [ -16993.2922] [Branch lengths ] . ( 305 sec) [ -16993.2906] [GTR parameters ] . ( 306 sec) [ -16993.2906] [Alpha ][ 0.362033] . ( 402 sec) [ -16993.2127] [ 3492] [depth= 1] . ( 454 sec) [ -16993.1371] [Branch lengths ] . ( 455 sec) [ -16993.1370] [GTR parameters ] . ( 455 sec) [ -16993.1370] [Alpha ][ 0.362033] . ( 455 sec) [ -16993.1370] [Topology ] . ( 458 sec) [ -16993.1346] [Topology ] . ( 461 sec) [ -16993.1338] [Topology ] . ( 462 sec) [ -16993.1338] [GTR parameters ] . ( 462 sec) [ -16993.1338] [Alpha ][ 0.362033] . ( 462 sec) [ -16993.1338] [Topology ] . ( 465 sec) [ -16993.1333] [Topology ] . ( 466 sec) [ -16993.1332] [GTR parameters ] . ( 466 sec) [ -16993.1332] [Alpha ][ 0.362033] . Checking for NNIs, optimizing five branches... . ( 489 sec) [ -16993.0241] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -16993.024125. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 7 sec) [ -18030.1538] [GTR parameters ] . ( 7 sec) [ -17741.2296] [Alpha ][ 0.500960] . ( 7 sec) [ -17741.2296] [Topology ] . ( 10 sec) [ -17315.9427] [Topology ] . ( 13 sec) [ -17203.4981] [Topology ] . ( 16 sec) [ -17151.0051] [Topology ] . ( 19 sec) [ -17128.8187] [Topology ] . ( 23 sec) [ -17112.6803] [Topology ] . ( 26 sec) [ -17105.8340] [Topology ] . ( 29 sec) [ -17101.2221] [Topology ] . ( 32 sec) [ -17099.3400] [Topology ] . ( 35 sec) [ -17097.6209] [Topology ] . Checking for NNIs, optimizing five branches... . ( 61 sec) [ -17091.2429] [Topology ] . ( 66 sec) [ -17076.1281] [GTR parameters ] . ( 66 sec) [ -17046.3688] [Alpha ][ 0.369311] . ( 66 sec) [ -17046.3688] [Topology ] . ( 70 sec) [ -17043.4664] [Topology ] . ( 73 sec) [ -17042.4267] [Topology ] . ( 76 sec) [ -17041.4778] [Topology ] . ( 79 sec) [ -17039.1772] [Topology ] . ( 82 sec) [ -17036.4185] [Topology ] . ( 86 sec) [ -17036.0413] [Topology ] . ( 89 sec) [ -17035.9335] [Topology ] . Checking for NNIs, optimizing five branches... . ( 114 sec) [ -17034.9214] [GTR parameters ] . ( 115 sec) [ -17034.8933] [Alpha ][ 0.365833] . ( 115 sec) [ -17034.8933] [Topology ] . ( 118 sec) [ -17034.7268] [Topology ] . ( 121 sec) [ -17034.6482] [Topology ] . ( 125 sec) [ -17034.5992] [Topology ] . ( 128 sec) [ -17034.5677] [Topology ] . ( 131 sec) [ -17034.5474] [Topology ] . ( 134 sec) [ -17034.5344] [Topology ] . Checking for NNIs, optimizing five branches... . ( 160 sec) [ -17034.5093] [GTR parameters ] . ( 160 sec) [ -17034.5092] [Alpha ][ 0.365468] . ( 160 sec) [ -17034.5092] [Topology ] . ( 164 sec) [ -17034.4950] [Topology ] . ( 167 sec) [ -17034.4865] [Topology ] . ( 170 sec) [ -17034.4811] [Topology ] . ( 173 sec) [ -17034.4776] [Topology ] . ( 176 sec) [ -17034.4753] [Topology ] . ( 180 sec) [ -17034.4739] [Topology ] . Checking for NNIs, optimizing five branches... . ( 203 sec) [ -17034.4722] [GTR parameters ] . ( 203 sec) [ -17034.4722] [Alpha ][ 0.365468] . ( 203 sec) [ -17034.4722] [Topology ] . ( 207 sec) [ -17034.4709] [Topology ] . ( 210 sec) [ -17034.4700] [Topology ] . Checking for NNIs, optimizing five branches... . ( 233 sec) [ -17034.4698] [GTR parameters ] . ( 234 sec) [ -17034.4698] [Alpha ][ 0.365468] . ( 234 sec) [ -17034.4698] [Topology ] . ( 237 sec) [ -17034.4693] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 291 sec) [ -18030.1538] [GTR parameters ] . ( 292 sec) [ -17741.2296] [Alpha ][ 0.500960] . ( 292 sec) [ -17732.2284] [ 3534] [depth= 1] . ( 292 sec) [ -17727.9520] [ 3536] [depth= 1] . ( 292 sec) [ -17720.9232] [ 3536] [depth= 2] . ( 293 sec) [ -17710.1407] [ 3534] [depth= 2] . ( 293 sec) [ -17687.4237] [ 3532] [depth= 1] . ( 293 sec) [ -17673.6169] [ 3523] [depth= 2] . ( 293 sec) [ -17672.1004] [ 3522] [depth= 1] . ( 295 sec) [ -17671.8543] [ 3522] [depth= 1] . ( 295 sec) [ -17668.2870] [ 3521] [depth= 1] . ( 296 sec) [ -17667.7826] [ 3521] [depth= 1] . ( 296 sec) [ -17665.2764] [ 3521] [depth= 1] . ( 296 sec) [ -17665.0808] [ 3521] [depth= 1] . ( 296 sec) [ -17662.2901] [ 3528] [depth= 1] . ( 297 sec) [ -17649.7618] [ 3529] [depth= 1] . ( 298 sec) [ -17647.0321] [ 3528] [depth= 2] . ( 298 sec) [ -17645.8889] [ 3528] [depth= 1] . ( 298 sec) [ -17645.5956] [ 3528] [depth= 1] . ( 298 sec) [ -17641.4722] [ 3525] [depth= 1] . ( 300 sec) [ -17641.0441] [ 3523] [depth= 1] . ( 300 sec) [ -17640.6873] [ 3523] [depth= 1] . ( 300 sec) [ -17638.6764] [ 3523] [depth= 1] . ( 300 sec) [ -17625.5744] [ 3522] [depth= 3] . ( 301 sec) [ -17625.1000] [ 3522] [depth= 1] . ( 301 sec) [ -17614.7584] [ 3520] [depth= 2] . ( 301 sec) [ -17614.6570] [ 3520] [depth= 1] . ( 302 sec) [ -17614.0769] [ 3522] [depth= 1] . ( 303 sec) [ -17606.7578] [ 3525] [depth= 1] . ( 303 sec) [ -17605.8674] [ 3522] [depth= 1] . ( 304 sec) [ -17603.1185] [ 3521] [depth= 1] . ( 304 sec) [ -17595.5106] [ 3522] [depth= 1] . ( 304 sec) [ -17591.3249] [ 3525] [depth= 1] . ( 305 sec) [ -17582.7946] [ 3523] [depth= 2] . ( 305 sec) [ -17581.4385] [ 3524] [depth= 1] . ( 306 sec) [ -17576.5902] [ 3521] [depth= 3] . ( 306 sec) [ -17570.1001] [ 3515] [depth= 2] . ( 306 sec) [ -17568.1545] [ 3514] [depth= 1] . ( 306 sec) [ -17565.9700] [ 3515] [depth= 2] . ( 307 sec) [ -17565.5582] [ 3515] [depth= 1] . ( 307 sec) [ -17556.2693] [ 3513] [depth= 1] . ( 307 sec) [ -17547.3723] [ 3509] [depth= 2] . ( 308 sec) [ -17546.3350] [ 3509] [depth= 1] . ( 308 sec) [ -17541.5026] [ 3509] [depth= 2] . ( 308 sec) [ -17528.9614] [ 3505] [depth= 1] . ( 309 sec) [ -17527.4592] [ 3508] [depth= 1] . ( 310 sec) [ -17527.3316] [ 3508] [depth= 1] . ( 310 sec) [ -17527.3063] [ 3512] [depth= 1] . ( 310 sec) [ -17527.2528] [ 3509] [depth= 1] . ( 310 sec) [ -17525.5769] [ 3510] [depth= 1] . ( 311 sec) [ -17522.0796] [ 3513] [depth= 1] . ( 311 sec) [ -17515.7045] [ 3513] [depth= 1] . ( 312 sec) [ -17512.0364] [ 3512] [depth= 1] . ( 312 sec) [ -17506.2200] [ 3513] [depth= 2] . ( 312 sec) [ -17502.5205] [ 3515] [depth= 1] . ( 312 sec) [ -17501.0224] [ 3515] [depth= 1] . ( 313 sec) [ -17498.9748] [ 3513] [depth= 1] . ( 313 sec) [ -17498.6457] [ 3515] [depth= 1] . ( 314 sec) [ -17497.8277] [ 3518] [depth= 2] . ( 314 sec) [ -17494.5538] [ 3516] [depth= 1] . ( 314 sec) [ -17493.8148] [ 3517] [depth= 1] . ( 314 sec) [ -17487.7673] [ 3516] [depth= 1] . ( 315 sec) [ -17477.0588] [ 3517] [depth= 2] . ( 315 sec) [ -17472.5607] [ 3513] [depth= 1] . ( 316 sec) [ -17447.2737] [ 3509] [depth= 2] . ( 316 sec) [ -17438.2099] [ 3509] [depth= 1] . ( 317 sec) [ -17432.9037] [ 3513] [depth= 1] . ( 317 sec) [ -17430.8153] [ 3509] [depth= 1] . ( 317 sec) [ -17428.4813] [ 3511] [depth= 1] . ( 317 sec) [ -17385.6114] [ 3509] [depth= 6] . ( 317 sec) [ -17383.2046] [ 3510] [depth= 1] . ( 317 sec) [ -17383.0598] [ 3509] [depth= 1] . ( 320 sec) [ -17362.7768] [ 3504] [depth= 1] . ( 320 sec) [ -17360.6969] [ 3508] [depth= 1] . ( 320 sec) [ -17353.4635] [ 3501] [depth= 1] . ( 321 sec) [ -17347.5013] [ 3497] [depth= 2] . ( 321 sec) [ -17344.2898] [ 3500] [depth= 2] . ( 321 sec) [ -17341.7376] [ 3505] [depth= 1] . ( 321 sec) [ -17332.8490] [ 3503] [depth= 1] . ( 322 sec) [ -17327.3566] [ 3499] [depth= 1] . ( 322 sec) [ -17320.9950] [ 3499] [depth= 1] . ( 322 sec) [ -17314.6835] [ 3495] [depth= 2] . ( 323 sec) [ -17314.4520] [ 3494] [depth= 1] . ( 324 sec) [ -17309.5389] [ 3495] [depth= 1] . ( 324 sec) [ -17307.8887] [ 3495] [depth= 1] . ( 324 sec) [ -17303.2636] [ 3494] [depth= 1] . ( 324 sec) [ -17302.2737] [ 3495] [depth= 4] . ( 325 sec) [ -17299.9575] [ 3495] [depth= 1] . ( 325 sec) [ -17297.3650] [ 3495] [depth= 1] . ( 325 sec) [ -17296.1814] [ 3494] [depth= 1] . ( 325 sec) [ -17291.1740] [ 3493] [depth= 1] . ( 326 sec) [ -17290.7274] [ 3494] [depth= 1] . ( 327 sec) [ -17289.4688] [ 3493] [depth= 1] . ( 327 sec) [ -17288.4265] [ 3492] [depth= 1] . ( 327 sec) [ -17288.1997] [ 3494] [depth= 1] . ( 328 sec) [ -17287.8339] [ 3496] [depth= 1] . ( 328 sec) [ -17285.6605] [ 3494] [depth= 1] . ( 328 sec) [ -17284.9520] [ 3496] [depth= 1] . ( 329 sec) [ -17283.8794] [ 3494] [depth= 1] . ( 331 sec) [ -17118.6287] [Branch lengths ] . ( 335 sec) [ -17106.5366] [GTR parameters ] . ( 336 sec) [ -17069.3882] [Alpha ][ 0.348580] . ( 338 sec) [ -17067.7315] [ 3496] [depth= 1] . ( 338 sec) [ -17060.2362] [ 3487] [depth= 1] . ( 340 sec) [ -17058.0829] [ 3483] [depth= 2] . ( 341 sec) [ -17055.7461] [ 3484] [depth= 1] . ( 342 sec) [ -17055.0689] [ 3486] [depth= 1] . ( 344 sec) [ -17052.7666] [ 3484] [depth= 1] . ( 344 sec) [ -17052.2562] [ 3483] [depth= 1] . ( 346 sec) [ -17050.8560] [ 3483] [depth= 1] . ( 354 sec) [ -17050.1894] [ 3486] [depth= 1] . ( 355 sec) [ -17050.0303] [ 3485] [depth= 1] . ( 360 sec) [ -17047.8575] [ 3484] [depth= 1] . ( 362 sec) [ -17047.7667] [ 3483] [depth= 1] . ( 363 sec) [ -17047.5997] [ 3484] [depth= 1] . ( 364 sec) [ -17045.3743] [ 3487] [depth= 1] . ( 366 sec) [ -17044.5819] [ 3487] [depth= 1] . ( 366 sec) [ -17043.8421] [ 3487] [depth= 5] . ( 367 sec) [ -17042.9538] [ 3487] [depth= 1] . ( 370 sec) [ -17042.4450] [ 3487] [depth= 1] . ( 375 sec) [ -17007.0987] [Branch lengths ] . ( 379 sec) [ -17005.3774] [GTR parameters ] . ( 380 sec) [ -17005.2591] [Alpha ][ 0.355080] . ( 388 sec) [ -17005.1982] [ 3485] [depth= 1] . ( 388 sec) [ -17005.1710] [ 3487] [depth= 1] . ( 411 sec) [ -17005.0176] [ 3489] [depth= 2] . ( 421 sec) [ -16996.3325] [Branch lengths ] . ( 425 sec) [ -16996.2585] [GTR parameters ] . ( 425 sec) [ -16996.2221] [Alpha ][ 0.358898] . ( 433 sec) [ -16996.2027] [ 3487] [depth= 1] . ( 466 sec) [ -16994.3391] [Branch lengths ] . ( 470 sec) [ -16994.3141] [GTR parameters ] . ( 470 sec) [ -16994.3061] [Alpha ][ 0.360657] . ( 513 sec) [ -16993.7035] [Branch lengths ] . ( 664 sec) [ -16993.5115] [Branch lengths ] . ( 664 sec) [ -16993.5115] [Topology ] . ( 667 sec) [ -16993.2548] [Topology ] . ( 671 sec) [ -16993.1930] [Topology ] . ( 674 sec) [ -16993.1147] [Topology ] . ( 678 sec) [ -16993.0677] [Topology ] . ( 681 sec) [ -16993.0509] [Topology ] . ( 685 sec) [ -16993.0441] [Topology ] . ( 688 sec) [ -16993.0410] [Topology ] . ( 691 sec) [ -16993.0012] [GTR parameters ] . ( 692 sec) [ -16992.9885] [Alpha ][ 0.362902] . ( 692 sec) [ -16992.9885] [Topology ] . ( 695 sec) [ -16992.9828] [Topology ] . ( 698 sec) [ -16992.9796] [Topology ] . ( 702 sec) [ -16992.9774] [Topology ] . ( 705 sec) [ -16992.9760] [Topology ] . ( 708 sec) [ -16992.9751] [Topology ] . ( 710 sec) [ -16992.9747] [GTR parameters ] . ( 710 sec) [ -16992.9747] [Alpha ][ 0.362902] . ( 711 sec) [ -16992.9747] [Topology ] . ( 714 sec) [ -16992.9739] [Topology ] . ( 715 sec) [ -16992.9739] [GTR parameters ] . ( 715 sec) [ -16992.9739] [Alpha ][ 0.362902] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -17034.469256 . Log likelihood obtained after SPR moves : -16992.973865 . Log likelihood of the current tree: -16992.973865. . Printing the most likely tree in file 'nucleic_M2946_110x1003_2006.phy_phyml_tree.txt'... . Best log likelihood : -16992.973865 . Time used 0h12m19s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 3343.73user 0.00system 56:38.44elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps