.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2716_79x1252_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 . 28 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 280 patterns found. (out of a total of 1252 sites) . 984 sites without polymorphism (78.59%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 12Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -11882.3282] [GTR parameters ] . ( 2 sec) [ -11695.5937] [Alpha ][ 0.500960] . ( 2 sec) [ -11518.0836] [ 989] [depth= 9] . ( 2 sec) [ -11430.3722] [ 989] [depth= 7] . ( 2 sec) [ -11414.4950] [ 989] [depth= 1] . ( 2 sec) [ -11294.4806] [ 975] [depth= 6] . ( 2 sec) [ -11221.6507] [ 966] [depth= 12] . ( 2 sec) [ -11061.0134] [ 963] [depth= 2] . ( 2 sec) [ -11039.4200] [ 961] [depth= 7] . ( 2 sec) [ -10989.7970] [ 956] [depth= 8] . ( 2 sec) [ -10890.3384] [ 956] [depth= 1] . ( 2 sec) [ -10456.1197] [ 950] [depth= 10] . ( 2 sec) [ -10276.1503] [ 950] [depth= 1] . ( 2 sec) [ -10145.7348] [ 942] [depth= 7] . ( 3 sec) [ -10145.4680] [ 942] [depth= 3] . ( 3 sec) [ -10124.1584] [ 942] [depth= 12] . ( 3 sec) [ -10108.5877] [ 942] [depth= 1] . ( 3 sec) [ -10074.9500] [ 940] [depth= 18] . ( 3 sec) [ -10073.0876] [ 940] [depth= 1] . ( 3 sec) [ -10050.0711] [ 932] [depth= 19] . ( 3 sec) [ -9924.1248] [ 931] [depth= 5] . ( 3 sec) [ -9465.6632] [ 930] [depth= 13] . ( 3 sec) [ -9225.8161] [ 934] [depth= 8] . ( 3 sec) [ -8922.0604] [ 916] [depth= 13] . ( 3 sec) [ -8916.5678] [ 913] [depth= 2] . ( 3 sec) [ -8899.6371] [ 910] [depth= 5] . ( 3 sec) [ -8879.2755] [ 910] [depth= 1] . ( 3 sec) [ -8852.3653] [ 910] [depth= 3] . ( 4 sec) [ -8799.4929] [ 910] [depth= 11] . ( 4 sec) [ -8795.6056] [ 896] [depth= 9] . ( 4 sec) [ -8763.7027] [ 896] [depth= 2] . ( 4 sec) [ -8714.4391] [ 876] [depth= 1] . ( 4 sec) [ -8486.0455] [ 852] [depth= 19] . ( 4 sec) [ -8357.2077] [ 852] [depth= 22] . ( 4 sec) [ -8347.4618] [ 853] [depth= 11] . ( 4 sec) [ -8336.3163] [ 851] [depth= 3] . ( 4 sec) [ -8323.2332] [ 851] [depth= 1] . ( 4 sec) [ -8308.4651] [ 851] [depth= 5] . ( 4 sec) [ -8239.0377] [ 830] [depth= 13] . ( 4 sec) [ -8156.7013] [ 809] [depth= 16] . ( 4 sec) [ -8142.0146] [ 809] [depth= 16] . ( 4 sec) [ -8116.0407] [ 809] [depth= 4] . ( 4 sec) [ -7939.3370] [ 799] [depth= 7] . ( 5 sec) [ -7889.0794] [ 793] [depth= 3] . ( 5 sec) [ -7854.3100] [ 782] [depth= 13] . ( 5 sec) [ -7820.9455] [ 781] [depth= 9] . ( 5 sec) [ -7677.5846] [ 776] [depth= 4] . ( 5 sec) [ -7571.0519] [ 775] [depth= 16] . ( 5 sec) [ -7547.1443] [ 762] [depth= 10] . ( 5 sec) [ -7508.7823] [ 762] [depth= 1] . ( 5 sec) [ -6910.4796] [ 755] [depth= 1] . ( 5 sec) [ -6821.7549] [ 739] [depth= 7] . ( 5 sec) [ -6817.8178] [ 739] [depth= 5] . ( 5 sec) [ -6797.7337] [ 736] [depth= 6] . ( 5 sec) [ -6793.3955] [ 736] [depth= 1] . ( 5 sec) [ -6791.5608] [ 736] [depth= 8] . ( 5 sec) [ -6679.6012] [ 723] [depth= 2] . ( 5 sec) [ -6315.1843] [ 719] [depth= 2] . ( 5 sec) [ -6257.2758] [ 719] [depth= 16] . ( 6 sec) [ -5974.9557] [ 717] [depth= 14] . ( 6 sec) [ -5865.1842] [ 698] [depth= 21] . ( 6 sec) [ -5856.4314] [ 698] [depth= 3] . ( 6 sec) [ -5777.4072] [ 698] [depth= 5] . ( 6 sec) [ -5776.2723] [ 698] [depth= 10] . ( 6 sec) [ -5738.5100] [ 684] [depth= 19] . ( 6 sec) [ -5734.5949] [ 684] [depth= 3] . ( 6 sec) [ -5701.2080] [ 678] [depth= 9] . ( 6 sec) [ -5695.9497] [ 678] [depth= 1] . ( 6 sec) [ -5695.6015] [ 678] [depth= 2] . ( 6 sec) [ -5692.3728] [ 678] [depth= 1] . ( 6 sec) [ -5637.2066] [ 672] [depth= 11] . ( 6 sec) [ -5537.9908] [ 671] [depth= 3] . ( 6 sec) [ -5523.4509] [ 669] [depth= 6] . ( 6 sec) [ -5493.5094] [ 669] [depth= 1] . ( 7 sec) [ -5443.0079] [ 668] [depth= 3] . ( 7 sec) [ -5354.1269] [ 648] [depth= 7] . ( 7 sec) [ -5347.5612] [ 648] [depth= 1] . ( 7 sec) [ -5187.4982] [ 645] [depth= 4] . ( 7 sec) [ -5073.7935] [ 632] [depth= 3] . ( 7 sec) [ -5071.7145] [ 637] [depth= 15] . ( 7 sec) [ -4948.9326] [ 610] [depth= 11] . ( 7 sec) [ -4948.3067] [ 610] [depth= 2] . ( 7 sec) [ -4943.3291] [ 610] [depth= 6] . ( 7 sec) [ -4925.8866] [ 609] [depth= 9] . ( 7 sec) [ -4903.2518] [ 604] [depth= 7] . ( 7 sec) [ -4902.0504] [ 604] [depth= 1] . ( 7 sec) [ -4880.2714] [ 602] [depth= 6] . ( 7 sec) [ -4879.9956] [ 602] [depth= 3] . ( 7 sec) [ -4819.6894] [ 589] [depth= 8] . ( 7 sec) [ -4802.5661] [ 589] [depth= 2] . ( 8 sec) [ -4797.8840] [ 589] [depth= 12] . ( 8 sec) [ -4797.8595] [ 589] [depth= 6] . ( 8 sec) [ -4795.0747] [ 589] [depth= 2] . ( 8 sec) [ -4709.0903] [ 575] [depth= 17] . ( 8 sec) [ -4703.3991] [ 574] [depth= 5] . ( 8 sec) [ -4700.5282] [ 574] [depth= 1] . ( 8 sec) [ -4697.8356] [ 571] [depth= 12] . ( 8 sec) [ -4693.9047] [ 571] [depth= 1] . ( 8 sec) [ -4693.1385] [ 566] [depth= 8] . ( 8 sec) [ -4692.7798] [ 566] [depth= 4] . ( 8 sec) [ -4692.4137] [ 566] [depth= 4] . ( 8 sec) [ -4687.3072] [ 565] [depth= 7] . ( 8 sec) [ -4687.0190] [ 565] [depth= 1] . ( 8 sec) [ -4673.0929] [ 557] [depth= 14] . ( 8 sec) [ -4672.9860] [ 557] [depth= 3] . ( 8 sec) [ -4668.4584] [ 557] [depth= 4] . ( 8 sec) [ -4666.2367] [ 557] [depth= 16] . ( 9 sec) [ -4640.1939] [ 554] [depth= 1] . ( 9 sec) [ -4635.2276] [ 554] [depth= 9] . ( 9 sec) [ -4633.6399] [ 553] [depth= 2] . ( 9 sec) [ -4628.1999] [ 550] [depth= 10] . ( 9 sec) [ -4617.5168] [ 550] [depth= 1] . ( 9 sec) [ -4614.7182] [ 550] [depth= 9] . ( 9 sec) [ -4605.7398] [ 551] [depth= 1] . ( 9 sec) [ -4600.3517] [ 550] [depth= 2] . ( 9 sec) [ -4570.1089] [ 539] [depth= 4] . ( 9 sec) [ -4528.4775] [ 531] [depth= 5] . ( 9 sec) [ -4523.4227] [ 531] [depth= 1] . ( 9 sec) [ -4522.1443] [ 531] [depth= 1] . ( 9 sec) [ -4515.9358] [ 531] [depth= 1] . ( 9 sec) [ -4506.9720] [ 531] [depth= 1] . ( 9 sec) [ -4506.4558] [ 531] [depth= 2] . ( 9 sec) [ -4366.3145] [ 504] [depth= 14] . ( 9 sec) [ -4364.3892] [ 504] [depth= 2] . ( 9 sec) [ -4363.6022] [ 504] [depth= 2] . ( 10 sec) [ -4363.4797] [ 503] [depth= 9] . ( 10 sec) [ -4363.0113] [ 503] [depth= 3] . ( 10 sec) [ -4276.4831] [ 484] [depth= 8] . ( 10 sec) [ -4269.3888] [ 481] [depth= 1] . ( 10 sec) [ -4248.8360] [ 476] [depth= 9] . ( 10 sec) [ -4218.4535] [ 473] [depth= 9] . ( 10 sec) [ -4218.3123] [ 473] [depth= 3] . ( 10 sec) [ -4217.9995] [ 473] [depth= 2] . ( 10 sec) [ -4217.8530] [ 473] [depth= 1] . ( 10 sec) [ -4186.7454] [ 473] [depth= 2] . ( 10 sec) [ -4182.9025] [ 470] [depth= 4] . ( 10 sec) [ -4168.6433] [ 468] [depth= 3] . ( 10 sec) [ -4165.0162] [ 468] [depth= 1] . ( 10 sec) [ -4157.2936] [ 468] [depth= 1] . ( 10 sec) [ -4156.6989] [ 468] [depth= 2] . ( 10 sec) [ -4111.0023] [ 458] [depth= 6] . ( 10 sec) [ -4100.2897] [ 457] [depth= 7] . ( 11 sec) [ -4069.1755] [ 457] [depth= 3] . ( 11 sec) [ -4068.2079] [ 457] [depth= 5] . ( 11 sec) [ -4046.5725] [ 452] [depth= 2] . ( 11 sec) [ -4046.4046] [ 452] [depth= 3] . ( 11 sec) [ -4043.1850] [ 452] [depth= 3] . ( 11 sec) [ -4022.1357] [ 451] [depth= 6] . ( 11 sec) [ -4021.8569] [ 451] [depth= 6] . ( 11 sec) [ -4018.7098] [ 451] [depth= 5] . ( 12 sec) [ -4015.4744] [ 451] [depth= 8] . ( 12 sec) [ -4012.6129] [ 451] [depth= 5] . ( 12 sec) [ -4011.3784] [ 451] [depth= 3] . ( 12 sec) [ -4010.6208] [ 451] [depth= 1] . ( 12 sec) [ -4010.5293] [ 451] [depth= 1] . ( 12 sec) [ -4009.8978] [ 451] [depth= 5] . ( 12 sec) [ -4009.2780] [ 451] [depth= 3] . ( 12 sec) [ -4008.2705] [ 451] [depth= 9] . ( 12 sec) [ -4006.8861] [ 451] [depth= 2] . ( 12 sec) [ -4006.8184] [ 451] [depth= 3] . ( 12 sec) [ -4006.1035] [ 451] [depth= 6] . ( 13 sec) [ -3981.4338] [ 447] [depth= 4] . ( 13 sec) [ -3961.1935] [ 446] [depth= 1] . ( 13 sec) [ -3944.8493] [ 424] [depth= 18] . ( 13 sec) [ -3894.4238] [ 425] [depth= 1] . ( 13 sec) [ -3881.6494] [ 425] [depth= 3] . ( 13 sec) [ -3880.8986] [ 425] [depth= 7] . ( 13 sec) [ -3861.4371] [ 425] [depth= 2] . ( 13 sec) [ -3860.9825] [ 425] [depth= 3] . ( 13 sec) [ -3836.9985] [ 419] [depth= 14] . ( 13 sec) [ -3825.9303] [ 419] [depth= 1] . ( 13 sec) [ -3825.5141] [ 419] [depth= 2] . ( 13 sec) [ -3818.9359] [ 418] [depth= 2] . ( 13 sec) [ -3818.9146] [ 418] [depth= 3] . ( 13 sec) [ -3818.8763] [ 418] [depth= 1] . ( 13 sec) [ -3818.8662] [ 418] [depth= 3] . ( 13 sec) [ -3818.7621] [ 418] [depth= 1] . ( 13 sec) [ -3818.0284] [ 418] [depth= 5] . ( 14 sec) [ -3815.1023] [ 418] [depth= 18] . ( 14 sec) [ -3814.8857] [ 418] [depth= 1] . ( 14 sec) [ -3814.8707] [ 418] [depth= 7] . ( 14 sec) [ -3813.9009] [ 418] [depth= 2] . ( 14 sec) [ -3813.7489] [ 418] [depth= 5] . ( 14 sec) [ -3813.7186] [ 418] [depth= 3] . ( 14 sec) [ -3813.1009] [ 413] [depth= 8] . ( 14 sec) [ -3812.7139] [ 410] [depth= 5] . ( 14 sec) [ -3809.1593] [ 410] [depth= 2] . ( 14 sec) [ -3794.3843] [ 410] [depth= 4] . ( 14 sec) [ -3794.2500] [ 410] [depth= 1] . ( 14 sec) [ -3794.1633] [ 410] [depth= 2] . ( 14 sec) [ -3793.7704] [ 410] [depth= 1] . ( 14 sec) [ -3793.6697] [ 410] [depth= 5] . ( 14 sec) [ -3792.8665] [ 410] [depth= 3] . ( 15 sec) [ -3761.5798] [ 403] [depth= 3] . ( 15 sec) [ -3753.2385] [ 403] [depth= 2] . ( 15 sec) [ -3703.1515] [ 395] [depth= 1] . ( 15 sec) [ -3700.8718] [ 395] [depth= 1] . ( 15 sec) [ -3700.5263] [ 395] [depth= 8] . ( 15 sec) [ -3700.3991] [ 395] [depth= 10] . ( 15 sec) [ -3690.2062] [ 395] [depth= 1] . ( 15 sec) [ -3685.5082] [ 395] [depth= 2] . ( 16 sec) [ -3684.5676] [ 395] [depth= 4] . ( 16 sec) [ -3684.0794] [ 395] [depth= 2] . ( 16 sec) [ -3682.3024] [ 395] [depth= 1] . ( 16 sec) [ -3628.2038] [ 380] [depth= 15] . ( 16 sec) [ -3628.1105] [ 380] [depth= 3] . ( 16 sec) [ -3579.4838] [Branch lengths ] . ( 20 sec) [ -3566.8209] [GTR parameters ] . ( 20 sec) [ -3543.6604] [Alpha ][ 0.250961] . ( 20 sec) [ -3543.6313] [ 380] [depth= 1] . ( 20 sec) [ -3543.6174] [ 380] [depth= 1] . ( 21 sec) [ -3543.6066] [ 380] [depth= 3] . ( 21 sec) [ -3540.2890] [ 380] [depth= 1] . ( 21 sec) [ -3538.7470] [ 380] [depth= 8] . ( 22 sec) [ -3538.7234] [ 379] [depth= 8] . ( 22 sec) [ -3535.3981] [ 377] [depth= 9] . ( 23 sec) [ -3533.6946] [ 376] [depth= 2] . ( 23 sec) [ -3529.8339] [ 374] [depth= 1] . ( 23 sec) [ -3512.2171] [ 374] [depth= 20] . ( 23 sec) [ -3490.0335] [ 365] [depth= 6] . ( 23 sec) [ -3490.0049] [ 365] [depth= 1] . ( 24 sec) [ -3489.9535] [ 365] [depth= 3] . ( 24 sec) [ -3489.0857] [ 365] [depth= 9] . ( 24 sec) [ -3488.9743] [ 365] [depth= 9] . ( 24 sec) [ -3488.9629] [ 365] [depth= 1] . ( 25 sec) [ -3488.9277] [ 365] [depth= 1] . ( 26 sec) [ -3488.8902] [ 365] [depth= 5] . ( 26 sec) [ -3456.9103] [ 354] [depth= 10] . ( 27 sec) [ -3456.6355] [ 356] [depth= 5] . ( 27 sec) [ -3456.6035] [ 356] [depth= 12] . ( 28 sec) [ -3456.0522] [ 356] [depth= 2] . ( 28 sec) [ -3456.0348] [ 356] [depth= 3] . ( 28 sec) [ -3455.7059] [ 361] [depth= 1] . ( 28 sec) [ -3453.5582] [ 358] [depth= 1] . ( 28 sec) [ -3453.1039] [ 358] [depth= 9] . ( 28 sec) [ -3453.0928] [ 358] [depth= 8] . ( 29 sec) [ -3452.9977] [ 358] [depth= 4] . ( 29 sec) [ -3452.9583] [ 358] [depth= 2] . ( 29 sec) [ -3452.2987] [ 355] [depth= 1] . ( 29 sec) [ -3452.2762] [ 355] [depth= 2] . ( 29 sec) [ -3452.2552] [ 355] [depth= 6] . ( 29 sec) [ -3452.2088] [ 355] [depth= 7] . ( 30 sec) [ -3452.1738] [ 355] [depth= 2] . ( 30 sec) [ -3452.1628] [ 355] [depth= 3] . ( 34 sec) [ -3452.1362] [ 355] [depth= 2] . ( 37 sec) [ -3451.4061] [ 355] [depth= 3] . ( 38 sec) [ -3442.9935] [ 352] [depth= 8] . ( 39 sec) [ -3442.9627] [ 352] [depth= 1] . ( 39 sec) [ -3442.9352] [ 350] [depth= 2] . ( 40 sec) [ -3442.4788] [ 350] [depth= 1] . ( 40 sec) [ -3442.0033] [ 350] [depth= 6] . ( 40 sec) [ -3441.8258] [ 350] [depth= 6] . ( 42 sec) [ -3441.8143] [ 350] [depth= 4] . ( 42 sec) [ -3441.3187] [ 350] [depth= 2] . ( 42 sec) [ -3441.2961] [ 350] [depth= 2] . ( 42 sec) [ -3441.0429] [ 350] [depth= 3] . ( 42 sec) [ -3440.8268] [ 350] [depth= 3] . ( 43 sec) [ -3439.7269] [ 350] [depth= 2] . ( 43 sec) [ -3439.7032] [ 350] [depth= 12] . ( 43 sec) [ -3439.6804] [ 350] [depth= 4] . ( 43 sec) [ -3439.6664] [ 350] [depth= 1] . ( 43 sec) [ -3439.6384] [ 350] [depth= 4] . ( 43 sec) [ -3439.5861] [ 351] [depth= 3] . ( 45 sec) [ -3439.2384] [ 351] [depth= 2] . ( 45 sec) [ -3439.2282] [ 351] [depth= 6] . ( 45 sec) [ -3434.9607] [ 350] [depth= 6] . ( 47 sec) [ -3434.9425] [ 350] [depth= 11] . ( 49 sec) [ -3434.9131] [ 350] [depth= 3] . ( 50 sec) [ -3434.0254] [ 350] [depth= 9] . ( 50 sec) [ -3433.9680] [ 350] [depth= 2] . ( 51 sec) [ -3433.8375] [ 350] [depth= 9] . ( 51 sec) [ -3433.7790] [ 350] [depth= 1] . ( 51 sec) [ -3433.7662] [ 350] [depth= 1] . ( 52 sec) [ -3433.7498] [ 350] [depth= 3] . ( 52 sec) [ -3433.4895] [ 350] [depth= 2] . ( 52 sec) [ -3433.1425] [ 350] [depth= 9] . ( 52 sec) [ -3433.0423] [ 350] [depth= 2] . ( 52 sec) [ -3433.0299] [ 350] [depth= 2] . ( 53 sec) [ -3433.0008] [ 350] [depth= 7] . ( 53 sec) [ -3432.9818] [ 350] [depth= 8] . ( 54 sec) [ -3432.9386] [ 350] [depth= 1] . ( 54 sec) [ -3420.3331] [ 344] [depth= 7] . ( 55 sec) [ -3408.0268] [ 341] [depth= 10] . ( 55 sec) [ -3408.0160] [ 341] [depth= 4] . ( 55 sec) [ -3406.6328] [ 341] [depth= 3] . ( 55 sec) [ -3406.5591] [ 341] [depth= 2] . ( 56 sec) [ -3406.3120] [ 341] [depth= 3] . ( 56 sec) [ -3405.3761] [ 341] [depth= 4] . ( 56 sec) [ -3402.6369] [ 342] [depth= 1] . ( 56 sec) [ -3402.2600] [ 342] [depth= 1] . ( 56 sec) [ -3402.0656] [ 342] [depth= 2] . ( 56 sec) [ -3402.0527] [ 342] [depth= 2] . ( 56 sec) [ -3402.0059] [ 342] [depth= 11] . ( 56 sec) [ -3401.9818] [ 342] [depth= 4] . ( 56 sec) [ -3399.8990] [ 341] [depth= 4] . ( 57 sec) [ -3399.6428] [ 341] [depth= 4] . ( 57 sec) [ -3399.5335] [ 341] [depth= 2] . ( 58 sec) [ -3399.3827] [ 341] [depth= 1] . ( 58 sec) [ -3399.2983] [ 341] [depth= 4] . ( 58 sec) [ -3399.2864] [ 341] [depth= 3] . ( 59 sec) [ -3399.2699] [ 341] [depth= 6] . ( 62 sec) [ -3395.2269] [Branch lengths ] . ( 65 sec) [ -3394.5122] [GTR parameters ] . ( 66 sec) [ -3394.2439] [Alpha ][ 0.223424] . ( 67 sec) [ -3394.2333] [ 341] [depth= 4] . ( 69 sec) [ -3393.1539] [ 341] [depth= 12] . ( 69 sec) [ -3393.1361] [ 341] [depth= 2] . ( 70 sec) [ -3393.1186] [ 341] [depth= 12] . ( 71 sec) [ -3392.9290] [ 341] [depth= 11] . ( 71 sec) [ -3392.8219] [ 341] [depth= 3] . ( 74 sec) [ -3392.7547] [ 341] [depth= 5] . ( 74 sec) [ -3392.6034] [ 340] [depth= 6] . ( 78 sec) [ -3392.1529] [ 340] [depth= 5] . ( 78 sec) [ -3392.0355] [ 340] [depth= 2] . ( 78 sec) [ -3391.6050] [ 342] [depth= 2] . ( 78 sec) [ -3391.5938] [ 342] [depth= 9] . ( 79 sec) [ -3391.4120] [ 342] [depth= 8] . ( 79 sec) [ -3390.6920] [ 342] [depth= 3] . ( 80 sec) [ -3390.6778] [ 342] [depth= 1] . ( 82 sec) [ -3390.6580] [ 342] [depth= 6] . ( 83 sec) [ -3389.5312] [ 341] [depth= 9] . ( 83 sec) [ -3388.9219] [ 341] [depth= 3] . ( 84 sec) [ -3387.4157] [ 341] [depth= 3] . ( 86 sec) [ -3387.3416] [ 341] [depth= 17] . ( 86 sec) [ -3387.1137] [ 341] [depth= 10] . ( 86 sec) [ -3386.8703] [ 341] [depth= 1] . ( 86 sec) [ -3386.6777] [ 341] [depth= 15] . ( 88 sec) [ -3386.6100] [ 341] [depth= 2] . ( 88 sec) [ -3386.5990] [ 341] [depth= 2] . ( 89 sec) [ -3386.5886] [ 341] [depth= 1] . ( 92 sec) [ -3386.3223] [ 341] [depth= 2] . ( 92 sec) [ -3385.9498] [ 341] [depth= 12] . ( 92 sec) [ -3385.9363] [ 341] [depth= 4] . ( 93 sec) [ -3385.8059] [ 341] [depth= 2] . ( 93 sec) [ -3385.7259] [ 341] [depth= 2] . ( 93 sec) [ -3385.5796] [ 341] [depth= 2] . ( 93 sec) [ -3385.4787] [ 341] [depth= 1] . ( 94 sec) [ -3385.4675] [ 341] [depth= 3] . ( 94 sec) [ -3385.3708] [ 341] [depth= 1] . ( 94 sec) [ -3385.2313] [ 341] [depth= 3] . ( 94 sec) [ -3385.1730] [ 341] [depth= 5] . ( 94 sec) [ -3385.1358] [ 341] [depth= 1] . ( 94 sec) [ -3385.0363] [ 341] [depth= 2] . ( 96 sec) [ -3384.9817] [ 341] [depth= 1] . ( 98 sec) [ -3384.9547] [ 341] [depth= 4] . ( 98 sec) [ -3384.8691] [ 341] [depth= 5] . ( 98 sec) [ -3384.8538] [ 341] [depth= 6] . ( 100 sec) [ -3384.7804] [ 341] [depth= 2] . ( 102 sec) [ -3384.5721] [ 341] [depth= 1] . ( 104 sec) [ -3384.5534] [ 341] [depth= 3] . ( 107 sec) [ -3384.5194] [ 341] [depth= 2] . ( 111 sec) [ -3384.5075] [ 343] [depth= 1] . ( 113 sec) [ -3384.1688] [Branch lengths ] . ( 115 sec) [ -3384.0676] [GTR parameters ] . ( 115 sec) [ -3384.0653] [Alpha ][ 0.225970] . ( 116 sec) [ -3383.5078] [ 343] [depth= 3] . ( 119 sec) [ -3382.3448] [ 342] [depth= 3] . ( 121 sec) [ -3382.2995] [ 342] [depth= 3] . ( 124 sec) [ -3382.2563] [ 342] [depth= 1] . ( 126 sec) [ -3382.2254] [ 342] [depth= 1] . ( 130 sec) [ -3380.3590] [ 342] [depth= 2] . ( 130 sec) [ -3380.3387] [ 340] [depth= 1] . ( 130 sec) [ -3380.3186] [ 340] [depth= 11] . ( 131 sec) [ -3379.4066] [ 340] [depth= 5] . ( 135 sec) [ -3379.3905] [ 340] [depth= 5] . ( 135 sec) [ -3378.9638] [ 340] [depth= 14] . ( 135 sec) [ -3378.9519] [ 340] [depth= 1] . ( 136 sec) [ -3378.9418] [ 340] [depth= 2] . ( 136 sec) [ -3378.8985] [ 340] [depth= 1] . ( 137 sec) [ -3378.8853] [ 340] [depth= 1] . ( 137 sec) [ -3378.7528] [ 340] [depth= 1] . ( 138 sec) [ -3378.6446] [ 340] [depth= 3] . ( 138 sec) [ -3378.6067] [ 340] [depth= 6] . ( 139 sec) [ -3378.5935] [ 340] [depth= 5] . ( 141 sec) [ -3378.5819] [ 340] [depth= 2] . ( 142 sec) [ -3378.5419] [ 340] [depth= 4] . ( 146 sec) [ -3378.5298] [ 340] [depth= 8] . ( 146 sec) [ -3378.3055] [ 340] [depth= 5] . ( 147 sec) [ -3378.2928] [ 340] [depth= 3] . ( 150 sec) [ -3376.6236] [ 340] [depth= 16] . ( 150 sec) [ -3375.8026] [ 340] [depth= 5] . ( 150 sec) [ -3375.3736] [ 340] [depth= 3] . ( 151 sec) [ -3375.3594] [ 340] [depth= 7] . ( 151 sec) [ -3375.3417] [ 340] [depth= 2] . ( 151 sec) [ -3375.3256] [ 340] [depth= 9] . ( 151 sec) [ -3375.3109] [ 340] [depth= 1] . ( 151 sec) [ -3375.2837] [ 340] [depth= 3] . ( 154 sec) [ -3374.4504] [ 340] [depth= 3] . ( 155 sec) [ -3374.1786] [ 340] [depth= 2] . ( 156 sec) [ -3374.1592] [ 340] [depth= 3] . ( 156 sec) [ -3374.1442] [ 340] [depth= 1] . ( 161 sec) [ -3374.0520] [ 340] [depth= 2] . ( 163 sec) [ -3373.9494] [ 340] [depth= 11] . ( 163 sec) [ -3373.8584] [ 340] [depth= 6] . ( 166 sec) [ -3371.7784] [Branch lengths ] . ( 167 sec) [ -3371.7637] [GTR parameters ] . ( 167 sec) [ -3371.7615] [Alpha ][ 0.228504] . ( 168 sec) [ -3357.0639] [ 335] [depth= 10] . ( 171 sec) [ -3357.0447] [ 335] [depth= 4] . ( 172 sec) [ -3356.9911] [ 335] [depth= 1] . ( 172 sec) [ -3356.9805] [ 335] [depth= 7] . ( 173 sec) [ -3356.8525] [ 335] [depth= 9] . ( 175 sec) [ -3356.8190] [ 335] [depth= 1] . ( 177 sec) [ -3356.7997] [ 335] [depth= 6] . ( 178 sec) [ -3356.5134] [ 335] [depth= 1] . ( 178 sec) [ -3352.9687] [ 334] [depth= 18] . ( 179 sec) [ -3352.8712] [ 334] [depth= 3] . ( 181 sec) [ -3352.8278] [ 334] [depth= 4] . ( 181 sec) [ -3352.7937] [ 334] [depth= 10] . ( 183 sec) [ -3352.7015] [ 334] [depth= 1] . ( 184 sec) [ -3352.6507] [ 334] [depth= 4] . ( 184 sec) [ -3352.6400] [ 334] [depth= 1] . ( 185 sec) [ -3352.6231] [ 334] [depth= 5] . ( 186 sec) [ -3352.5769] [ 334] [depth= 2] . ( 187 sec) [ -3352.5428] [ 334] [depth= 8] . ( 187 sec) [ -3351.7729] [ 334] [depth= 1] . ( 189 sec) [ -3351.7404] [ 334] [depth= 3] . ( 189 sec) [ -3351.6894] [ 334] [depth= 1] . ( 189 sec) [ -3351.6368] [ 334] [depth= 4] . ( 190 sec) [ -3351.5561] [ 334] [depth= 9] . ( 190 sec) [ -3351.5417] [ 334] [depth= 10] . ( 192 sec) [ -3351.5272] [ 334] [depth= 9] . ( 192 sec) [ -3347.2551] [ 334] [depth= 4] . ( 193 sec) [ -3347.2291] [ 334] [depth= 7] . ( 193 sec) [ -3347.2038] [ 334] [depth= 7] . ( 194 sec) [ -3347.1933] [ 334] [depth= 1] . ( 205 sec) [ -3347.1821] [ 334] [depth= 4] . ( 222 sec) [ -3347.1598] [ 334] [depth= 3] . ( 226 sec) [ -3346.5733] [Branch lengths ] . ( 229 sec) [ -3346.5376] [GTR parameters ] . ( 230 sec) [ -3346.5008] [Alpha ][ 0.239332] . ( 234 sec) [ -3346.4830] [ 334] [depth= 6] . ( 300 sec) [ -3346.4667] [Branch lengths ] . ( 301 sec) [ -3346.4660] [GTR parameters ] . ( 301 sec) [ -3346.4656] [Alpha ][ 0.240430] . ( 311 sec) [ -3346.4542] [ 334] [depth= 8] . ( 351 sec) [ -3346.4505] [Branch lengths ] . ( 352 sec) [ -3346.4504] [GTR parameters ] . ( 352 sec) [ -3346.4504] [Alpha ][ 0.240430] . ( 352 sec) [ -3346.4504] [Topology ] . ( 353 sec) [ -3346.4490] [Topology ] . ( 354 sec) [ -3346.4481] [Topology ] . ( 354 sec) [ -3346.4481] [GTR parameters ] . ( 354 sec) [ -3346.4481] [Alpha ][ 0.240430] . ( 354 sec) [ -3346.4481] [Topology ] . ( 355 sec) [ -3346.4475] [Topology ] . ( 355 sec) [ -3346.4475] [GTR parameters ] . ( 355 sec) [ -3346.4475] [Alpha ][ 0.240430] . Checking for NNIs, optimizing five branches... . ( 361 sec) [ -3346.4471] [Topology ] . Checking for NNIs, optimizing five branches... . ( 367 sec) [ -3346.4462] [Topology ] . Checking for NNIs, optimizing five branches... . ( 372 sec) [ -3346.4372] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3346.437213. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -12336.3949] [GTR parameters ] . ( 1 sec) [ -12122.1128] [Alpha ][ 0.500960] . ( 1 sec) [ -11993.0546] [ 991] [depth= 4] . ( 2 sec) [ -11492.9853] [ 959] [depth= 10] . ( 2 sec) [ -11340.9343] [ 959] [depth= 1] . ( 2 sec) [ -11259.4204] [ 957] [depth= 5] . ( 2 sec) [ -11010.7023] [ 956] [depth= 1] . ( 2 sec) [ -10911.5696] [ 956] [depth= 3] . ( 2 sec) [ -10839.3304] [ 955] [depth= 7] . ( 2 sec) [ -10793.8299] [ 955] [depth= 2] . ( 2 sec) [ -10534.3532] [ 954] [depth= 4] . ( 2 sec) [ -10473.9971] [ 954] [depth= 1] . ( 2 sec) [ -10472.3701] [ 941] [depth= 11] . ( 3 sec) [ -10461.8207] [ 941] [depth= 1] . ( 3 sec) [ -10460.6869] [ 941] [depth= 13] . ( 3 sec) [ -10280.1358] [ 926] [depth= 7] . ( 3 sec) [ -10280.0344] [ 926] [depth= 13] . ( 3 sec) [ -10208.5838] [ 909] [depth= 11] . ( 3 sec) [ -10180.4346] [ 909] [depth= 11] . ( 3 sec) [ -10180.3000] [ 909] [depth= 5] . ( 3 sec) [ -10074.1093] [ 901] [depth= 7] . ( 3 sec) [ -10067.7291] [ 886] [depth= 9] . ( 3 sec) [ -9880.8912] [ 872] [depth= 10] . ( 3 sec) [ -9867.2270] [ 872] [depth= 1] . ( 3 sec) [ -9806.7038] [ 867] [depth= 17] . ( 3 sec) [ -9732.4951] [ 857] [depth= 4] . ( 4 sec) [ -9718.3306] [ 855] [depth= 6] . ( 4 sec) [ -9712.4282] [ 855] [depth= 4] . ( 4 sec) [ -9674.2408] [ 848] [depth= 9] . ( 4 sec) [ -9671.4858] [ 848] [depth= 1] . ( 4 sec) [ -9648.4282] [ 848] [depth= 4] . ( 4 sec) [ -9628.8295] [ 848] [depth= 1] . ( 4 sec) [ -9611.8822] [ 848] [depth= 1] . ( 4 sec) [ -9556.3257] [ 854] [depth= 1] . ( 4 sec) [ -9505.0170] [ 854] [depth= 2] . ( 4 sec) [ -9447.2392] [ 854] [depth= 7] . ( 4 sec) [ -9436.5708] [ 854] [depth= 2] . ( 5 sec) [ -9415.7055] [ 854] [depth= 8] . ( 5 sec) [ -9349.2822] [ 854] [depth= 1] . ( 5 sec) [ -9307.2139] [ 839] [depth= 17] . ( 5 sec) [ -9210.8446] [ 824] [depth= 6] . ( 5 sec) [ -9148.9314] [ 823] [depth= 10] . ( 5 sec) [ -8974.4914] [ 823] [depth= 13] . ( 5 sec) [ -8418.8947] [ 808] [depth= 14] . ( 5 sec) [ -8352.8926] [ 808] [depth= 13] . ( 5 sec) [ -8307.2779] [ 804] [depth= 9] . ( 5 sec) [ -8290.8231] [ 804] [depth= 1] . ( 5 sec) [ -8263.3136] [ 801] [depth= 1] . ( 6 sec) [ -8226.7836] [ 801] [depth= 1] . ( 6 sec) [ -8215.4393] [ 793] [depth= 2] . ( 6 sec) [ -8165.1506] [ 791] [depth= 9] . ( 6 sec) [ -7886.4222] [ 757] [depth= 14] . ( 6 sec) [ -7884.8986] [ 757] [depth= 2] . ( 6 sec) [ -7839.4961] [ 748] [depth= 10] . ( 6 sec) [ -7831.5918] [ 748] [depth= 1] . ( 6 sec) [ -7815.1331] [ 746] [depth= 17] . ( 6 sec) [ -7811.1201] [ 746] [depth= 2] . ( 6 sec) [ -7756.2049] [ 746] [depth= 6] . ( 6 sec) [ -7748.5502] [ 740] [depth= 12] . ( 7 sec) [ -7743.1954] [ 740] [depth= 16] . ( 7 sec) [ -7742.7490] [ 740] [depth= 16] . ( 7 sec) [ -7706.2307] [ 734] [depth= 14] . ( 7 sec) [ -7704.6359] [ 734] [depth= 4] . ( 7 sec) [ -7695.5147] [ 733] [depth= 7] . ( 7 sec) [ -7675.0060] [ 733] [depth= 1] . ( 7 sec) [ -7603.5589] [ 713] [depth= 15] . ( 7 sec) [ -7580.5443] [ 714] [depth= 1] . ( 7 sec) [ -7509.8437] [ 705] [depth= 16] . ( 7 sec) [ -7464.3854] [ 705] [depth= 16] . ( 7 sec) [ -7441.0424] [ 705] [depth= 19] . ( 8 sec) [ -7426.6437] [ 705] [depth= 1] . ( 8 sec) [ -7292.6765] [ 669] [depth= 18] . ( 8 sec) [ -6968.7704] [ 660] [depth= 4] . ( 8 sec) [ -6962.6467] [ 660] [depth= 1] . ( 8 sec) [ -6182.7843] [ 648] [depth= 7] . ( 8 sec) [ -6174.0494] [ 648] [depth= 1] . ( 8 sec) [ -6142.3690] [ 643] [depth= 22] . ( 8 sec) [ -6118.9867] [ 644] [depth= 4] . ( 8 sec) [ -5991.0352] [ 642] [depth= 3] . ( 8 sec) [ -5981.9660] [ 641] [depth= 7] . ( 8 sec) [ -5978.5356] [ 641] [depth= 13] . ( 8 sec) [ -5936.3765] [ 641] [depth= 4] . ( 9 sec) [ -5931.8323] [ 641] [depth= 2] . ( 9 sec) [ -5931.8104] [ 641] [depth= 3] . ( 9 sec) [ -5853.2770] [ 641] [depth= 3] . ( 9 sec) [ -5822.0889] [ 641] [depth= 1] . ( 9 sec) [ -5819.4659] [ 631] [depth= 3] . ( 9 sec) [ -5804.4353] [ 631] [depth= 1] . ( 9 sec) [ -5718.8682] [ 620] [depth= 18] . ( 9 sec) [ -5691.2333] [ 605] [depth= 4] . ( 9 sec) [ -5666.8250] [ 609] [depth= 7] . ( 9 sec) [ -5666.5629] [ 609] [depth= 17] . ( 10 sec) [ -5626.5354] [ 609] [depth= 14] . ( 10 sec) [ -5581.3597] [ 603] [depth= 10] . ( 10 sec) [ -5580.1334] [ 603] [depth= 3] . ( 10 sec) [ -5580.1169] [ 603] [depth= 16] . ( 10 sec) [ -5534.5645] [ 588] [depth= 13] . ( 10 sec) [ -5534.4528] [ 588] [depth= 1] . ( 10 sec) [ -5513.6677] [ 576] [depth= 4] . ( 10 sec) [ -5441.6146] [ 566] [depth= 3] . ( 10 sec) [ -5435.4478] [ 566] [depth= 6] . ( 10 sec) [ -5435.4041] [ 566] [depth= 2] . ( 10 sec) [ -5432.6871] [ 566] [depth= 1] . ( 11 sec) [ -5430.3799] [ 566] [depth= 1] . ( 11 sec) [ -5315.6964] [ 552] [depth= 18] . ( 11 sec) [ -5312.6482] [ 552] [depth= 3] . ( 11 sec) [ -5220.8802] [ 545] [depth= 13] . ( 11 sec) [ -5146.0772] [ 544] [depth= 3] . ( 11 sec) [ -5141.4876] [ 545] [depth= 4] . ( 11 sec) [ -5105.7499] [ 537] [depth= 9] . ( 11 sec) [ -5093.1859] [ 534] [depth= 3] . ( 12 sec) [ -5090.0559] [ 539] [depth= 1] . ( 12 sec) [ -5089.8217] [ 539] [depth= 1] . ( 12 sec) [ -5087.0562] [ 539] [depth= 10] . ( 12 sec) [ -5031.5988] [ 520] [depth= 11] . ( 12 sec) [ -5029.6625] [ 520] [depth= 13] . ( 13 sec) [ -5021.5176] [ 518] [depth= 5] . ( 13 sec) [ -5003.9735] [ 518] [depth= 1] . ( 13 sec) [ -4980.2841] [ 517] [depth= 4] . ( 13 sec) [ -4978.3239] [ 517] [depth= 4] . ( 13 sec) [ -4978.1898] [ 517] [depth= 1] . ( 13 sec) [ -4967.5177] [ 517] [depth= 10] . ( 13 sec) [ -4946.4308] [ 517] [depth= 8] . ( 13 sec) [ -4931.2433] [ 512] [depth= 4] . ( 13 sec) [ -4930.2902] [ 512] [depth= 1] . ( 13 sec) [ -4881.6638] [ 512] [depth= 1] . ( 14 sec) [ -4881.6113] [ 512] [depth= 1] . ( 14 sec) [ -4881.5399] [ 512] [depth= 3] . ( 14 sec) [ -4881.5189] [ 512] [depth= 4] . ( 14 sec) [ -4871.8108] [ 512] [depth= 5] . ( 14 sec) [ -4859.3207] [ 512] [depth= 1] . ( 14 sec) [ -4859.0083] [ 512] [depth= 2] . ( 14 sec) [ -4848.6427] [ 512] [depth= 1] . ( 14 sec) [ -4821.0598] [ 507] [depth= 18] . ( 14 sec) [ -4820.0771] [ 507] [depth= 3] . ( 14 sec) [ -4814.2034] [ 506] [depth= 10] . ( 14 sec) [ -4807.5424] [ 506] [depth= 2] . ( 14 sec) [ -4804.4415] [ 506] [depth= 3] . ( 14 sec) [ -4803.7924] [ 506] [depth= 5] . ( 14 sec) [ -4803.7471] [ 506] [depth= 2] . ( 14 sec) [ -4784.0541] [ 503] [depth= 5] . ( 15 sec) [ -4732.4517] [ 488] [depth= 7] . ( 15 sec) [ -4702.4762] [ 483] [depth= 11] . ( 15 sec) [ -4697.1713] [ 474] [depth= 1] . ( 15 sec) [ -4697.1351] [ 474] [depth= 2] . ( 15 sec) [ -4696.9963] [ 474] [depth= 2] . ( 15 sec) [ -4696.7616] [ 474] [depth= 4] . ( 15 sec) [ -4695.0733] [ 471] [depth= 8] . ( 15 sec) [ -4677.8008] [ 467] [depth= 1] . ( 15 sec) [ -4602.0003] [ 466] [depth= 2] . ( 15 sec) [ -4583.4413] [ 466] [depth= 2] . ( 16 sec) [ -4583.3566] [ 466] [depth= 4] . ( 16 sec) [ -4559.4088] [ 456] [depth= 3] . ( 16 sec) [ -4554.9951] [ 456] [depth= 2] . ( 16 sec) [ -4519.3497] [ 456] [depth= 2] . ( 16 sec) [ -4518.7830] [ 456] [depth= 10] . ( 16 sec) [ -4476.2317] [ 447] [depth= 2] . ( 16 sec) [ -4471.1947] [ 439] [depth= 12] . ( 16 sec) [ -4414.9620] [ 439] [depth= 5] . ( 16 sec) [ -4412.0901] [ 439] [depth= 21] . ( 16 sec) [ -4412.0589] [ 439] [depth= 1] . ( 17 sec) [ -4411.3461] [ 439] [depth= 2] . ( 17 sec) [ -4410.9507] [ 439] [depth= 4] . ( 17 sec) [ -4388.2734] [ 442] [depth= 6] . ( 17 sec) [ -4383.7847] [ 439] [depth= 10] . ( 17 sec) [ -4383.5219] [ 439] [depth= 5] . ( 17 sec) [ -4379.1347] [ 439] [depth= 7] . ( 17 sec) [ -4378.9979] [ 439] [depth= 3] . ( 17 sec) [ -4377.5551] [ 439] [depth= 2] . ( 17 sec) [ -4375.8178] [ 439] [depth= 2] . ( 18 sec) [ -4374.1832] [ 439] [depth= 3] . ( 18 sec) [ -4373.0113] [ 439] [depth= 1] . ( 18 sec) [ -4372.4112] [ 439] [depth= 12] . ( 18 sec) [ -4351.8210] [ 440] [depth= 5] . ( 18 sec) [ -4351.6418] [ 440] [depth= 3] . ( 18 sec) [ -4351.4146] [ 440] [depth= 1] . ( 18 sec) [ -4351.3730] [ 440] [depth= 2] . ( 18 sec) [ -4348.2936] [ 438] [depth= 5] . ( 18 sec) [ -4340.9756] [ 428] [depth= 5] . ( 18 sec) [ -3928.2391] [ 432] [depth= 1] . ( 18 sec) [ -3921.9391] [ 428] [depth= 1] . ( 19 sec) [ -3882.9595] [ 419] [depth= 5] . ( 19 sec) [ -3875.3417] [ 419] [depth= 1] . ( 19 sec) [ -3849.6037] [ 411] [depth= 5] . ( 19 sec) [ -3847.2522] [ 409] [depth= 2] . ( 19 sec) [ -3795.0182] [ 400] [depth= 9] . ( 19 sec) [ -3791.0195] [ 398] [depth= 3] . ( 19 sec) [ -3780.8311] [ 399] [depth= 1] . ( 19 sec) [ -3780.0845] [ 399] [depth= 2] . ( 19 sec) [ -3778.5100] [ 399] [depth= 2] . ( 19 sec) [ -3778.2860] [ 399] [depth= 3] . ( 20 sec) [ -3778.2626] [ 399] [depth= 7] . ( 20 sec) [ -3741.2882] [ 384] [depth= 7] . ( 20 sec) [ -3740.5893] [ 384] [depth= 1] . ( 20 sec) [ -3732.9306] [ 378] [depth= 6] . ( 20 sec) [ -3732.0618] [ 377] [depth= 3] . ( 20 sec) [ -3717.5539] [ 377] [depth= 3] . ( 20 sec) [ -3717.3609] [ 377] [depth= 1] . ( 20 sec) [ -3717.1918] [ 377] [depth= 4] . ( 20 sec) [ -3709.6326] [ 377] [depth= 3] . ( 21 sec) [ -3699.0360] [ 377] [depth= 7] . ( 21 sec) [ -3693.2798] [ 377] [depth= 28] . ( 21 sec) [ -3686.1535] [ 376] [depth= 17] . ( 21 sec) [ -3685.8685] [ 376] [depth= 28] . ( 21 sec) [ -3685.4406] [ 376] [depth= 1] . ( 22 sec) [ -3615.9080] [Branch lengths ] . ( 25 sec) [ -3595.1288] [GTR parameters ] . ( 25 sec) [ -3578.8097] [Alpha ][ 0.250961] . ( 26 sec) [ -3578.5170] [ 376] [depth= 1] . ( 26 sec) [ -3575.4960] [ 375] [depth= 3] . ( 26 sec) [ -3569.5073] [ 372] [depth= 1] . ( 27 sec) [ -3569.1943] [ 372] [depth= 2] . ( 27 sec) [ -3568.7197] [ 372] [depth= 1] . ( 27 sec) [ -3568.5539] [ 372] [depth= 2] . ( 27 sec) [ -3568.5329] [ 372] [depth= 22] . ( 28 sec) [ -3568.1813] [ 372] [depth= 5] . ( 28 sec) [ -3568.1686] [ 372] [depth= 1] . ( 28 sec) [ -3568.1542] [ 372] [depth= 4] . ( 28 sec) [ -3568.1397] [ 372] [depth= 2] . ( 29 sec) [ -3568.1048] [ 372] [depth= 3] . ( 29 sec) [ -3568.0912] [ 372] [depth= 3] . ( 29 sec) [ -3568.0684] [ 372] [depth= 5] . ( 31 sec) [ -3567.1774] [ 372] [depth= 24] . ( 31 sec) [ -3567.1626] [ 372] [depth= 1] . ( 31 sec) [ -3566.8737] [ 372] [depth= 2] . ( 31 sec) [ -3566.7725] [ 372] [depth= 1] . ( 32 sec) [ -3566.4623] [ 373] [depth= 4] . ( 32 sec) [ -3565.7850] [ 373] [depth= 7] . ( 33 sec) [ -3565.7337] [ 373] [depth= 2] . ( 33 sec) [ -3565.6586] [ 373] [depth= 14] . ( 34 sec) [ -3560.1894] [ 370] [depth= 6] . ( 34 sec) [ -3559.5448] [ 370] [depth= 2] . ( 34 sec) [ -3559.3452] [ 370] [depth= 1] . ( 34 sec) [ -3559.3233] [ 370] [depth= 1] . ( 35 sec) [ -3559.1898] [ 370] [depth= 5] . ( 35 sec) [ -3559.1775] [ 370] [depth= 1] . ( 37 sec) [ -3559.1025] [ 370] [depth= 5] . ( 38 sec) [ -3558.8029] [ 370] [depth= 1] . ( 38 sec) [ -3558.6481] [ 370] [depth= 4] . ( 39 sec) [ -3557.7816] [ 371] [depth= 9] . ( 39 sec) [ -3557.7071] [ 371] [depth= 3] . ( 40 sec) [ -3557.6941] [ 371] [depth= 3] . ( 40 sec) [ -3538.2151] [ 367] [depth= 11] . ( 41 sec) [ -3535.5501] [ 367] [depth= 5] . ( 41 sec) [ -3535.4675] [ 367] [depth= 2] . ( 42 sec) [ -3535.4516] [ 367] [depth= 1] . ( 42 sec) [ -3535.0352] [ 367] [depth= 1] . ( 43 sec) [ -3535.0189] [ 367] [depth= 28] . ( 43 sec) [ -3533.2989] [ 367] [depth= 2] . ( 43 sec) [ -3533.2883] [ 367] [depth= 4] . ( 44 sec) [ -3532.5739] [ 367] [depth= 3] . ( 44 sec) [ -3532.5306] [ 367] [depth= 30] . ( 44 sec) [ -3532.5155] [ 367] [depth= 28] . ( 44 sec) [ -3531.7197] [ 367] [depth= 2] . ( 45 sec) [ -3531.7073] [ 367] [depth= 1] . ( 45 sec) [ -3531.6376] [ 367] [depth= 3] . ( 45 sec) [ -3531.5963] [ 367] [depth= 2] . ( 46 sec) [ -3531.5668] [ 367] [depth= 4] . ( 46 sec) [ -3531.5430] [ 367] [depth= 18] . ( 46 sec) [ -3531.1444] [ 367] [depth= 1] . ( 46 sec) [ -3527.0813] [ 365] [depth= 2] . ( 47 sec) [ -3527.0266] [ 365] [depth= 2] . ( 47 sec) [ -3526.9860] [ 365] [depth= 1] . ( 47 sec) [ -3526.9232] [ 365] [depth= 2] . ( 47 sec) [ -3526.8311] [ 365] [depth= 4] . ( 48 sec) [ -3526.8175] [ 365] [depth= 1] . ( 48 sec) [ -3526.7993] [ 365] [depth= 1] . ( 48 sec) [ -3526.7699] [ 365] [depth= 1] . ( 48 sec) [ -3526.7519] [ 365] [depth= 3] . ( 53 sec) [ -3525.1628] [ 364] [depth= 1] . ( 56 sec) [ -3525.1286] [ 364] [depth= 1] . ( 56 sec) [ -3525.1173] [ 364] [depth= 3] . ( 57 sec) [ -3525.0433] [ 364] [depth= 1] . ( 58 sec) [ -3524.3804] [ 363] [depth= 6] . ( 59 sec) [ -3522.2058] [ 360] [depth= 1] . ( 59 sec) [ -3522.1885] [ 360] [depth= 4] . ( 59 sec) [ -3517.7960] [ 360] [depth= 2] . ( 61 sec) [ -3517.7762] [ 360] [depth= 2] . ( 61 sec) [ -3517.7062] [ 360] [depth= 4] . ( 64 sec) [ -3516.7053] [ 360] [depth= 27] . ( 64 sec) [ -3516.6639] [ 360] [depth= 24] . ( 65 sec) [ -3516.5424] [ 360] [depth= 1] . ( 66 sec) [ -3516.4988] [ 360] [depth= 1] . ( 66 sec) [ -3516.3777] [ 360] [depth= 2] . ( 68 sec) [ -3516.3567] [ 360] [depth= 2] . ( 69 sec) [ -3515.2912] [ 360] [depth= 3] . ( 69 sec) [ -3515.1647] [ 360] [depth= 1] . ( 70 sec) [ -3515.0249] [ 360] [depth= 1] . ( 70 sec) [ -3514.5883] [ 360] [depth= 3] . ( 70 sec) [ -3514.3438] [ 360] [depth= 21] . ( 71 sec) [ -3504.2245] [Branch lengths ] . ( 74 sec) [ -3503.8889] [GTR parameters ] . ( 74 sec) [ -3502.6399] [Alpha ][ 0.199932] . ( 75 sec) [ -3502.4992] [ 360] [depth= 3] . ( 75 sec) [ -3502.4350] [ 360] [depth= 3] . ( 76 sec) [ -3502.2160] [ 360] [depth= 2] . ( 76 sec) [ -3502.1381] [ 360] [depth= 2] . ( 77 sec) [ -3502.1216] [ 360] [depth= 16] . ( 79 sec) [ -3500.0518] [ 360] [depth= 1] . ( 79 sec) [ -3499.8480] [ 360] [depth= 2] . ( 81 sec) [ -3499.8158] [ 360] [depth= 2] . ( 81 sec) [ -3499.7991] [ 360] [depth= 2] . ( 81 sec) [ -3499.7150] [ 360] [depth= 4] . ( 82 sec) [ -3438.1642] [ 353] [depth= 25] . ( 82 sec) [ -3432.4062] [ 353] [depth= 9] . ( 82 sec) [ -3431.7850] [ 353] [depth= 1] . ( 82 sec) [ -3431.6763] [ 353] [depth= 2] . ( 83 sec) [ -3431.6584] [ 353] [depth= 1] . ( 83 sec) [ -3431.5474] [ 353] [depth= 4] . ( 83 sec) [ -3431.5228] [ 353] [depth= 1] . ( 84 sec) [ -3431.4959] [ 353] [depth= 13] . ( 87 sec) [ -3431.4370] [ 353] [depth= 6] . ( 87 sec) [ -3431.4195] [ 353] [depth= 4] . ( 88 sec) [ -3431.4072] [ 353] [depth= 3] . ( 89 sec) [ -3431.3311] [ 353] [depth= 6] . ( 92 sec) [ -3431.2144] [ 351] [depth= 4] . ( 92 sec) [ -3431.1879] [ 351] [depth= 3] . ( 95 sec) [ -3431.1260] [ 351] [depth= 7] . ( 95 sec) [ -3429.7092] [ 351] [depth= 2] . ( 96 sec) [ -3429.3275] [ 351] [depth= 16] . ( 96 sec) [ -3429.1249] [ 351] [depth= 2] . ( 97 sec) [ -3427.9624] [ 351] [depth= 2] . ( 97 sec) [ -3427.8281] [ 351] [depth= 16] . ( 97 sec) [ -3427.8003] [ 351] [depth= 1] . ( 97 sec) [ -3426.3629] [ 351] [depth= 1] . ( 98 sec) [ -3426.2725] [ 351] [depth= 2] . ( 98 sec) [ -3426.2585] [ 351] [depth= 6] . ( 99 sec) [ -3426.1821] [ 351] [depth= 16] . ( 99 sec) [ -3426.1663] [ 351] [depth= 2] . ( 102 sec) [ -3425.6893] [ 352] [depth= 4] . ( 103 sec) [ -3425.5084] [ 352] [depth= 2] . ( 103 sec) [ -3425.4281] [ 352] [depth= 4] . ( 103 sec) [ -3425.1351] [ 352] [depth= 2] . ( 103 sec) [ -3424.9240] [ 352] [depth= 2] . ( 103 sec) [ -3424.8919] [ 352] [depth= 3] . ( 104 sec) [ -3424.8772] [ 352] [depth= 26] . ( 105 sec) [ -3424.7413] [ 352] [depth= 4] . ( 105 sec) [ -3424.5829] [ 352] [depth= 2] . ( 108 sec) [ -3424.2848] [ 352] [depth= 1] . ( 108 sec) [ -3423.7486] [ 352] [depth= 7] . ( 109 sec) [ -3423.7262] [ 352] [depth= 1] . ( 109 sec) [ -3423.6398] [ 352] [depth= 24] . ( 110 sec) [ -3421.9278] [ 351] [depth= 1] . ( 110 sec) [ -3421.9177] [ 351] [depth= 1] . ( 110 sec) [ -3418.6017] [ 343] [depth= 21] . ( 111 sec) [ -3418.5640] [ 343] [depth= 4] . ( 112 sec) [ -3418.1422] [ 343] [depth= 10] . ( 113 sec) [ -3418.1299] [ 343] [depth= 1] . ( 113 sec) [ -3418.1189] [ 343] [depth= 3] . ( 114 sec) [ -3418.0734] [ 343] [depth= 7] . ( 115 sec) [ -3416.0337] [Branch lengths ] . ( 116 sec) [ -3416.0307] [GTR parameters ] . ( 116 sec) [ -3415.8594] [Alpha ][ 0.220108] . ( 117 sec) [ -3415.8134] [ 343] [depth= 2] . ( 118 sec) [ -3415.8005] [ 343] [depth= 7] . ( 126 sec) [ -3413.6028] [ 342] [depth= 3] . ( 131 sec) [ -3413.5088] [ 342] [depth= 1] . ( 135 sec) [ -3413.4300] [ 343] [depth= 1] . ( 136 sec) [ -3413.3796] [ 343] [depth= 12] . ( 139 sec) [ -3413.2234] [ 343] [depth= 3] . ( 140 sec) [ -3412.9271] [ 343] [depth= 5] . ( 141 sec) [ -3412.5559] [ 343] [depth= 1] . ( 148 sec) [ -3412.5273] [ 343] [depth= 2] . ( 150 sec) [ -3406.6919] [ 342] [depth= 8] . ( 152 sec) [ -3406.6744] [ 342] [depth= 8] . ( 153 sec) [ -3406.3390] [ 342] [depth= 1] . ( 154 sec) [ -3406.0260] [ 342] [depth= 13] . ( 158 sec) [ -3405.8621] [ 343] [depth= 1] . ( 159 sec) [ -3405.7362] [ 343] [depth= 9] . ( 161 sec) [ -3404.8080] [ 343] [depth= 3] . ( 161 sec) [ -3404.7390] [ 343] [depth= 2] . ( 170 sec) [ -3404.7253] [ 343] [depth= 3] . ( 171 sec) [ -3404.6897] [ 343] [depth= 20] . ( 172 sec) [ -3404.5857] [ 343] [depth= 20] . ( 173 sec) [ -3404.0273] [ 345] [depth= 1] . ( 175 sec) [ -3403.9800] [ 343] [depth= 1] . ( 176 sec) [ -3403.9545] [ 343] [depth= 3] . ( 177 sec) [ -3403.9319] [ 343] [depth= 4] . ( 177 sec) [ -3373.4041] [ 338] [depth= 20] . ( 177 sec) [ -3373.3710] [ 338] [depth= 1] . ( 177 sec) [ -3373.3206] [ 338] [depth= 2] . ( 178 sec) [ -3373.2997] [ 338] [depth= 2] . ( 178 sec) [ -3373.2790] [ 338] [depth= 10] . ( 181 sec) [ -3368.6121] [Branch lengths ] . ( 185 sec) [ -3368.2079] [GTR parameters ] . ( 185 sec) [ -3368.1469] [Alpha ][ 0.233310] . ( 197 sec) [ -3364.9817] [ 338] [depth= 14] . ( 198 sec) [ -3364.9651] [ 338] [depth= 3] . ( 198 sec) [ -3364.9543] [ 338] [depth= 1] . ( 201 sec) [ -3364.8825] [ 338] [depth= 9] . ( 208 sec) [ -3364.5806] [ 337] [depth= 1] . ( 209 sec) [ -3364.5340] [ 337] [depth= 1] . ( 210 sec) [ -3364.1692] [ 337] [depth= 1] . ( 210 sec) [ -3364.1302] [ 337] [depth= 2] . ( 213 sec) [ -3364.1167] [ 337] [depth= 2] . ( 216 sec) [ -3364.1039] [ 337] [depth= 2] . ( 217 sec) [ -3364.0914] [ 337] [depth= 1] . ( 221 sec) [ -3363.0018] [ 337] [depth= 2] . ( 222 sec) [ -3362.7065] [ 337] [depth= 1] . ( 226 sec) [ -3362.6857] [ 337] [depth= 4] . ( 230 sec) [ -3360.6820] [ 337] [depth= 1] . ( 231 sec) [ -3360.4757] [ 337] [depth= 1] . ( 232 sec) [ -3360.4655] [ 337] [depth= 5] . ( 234 sec) [ -3360.4517] [ 337] [depth= 1] . ( 244 sec) [ -3360.1861] [ 337] [depth= 2] . ( 245 sec) [ -3360.1421] [ 337] [depth= 1] . ( 249 sec) [ -3360.1009] [ 337] [depth= 15] . ( 249 sec) [ -3360.0427] [ 337] [depth= 1] . ( 249 sec) [ -3359.9683] [ 337] [depth= 1] . ( 253 sec) [ -3359.1010] [Branch lengths ] . ( 255 sec) [ -3359.0923] [GTR parameters ] . ( 255 sec) [ -3359.0888] [Alpha ][ 0.236649] . ( 267 sec) [ -3359.0783] [ 337] [depth= 1] . ( 275 sec) [ -3359.0564] [ 337] [depth= 1] . ( 280 sec) [ -3359.0441] [ 337] [depth= 3] . ( 289 sec) [ -3359.0328] [ 337] [depth= 2] . ( 316 sec) [ -3358.9904] [ 337] [depth= 3] . ( 326 sec) [ -3358.9724] [Branch lengths ] . ( 327 sec) [ -3358.9719] [GTR parameters ] . ( 327 sec) [ -3358.9718] [Alpha ][ 0.237136] . ( 372 sec) [ -3358.9688] [Branch lengths ] . ( 372 sec) [ -3358.9688] [Topology ] . ( 373 sec) [ -3358.9684] [Topology ] . ( 373 sec) [ -3358.9684] [GTR parameters ] . ( 373 sec) [ -3358.9684] [Alpha ][ 0.237136] . Checking for NNIs, optimizing five branches... . ( 379 sec) [ -3358.9676] [Topology ] . Checking for NNIs, optimizing five branches... . ( 385 sec) [ -3358.9675] [Topology ] . Checking for NNIs, optimizing five branches... . ( 390 sec) [ -3358.9616] [Topology ] . Checking for NNIs, optimizing five branches... . ( 396 sec) [ -3358.9452] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3358.945206. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -11611.7782] [GTR parameters ] . ( 2 sec) [ -11405.4260] [Alpha ][ 0.500960] . ( 2 sec) [ -11272.3843] [ 1000] [depth= 5] . ( 2 sec) [ -10613.2984] [ 965] [depth= 13] . ( 2 sec) [ -10599.0748] [ 965] [depth= 1] . ( 2 sec) [ -10522.2178] [ 959] [depth= 3] . ( 2 sec) [ -10484.2193] [ 949] [depth= 2] . ( 2 sec) [ -10474.2253] [ 941] [depth= 16] . ( 2 sec) [ -10347.6619] [ 937] [depth= 2] . ( 2 sec) [ -10269.4927] [ 933] [depth= 10] . ( 3 sec) [ -10255.0519] [ 933] [depth= 2] . ( 3 sec) [ -10246.8141] [ 933] [depth= 3] . ( 3 sec) [ -10211.0023] [ 927] [depth= 7] . ( 3 sec) [ -10209.1349] [ 927] [depth= 1] . ( 3 sec) [ -10061.5614] [ 927] [depth= 1] . ( 3 sec) [ -9972.9467] [ 927] [depth= 1] . ( 3 sec) [ -9934.4509] [ 924] [depth= 12] . ( 3 sec) [ -9894.8257] [ 924] [depth= 6] . ( 3 sec) [ -9870.8826] [ 924] [depth= 8] . ( 3 sec) [ -9756.9436] [ 913] [depth= 2] . ( 3 sec) [ -9717.9988] [ 913] [depth= 2] . ( 4 sec) [ -9636.1203] [ 905] [depth= 2] . ( 4 sec) [ -9560.5317] [ 890] [depth= 7] . ( 4 sec) [ -9560.4053] [ 890] [depth= 1] . ( 4 sec) [ -9534.2305] [ 887] [depth= 8] . ( 4 sec) [ -9427.6670] [ 887] [depth= 6] . ( 4 sec) [ -9155.9042] [ 883] [depth= 7] . ( 4 sec) [ -9033.5260] [ 883] [depth= 1] . ( 4 sec) [ -8805.3689] [ 859] [depth= 7] . ( 4 sec) [ -8710.1566] [ 853] [depth= 5] . ( 4 sec) [ -8609.8781] [ 833] [depth= 1] . ( 5 sec) [ -8567.5924] [ 833] [depth= 1] . ( 5 sec) [ -8531.0145] [ 827] [depth= 7] . ( 5 sec) [ -8425.6878] [ 819] [depth= 6] . ( 5 sec) [ -8421.9266] [ 819] [depth= 1] . ( 5 sec) [ -8340.8337] [ 813] [depth= 12] . ( 5 sec) [ -8318.1206] [ 812] [depth= 3] . ( 5 sec) [ -8312.7772] [ 812] [depth= 17] . ( 5 sec) [ -8273.1074] [ 813] [depth= 1] . ( 5 sec) [ -8257.1646] [ 810] [depth= 21] . ( 6 sec) [ -8137.9467] [ 809] [depth= 1] . ( 6 sec) [ -8128.3495] [ 809] [depth= 3] . ( 6 sec) [ -8127.1553] [ 807] [depth= 3] . ( 6 sec) [ -8101.7059] [ 802] [depth= 4] . ( 6 sec) [ -8101.6260] [ 801] [depth= 29] . ( 6 sec) [ -8101.1955] [ 801] [depth= 6] . ( 6 sec) [ -8069.5084] [ 796] [depth= 11] . ( 6 sec) [ -7966.7380] [ 775] [depth= 6] . ( 6 sec) [ -7936.3290] [ 768] [depth= 6] . ( 7 sec) [ -7914.6365] [ 772] [depth= 2] . ( 7 sec) [ -7876.3192] [ 765] [depth= 3] . ( 7 sec) [ -7854.2058] [ 759] [depth= 21] . ( 7 sec) [ -7783.4585] [ 744] [depth= 7] . ( 7 sec) [ -7761.1262] [ 744] [depth= 1] . ( 7 sec) [ -7753.2944] [ 746] [depth= 2] . ( 7 sec) [ -7704.1505] [ 744] [depth= 7] . ( 7 sec) [ -7701.6652] [ 744] [depth= 10] . ( 7 sec) [ -7698.0584] [ 744] [depth= 10] . ( 7 sec) [ -7683.0477] [ 741] [depth= 5] . ( 8 sec) [ -7668.9898] [ 741] [depth= 4] . ( 8 sec) [ -7662.2818] [ 741] [depth= 11] . ( 8 sec) [ -7397.5472] [ 740] [depth= 13] . ( 8 sec) [ -7395.7801] [ 740] [depth= 1] . ( 8 sec) [ -7278.1187] [ 713] [depth= 9] . ( 8 sec) [ -7259.5512] [ 713] [depth= 1] . ( 8 sec) [ -7179.0716] [ 704] [depth= 9] . ( 8 sec) [ -7173.2180] [ 703] [depth= 19] . ( 8 sec) [ -7170.4490] [ 703] [depth= 17] . ( 9 sec) [ -7135.7948] [ 698] [depth= 10] . ( 9 sec) [ -7128.0241] [ 698] [depth= 16] . ( 9 sec) [ -7118.5641] [ 697] [depth= 4] . ( 9 sec) [ -7116.5494] [ 697] [depth= 1] . ( 9 sec) [ -6923.4678] [ 700] [depth= 19] . ( 9 sec) [ -6633.2877] [ 698] [depth= 4] . ( 9 sec) [ -6529.8462] [ 698] [depth= 8] . ( 9 sec) [ -6405.4329] [ 681] [depth= 8] . ( 10 sec) [ -6374.6465] [ 681] [depth= 8] . ( 10 sec) [ -6370.9859] [ 681] [depth= 11] . ( 10 sec) [ -6364.3190] [ 681] [depth= 20] . ( 10 sec) [ -6359.5901] [ 681] [depth= 10] . ( 10 sec) [ -6358.9408] [ 681] [depth= 1] . ( 10 sec) [ -6240.7613] [ 671] [depth= 16] . ( 10 sec) [ -6220.0279] [ 667] [depth= 1] . ( 10 sec) [ -5579.3131] [ 659] [depth= 22] . ( 10 sec) [ -5568.2037] [ 659] [depth= 4] . ( 11 sec) [ -5567.3615] [ 659] [depth= 1] . ( 11 sec) [ -5564.5426] [ 659] [depth= 2] . ( 11 sec) [ -5564.2765] [ 659] [depth= 10] . ( 11 sec) [ -5561.4702] [ 659] [depth= 1] . ( 11 sec) [ -5534.9075] [ 649] [depth= 8] . ( 11 sec) [ -5498.9890] [ 639] [depth= 16] . ( 11 sec) [ -5489.0140] [ 639] [depth= 1] . ( 11 sec) [ -5486.9423] [ 639] [depth= 9] . ( 11 sec) [ -5459.4274] [ 639] [depth= 1] . ( 11 sec) [ -5378.7989] [ 637] [depth= 23] . ( 12 sec) [ -5376.0226] [ 638] [depth= 12] . ( 12 sec) [ -5321.2844] [ 626] [depth= 10] . ( 12 sec) [ -5287.4931] [ 620] [depth= 18] . ( 12 sec) [ -5285.2682] [ 620] [depth= 2] . ( 12 sec) [ -5285.2038] [ 620] [depth= 12] . ( 12 sec) [ -5281.4728] [ 616] [depth= 1] . ( 12 sec) [ -5281.3088] [ 616] [depth= 1] . ( 12 sec) [ -5133.8435] [ 616] [depth= 2] . ( 12 sec) [ -5118.5155] [ 615] [depth= 18] . ( 13 sec) [ -5095.2463] [ 608] [depth= 2] . ( 13 sec) [ -5055.6092] [ 593] [depth= 14] . ( 13 sec) [ -5011.0441] [ 574] [depth= 9] . ( 13 sec) [ -4985.4577] [ 573] [depth= 9] . ( 13 sec) [ -4985.3929] [ 573] [depth= 12] . ( 13 sec) [ -4984.9408] [ 573] [depth= 13] . ( 13 sec) [ -4984.0729] [ 573] [depth= 7] . ( 13 sec) [ -4983.4101] [ 573] [depth= 7] . ( 14 sec) [ -4965.2829] [ 562] [depth= 8] . ( 14 sec) [ -4962.4479] [ 562] [depth= 4] . ( 14 sec) [ -4962.3524] [ 562] [depth= 3] . ( 14 sec) [ -4876.8435] [ 549] [depth= 15] . ( 14 sec) [ -4842.9744] [ 549] [depth= 1] . ( 14 sec) [ -4715.2724] [ 549] [depth= 2] . ( 14 sec) [ -4689.3090] [ 549] [depth= 3] . ( 14 sec) [ -4593.7460] [ 533] [depth= 13] . ( 14 sec) [ -4585.6134] [ 533] [depth= 9] . ( 15 sec) [ -4583.3503] [ 533] [depth= 12] . ( 15 sec) [ -4525.0177] [ 509] [depth= 14] . ( 15 sec) [ -4390.9044] [ 475] [depth= 16] . ( 15 sec) [ -4367.5377] [ 469] [depth= 1] . ( 15 sec) [ -4308.5213] [ 469] [depth= 1] . ( 15 sec) [ -4247.9992] [ 469] [depth= 3] . ( 15 sec) [ -4237.4859] [ 468] [depth= 1] . ( 15 sec) [ -4234.9734] [ 468] [depth= 9] . ( 16 sec) [ -4184.2953] [ 452] [depth= 17] . ( 16 sec) [ -4180.8372] [ 450] [depth= 1] . ( 16 sec) [ -4180.2292] [ 450] [depth= 4] . ( 16 sec) [ -4172.2233] [ 450] [depth= 1] . ( 16 sec) [ -4102.6008] [ 447] [depth= 6] . ( 16 sec) [ -4100.7857] [ 447] [depth= 7] . ( 16 sec) [ -4085.8560] [ 447] [depth= 3] . ( 16 sec) [ -4040.4000] [ 436] [depth= 11] . ( 16 sec) [ -4038.9227] [ 436] [depth= 1] . ( 17 sec) [ -4026.8254] [ 431] [depth= 7] . ( 17 sec) [ -4022.2138] [ 431] [depth= 1] . ( 17 sec) [ -4007.8696] [ 431] [depth= 1] . ( 17 sec) [ -3998.7555] [ 431] [depth= 1] . ( 17 sec) [ -3997.9802] [ 432] [depth= 1] . ( 17 sec) [ -3996.1226] [ 432] [depth= 1] . ( 17 sec) [ -3994.9381] [ 432] [depth= 2] . ( 17 sec) [ -3975.3769] [ 432] [depth= 4] . ( 17 sec) [ -3970.0319] [ 432] [depth= 3] . ( 17 sec) [ -3968.0119] [ 432] [depth= 3] . ( 17 sec) [ -3910.2935] [ 430] [depth= 8] . ( 18 sec) [ -3910.2813] [ 430] [depth= 5] . ( 18 sec) [ -3909.6751] [ 430] [depth= 2] . ( 18 sec) [ -3908.9530] [ 430] [depth= 8] . ( 18 sec) [ -3899.9198] [ 430] [depth= 2] . ( 18 sec) [ -3899.0109] [ 430] [depth= 1] . ( 18 sec) [ -3895.7026] [ 430] [depth= 3] . ( 18 sec) [ -3873.3845] [ 425] [depth= 9] . ( 18 sec) [ -3872.3778] [ 425] [depth= 5] . ( 18 sec) [ -3868.3108] [ 424] [depth= 8] . ( 19 sec) [ -3868.2863] [ 424] [depth= 5] . ( 19 sec) [ -3868.0675] [ 424] [depth= 3] . ( 19 sec) [ -3868.0360] [ 424] [depth= 5] . ( 19 sec) [ -3867.9700] [ 424] [depth= 4] . ( 19 sec) [ -3865.2700] [ 424] [depth= 1] . ( 19 sec) [ -3865.0936] [ 424] [depth= 10] . ( 19 sec) [ -3854.7417] [ 423] [depth= 23] . ( 19 sec) [ -3847.1219] [ 423] [depth= 2] . ( 19 sec) [ -3845.6780] [ 423] [depth= 9] . ( 20 sec) [ -3845.5924] [ 423] [depth= 13] . ( 20 sec) [ -3845.5237] [ 423] [depth= 10] . ( 20 sec) [ -3844.1654] [ 423] [depth= 2] . ( 20 sec) [ -3842.4993] [ 422] [depth= 4] . ( 20 sec) [ -3819.4095] [ 414] [depth= 11] . ( 20 sec) [ -3819.2627] [ 414] [depth= 7] . ( 20 sec) [ -3819.0282] [ 414] [depth= 1] . ( 20 sec) [ -3817.3467] [ 415] [depth= 1] . ( 20 sec) [ -3813.7219] [ 415] [depth= 3] . ( 21 sec) [ -3812.0595] [ 415] [depth= 1] . ( 21 sec) [ -3811.3633] [ 415] [depth= 3] . ( 21 sec) [ -3811.2716] [ 415] [depth= 3] . ( 21 sec) [ -3809.4171] [ 415] [depth= 3] . ( 21 sec) [ -3808.8404] [ 415] [depth= 4] . ( 21 sec) [ -3808.8186] [ 415] [depth= 1] . ( 22 sec) [ -3808.5957] [ 415] [depth= 4] . ( 22 sec) [ -3808.3278] [ 415] [depth= 4] . ( 22 sec) [ -3807.9807] [ 415] [depth= 2] . ( 22 sec) [ -3807.1821] [ 415] [depth= 7] . ( 22 sec) [ -3806.7972] [ 415] [depth= 1] . ( 22 sec) [ -3806.6218] [ 415] [depth= 11] . ( 22 sec) [ -3805.5186] [ 415] [depth= 4] . ( 22 sec) [ -3801.4670] [ 414] [depth= 7] . ( 23 sec) [ -3800.8764] [ 414] [depth= 11] . ( 23 sec) [ -3798.9331] [ 414] [depth= 1] . ( 23 sec) [ -3792.8521] [ 414] [depth= 2] . ( 23 sec) [ -3792.4741] [ 414] [depth= 4] . ( 23 sec) [ -3792.4310] [ 414] [depth= 4] . ( 23 sec) [ -3791.3621] [ 414] [depth= 4] . ( 23 sec) [ -3788.9949] [ 413] [depth= 4] . ( 24 sec) [ -3788.7702] [ 413] [depth= 4] . ( 24 sec) [ -3788.4149] [ 413] [depth= 4] . ( 24 sec) [ -3782.6846] [ 412] [depth= 6] . ( 24 sec) [ -3782.6588] [ 412] [depth= 4] . ( 24 sec) [ -3781.5854] [ 412] [depth= 1] . ( 24 sec) [ -3779.3228] [ 412] [depth= 2] . ( 24 sec) [ -3768.2582] [ 409] [depth= 3] . ( 24 sec) [ -3765.9093] [ 409] [depth= 1] . ( 24 sec) [ -3765.0241] [ 408] [depth= 21] . ( 25 sec) [ -3698.6797] [Branch lengths ] . ( 26 sec) [ -3681.4247] [GTR parameters ] . ( 26 sec) [ -3652.5479] [Alpha ][ 0.250961] . ( 27 sec) [ -3652.5336] [ 408] [depth= 3] . ( 27 sec) [ -3652.5204] [ 408] [depth= 1] . ( 30 sec) [ -3652.4824] [ 408] [depth= 3] . ( 30 sec) [ -3650.0180] [ 407] [depth= 2] . ( 31 sec) [ -3649.9327] [ 407] [depth= 1] . ( 32 sec) [ -3649.9167] [ 405] [depth= 5] . ( 32 sec) [ -3635.5521] [ 400] [depth= 3] . ( 33 sec) [ -3635.4614] [ 400] [depth= 6] . ( 33 sec) [ -3631.9559] [ 399] [depth= 2] . ( 33 sec) [ -3627.9369] [ 399] [depth= 3] . ( 34 sec) [ -3627.8486] [ 399] [depth= 3] . ( 34 sec) [ -3627.6815] [ 399] [depth= 1] . ( 34 sec) [ -3627.5157] [ 399] [depth= 4] . ( 35 sec) [ -3627.4613] [ 399] [depth= 5] . ( 35 sec) [ -3627.3271] [ 399] [depth= 3] . ( 36 sec) [ -3576.2370] [ 380] [depth= 18] . ( 36 sec) [ -3573.8286] [ 380] [depth= 18] . ( 39 sec) [ -3572.8740] [ 380] [depth= 1] . ( 42 sec) [ -3572.8520] [ 380] [depth= 1] . ( 42 sec) [ -3516.9473] [ 369] [depth= 6] . ( 42 sec) [ -3516.9170] [ 369] [depth= 3] . ( 42 sec) [ -3480.2216] [ 353] [depth= 15] . ( 42 sec) [ -3480.0261] [ 353] [depth= 4] . ( 42 sec) [ -3479.7276] [ 353] [depth= 1] . ( 42 sec) [ -3479.7039] [ 353] [depth= 1] . ( 42 sec) [ -3477.1225] [ 353] [depth= 3] . ( 43 sec) [ -3476.8852] [ 353] [depth= 7] . ( 43 sec) [ -3476.8339] [ 353] [depth= 1] . ( 44 sec) [ -3476.7798] [ 353] [depth= 1] . ( 44 sec) [ -3476.2171] [ 353] [depth= 1] . ( 45 sec) [ -3475.7196] [ 353] [depth= 3] . ( 45 sec) [ -3474.9856] [ 353] [depth= 5] . ( 46 sec) [ -3474.6600] [ 355] [depth= 4] . ( 46 sec) [ -3474.5824] [ 355] [depth= 1] . ( 47 sec) [ -3474.4011] [ 355] [depth= 1] . ( 47 sec) [ -3468.6828] [ 354] [depth= 3] . ( 47 sec) [ -3468.5429] [ 354] [depth= 3] . ( 47 sec) [ -3468.3893] [ 354] [depth= 6] . ( 48 sec) [ -3468.2484] [ 354] [depth= 8] . ( 48 sec) [ -3467.5300] [ 354] [depth= 4] . ( 49 sec) [ -3455.1934] [ 354] [depth= 2] . ( 49 sec) [ -3455.1704] [ 354] [depth= 8] . ( 50 sec) [ -3455.0212] [ 354] [depth= 1] . ( 50 sec) [ -3453.1114] [ 353] [depth= 4] . ( 50 sec) [ -3453.0980] [ 353] [depth= 1] . ( 51 sec) [ -3448.8925] [ 348] [depth= 1] . ( 51 sec) [ -3443.0662] [ 347] [depth= 3] . ( 52 sec) [ -3442.9614] [ 347] [depth= 4] . ( 52 sec) [ -3442.9452] [ 347] [depth= 6] . ( 52 sec) [ -3442.9338] [ 347] [depth= 2] . ( 53 sec) [ -3442.2261] [ 346] [depth= 2] . ( 53 sec) [ -3441.9719] [ 346] [depth= 1] . ( 54 sec) [ -3441.8642] [ 346] [depth= 1] . ( 54 sec) [ -3441.6898] [ 346] [depth= 1] . ( 54 sec) [ -3441.4971] [ 346] [depth= 2] . ( 55 sec) [ -3439.6103] [ 346] [depth= 3] . ( 55 sec) [ -3439.2743] [ 346] [depth= 5] . ( 55 sec) [ -3437.4736] [ 346] [depth= 1] . ( 56 sec) [ -3436.8843] [ 346] [depth= 1] . ( 57 sec) [ -3436.8401] [ 346] [depth= 5] . ( 57 sec) [ -3435.7441] [ 346] [depth= 3] . ( 58 sec) [ -3435.7115] [ 346] [depth= 5] . ( 58 sec) [ -3431.9817] [ 346] [depth= 1] . ( 58 sec) [ -3431.5857] [ 346] [depth= 3] . ( 58 sec) [ -3430.6154] [ 347] [depth= 1] . ( 59 sec) [ -3422.4805] [ 345] [depth= 3] . ( 59 sec) [ -3422.4564] [ 345] [depth= 3] . ( 60 sec) [ -3422.4259] [ 345] [depth= 1] . ( 61 sec) [ -3422.3292] [ 345] [depth= 1] . ( 61 sec) [ -3422.2981] [ 345] [depth= 7] . ( 62 sec) [ -3422.1961] [ 345] [depth= 5] . ( 63 sec) [ -3422.1829] [ 345] [depth= 1] . ( 63 sec) [ -3422.1488] [ 345] [depth= 3] . ( 63 sec) [ -3422.1326] [ 345] [depth= 6] . ( 63 sec) [ -3422.1065] [ 345] [depth= 6] . ( 63 sec) [ -3422.0956] [ 345] [depth= 4] . ( 63 sec) [ -3421.6091] [ 345] [depth= 1] . ( 64 sec) [ -3421.4492] [ 345] [depth= 4] . ( 64 sec) [ -3420.9608] [ 345] [depth= 2] . ( 64 sec) [ -3420.9256] [ 345] [depth= 5] . ( 64 sec) [ -3420.8890] [ 345] [depth= 1] . ( 64 sec) [ -3420.7918] [ 345] [depth= 16] . ( 65 sec) [ -3420.1701] [ 345] [depth= 2] . ( 65 sec) [ -3420.1589] [ 345] [depth= 4] . ( 65 sec) [ -3420.1470] [ 345] [depth= 1] . ( 65 sec) [ -3419.5982] [ 345] [depth= 1] . ( 66 sec) [ -3419.5648] [ 345] [depth= 1] . ( 66 sec) [ -3419.3923] [ 345] [depth= 4] . ( 67 sec) [ -3419.3088] [ 345] [depth= 10] . ( 67 sec) [ -3419.2919] [ 345] [depth= 4] . ( 67 sec) [ -3419.2581] [ 345] [depth= 7] . ( 68 sec) [ -3419.2255] [ 345] [depth= 3] . ( 68 sec) [ -3419.1392] [ 345] [depth= 5] . ( 68 sec) [ -3419.1167] [ 345] [depth= 5] . ( 68 sec) [ -3418.9461] [ 345] [depth= 23] . ( 69 sec) [ -3418.8629] [ 345] [depth= 2] . ( 69 sec) [ -3418.8504] [ 345] [depth= 6] . ( 70 sec) [ -3418.8362] [ 345] [depth= 2] . ( 70 sec) [ -3418.4294] [ 345] [depth= 1] . ( 70 sec) [ -3418.2403] [ 345] [depth= 3] . ( 70 sec) [ -3418.1417] [ 345] [depth= 12] . ( 70 sec) [ -3418.1261] [ 345] [depth= 3] . ( 71 sec) [ -3418.0684] [ 345] [depth= 17] . ( 72 sec) [ -3417.6111] [ 347] [depth= 1] . ( 72 sec) [ -3417.4811] [ 347] [depth= 1] . ( 72 sec) [ -3417.4133] [ 347] [depth= 7] . ( 72 sec) [ -3417.2773] [ 347] [depth= 2] . ( 72 sec) [ -3417.2630] [ 347] [depth= 8] . ( 73 sec) [ -3417.2479] [ 347] [depth= 2] . ( 73 sec) [ -3417.2171] [ 347] [depth= 6] . ( 74 sec) [ -3417.1722] [ 347] [depth= 3] . ( 74 sec) [ -3412.5693] [ 347] [depth= 9] . ( 74 sec) [ -3398.6825] [Branch lengths ] . ( 75 sec) [ -3397.7601] [GTR parameters ] . ( 75 sec) [ -3397.4545] [Alpha ][ 0.221905] . ( 78 sec) [ -3397.3645] [ 347] [depth= 5] . ( 78 sec) [ -3397.3357] [ 347] [depth= 19] . ( 84 sec) [ -3397.2943] [ 345] [depth= 1] . ( 98 sec) [ -3393.7999] [ 342] [depth= 3] . ( 98 sec) [ -3393.7766] [ 342] [depth= 2] . ( 101 sec) [ -3393.6684] [ 342] [depth= 7] . ( 102 sec) [ -3393.6520] [ 342] [depth= 5] . ( 104 sec) [ -3393.6069] [ 342] [depth= 8] . ( 104 sec) [ -3393.5960] [ 342] [depth= 2] . ( 112 sec) [ -3393.5457] [ 342] [depth= 5] . ( 115 sec) [ -3393.5107] [ 342] [depth= 1] . ( 135 sec) [ -3391.2235] [ 342] [depth= 6] . ( 136 sec) [ -3389.9693] [ 342] [depth= 3] . ( 136 sec) [ -3389.9579] [ 342] [depth= 13] . ( 138 sec) [ -3389.6518] [ 342] [depth= 2] . ( 140 sec) [ -3388.8992] [Branch lengths ] . ( 140 sec) [ -3388.8522] [GTR parameters ] . ( 141 sec) [ -3388.8515] [Alpha ][ 0.220513] . ( 161 sec) [ -3387.5007] [ 342] [depth= 3] . ( 162 sec) [ -3387.4895] [ 342] [depth= 5] . ( 162 sec) [ -3387.0711] [ 342] [depth= 1] . ( 164 sec) [ -3386.3924] [ 342] [depth= 2] . ( 167 sec) [ -3386.2415] [ 342] [depth= 2] . ( 168 sec) [ -3385.8649] [ 342] [depth= 15] . ( 169 sec) [ -3385.5316] [ 342] [depth= 1] . ( 176 sec) [ -3385.5058] [ 342] [depth= 2] . ( 178 sec) [ -3384.5249] [ 342] [depth= 2] . ( 181 sec) [ -3384.2424] [ 342] [depth= 1] . ( 183 sec) [ -3383.9143] [ 342] [depth= 11] . ( 184 sec) [ -3383.8008] [ 342] [depth= 2] . ( 199 sec) [ -3383.7899] [ 342] [depth= 14] . ( 204 sec) [ -3383.2118] [Branch lengths ] . ( 204 sec) [ -3383.2110] [GTR parameters ] . ( 204 sec) [ -3383.2109] [Alpha ][ 0.220763] . ( 213 sec) [ -3382.9868] [ 342] [depth= 2] . ( 213 sec) [ -3382.0845] [ 342] [depth= 3] . ( 217 sec) [ -3382.0348] [ 342] [depth= 2] . ( 219 sec) [ -3380.9657] [ 342] [depth= 1] . ( 231 sec) [ -3379.1456] [ 342] [depth= 1] . ( 231 sec) [ -3378.9806] [ 342] [depth= 1] . ( 237 sec) [ -3378.9566] [ 342] [depth= 3] . ( 239 sec) [ -3378.9257] [ 342] [depth= 2] . ( 239 sec) [ -3378.7719] [ 342] [depth= 2] . ( 244 sec) [ -3375.1452] [ 342] [depth= 2] . ( 245 sec) [ -3375.1242] [ 342] [depth= 2] . ( 246 sec) [ -3375.1124] [ 342] [depth= 1] . ( 249 sec) [ -3375.0681] [ 342] [depth= 2] . ( 253 sec) [ -3374.3240] [ 342] [depth= 2] . ( 255 sec) [ -3374.3119] [ 342] [depth= 1] . ( 258 sec) [ -3351.8314] [ 337] [depth= 12] . ( 258 sec) [ -3351.7979] [ 337] [depth= 4] . ( 258 sec) [ -3351.1392] [ 337] [depth= 2] . ( 258 sec) [ -3350.1217] [ 337] [depth= 7] . ( 258 sec) [ -3349.7850] [ 337] [depth= 9] . ( 259 sec) [ -3349.7746] [ 337] [depth= 4] . ( 259 sec) [ -3349.0495] [ 337] [depth= 15] . ( 259 sec) [ -3348.4880] [ 337] [depth= 11] . ( 260 sec) [ -3348.3863] [ 337] [depth= 4] . ( 263 sec) [ -3348.0834] [ 337] [depth= 3] . ( 264 sec) [ -3348.0332] [ 337] [depth= 3] . ( 264 sec) [ -3348.0192] [ 337] [depth= 11] . ( 266 sec) [ -3347.9989] [ 337] [depth= 9] . ( 267 sec) [ -3347.8876] [ 337] [depth= 5] . ( 267 sec) [ -3347.7638] [ 337] [depth= 2] . ( 267 sec) [ -3347.7511] [ 337] [depth= 7] . ( 267 sec) [ -3347.7379] [ 337] [depth= 6] . ( 267 sec) [ -3347.7271] [ 337] [depth= 10] . ( 272 sec) [ -3347.6954] [ 337] [depth= 1] . ( 275 sec) [ -3346.1485] [Branch lengths ] . ( 275 sec) [ -3346.0962] [GTR parameters ] . ( 276 sec) [ -3346.0520] [Alpha ][ 0.231768] . ( 277 sec) [ -3346.0344] [ 337] [depth= 2] . ( 284 sec) [ -3345.9806] [ 337] [depth= 1] . ( 300 sec) [ -3345.9514] [ 337] [depth= 1] . ( 359 sec) [ -3345.9221] [Branch lengths ] . ( 359 sec) [ -3345.9206] [GTR parameters ] . ( 359 sec) [ -3345.9201] [Alpha ][ 0.232986] . ( 397 sec) [ -3345.9017] [ 337] [depth= 2] . ( 404 sec) [ -3345.9001] [Branch lengths ] . ( 404 sec) [ -3345.9000] [GTR parameters ] . ( 405 sec) [ -3345.9000] [Alpha ][ 0.233299] . ( 405 sec) [ -3345.9000] [Topology ] . ( 405 sec) [ -3345.8998] [Topology ] . ( 405 sec) [ -3345.8998] [GTR parameters ] . ( 406 sec) [ -3345.8998] [Alpha ][ 0.233299] . Checking for NNIs, optimizing five branches... . ( 410 sec) [ -3345.8997] [Topology ] . Checking for NNIs, optimizing five branches... . ( 417 sec) [ -3345.8996] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3345.899572. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -11407.1404] [GTR parameters ] . ( 1 sec) [ -11229.6420] [Alpha ][ 0.500960] . ( 1 sec) [ -11146.1734] [ 1012] [depth= 6] . ( 1 sec) [ -10759.8094] [ 981] [depth= 5] . ( 1 sec) [ -10718.8636] [ 984] [depth= 2] . ( 1 sec) [ -10570.2798] [ 955] [depth= 6] . ( 1 sec) [ -10557.2620] [ 953] [depth= 3] . ( 1 sec) [ -10427.4691] [ 921] [depth= 18] . ( 1 sec) [ -10390.1213] [ 910] [depth= 2] . ( 1 sec) [ -10221.4677] [ 910] [depth= 2] . ( 1 sec) [ -10196.2131] [ 906] [depth= 3] . ( 2 sec) [ -10058.1731] [ 906] [depth= 1] . ( 2 sec) [ -10022.2348] [ 904] [depth= 5] . ( 2 sec) [ -10005.9558] [ 904] [depth= 3] . ( 2 sec) [ -10001.1589] [ 901] [depth= 8] . ( 2 sec) [ -9945.1482] [ 901] [depth= 2] . ( 2 sec) [ -9828.3162] [ 901] [depth= 1] . ( 2 sec) [ -9583.5572] [ 901] [depth= 3] . ( 2 sec) [ -9505.5180] [ 894] [depth= 11] . ( 2 sec) [ -9444.2399] [ 894] [depth= 1] . ( 2 sec) [ -9299.8381] [ 884] [depth= 16] . ( 2 sec) [ -9176.7196] [ 884] [depth= 1] . ( 2 sec) [ -9149.0256] [ 875] [depth= 3] . ( 2 sec) [ -9132.9119] [ 875] [depth= 1] . ( 2 sec) [ -9078.4196] [ 874] [depth= 6] . ( 2 sec) [ -8949.4920] [ 875] [depth= 2] . ( 2 sec) [ -8851.0604] [ 863] [depth= 26] . ( 2 sec) [ -8835.1802] [ 863] [depth= 1] . ( 3 sec) [ -8807.8634] [ 858] [depth= 23] . ( 3 sec) [ -8703.1207] [ 861] [depth= 1] . ( 3 sec) [ -8633.6464] [ 839] [depth= 11] . ( 3 sec) [ -8529.0133] [ 837] [depth= 9] . ( 3 sec) [ -8524.3233] [ 836] [depth= 11] . ( 3 sec) [ -8507.5686] [ 836] [depth= 2] . ( 3 sec) [ -8507.4130] [ 836] [depth= 2] . ( 3 sec) [ -8491.3379] [ 833] [depth= 13] . ( 3 sec) [ -8427.3224] [ 818] [depth= 17] . ( 3 sec) [ -8370.7401] [ 805] [depth= 29] . ( 3 sec) [ -8368.3423] [ 805] [depth= 1] . ( 3 sec) [ -8358.5379] [ 805] [depth= 1] . ( 3 sec) [ -8163.5128] [ 784] [depth= 10] . ( 4 sec) [ -8043.9207] [ 784] [depth= 15] . ( 4 sec) [ -7999.7655] [ 781] [depth= 9] . ( 4 sec) [ -7944.9441] [ 764] [depth= 9] . ( 4 sec) [ -7920.1340] [ 759] [depth= 21] . ( 4 sec) [ -7919.0073] [ 759] [depth= 1] . ( 4 sec) [ -7884.9042] [ 753] [depth= 20] . ( 4 sec) [ -7884.0611] [ 753] [depth= 1] . ( 4 sec) [ -7734.1549] [ 733] [depth= 6] . ( 4 sec) [ -7733.1555] [ 733] [depth= 1] . ( 4 sec) [ -7732.6773] [ 733] [depth= 7] . ( 5 sec) [ -7462.7382] [ 715] [depth= 14] . ( 5 sec) [ -7462.2146] [ 715] [depth= 1] . ( 5 sec) [ -7446.8312] [ 715] [depth= 8] . ( 5 sec) [ -7292.3499] [ 710] [depth= 20] . ( 5 sec) [ -7292.0759] [ 710] [depth= 8] . ( 5 sec) [ -7292.0458] [ 710] [depth= 6] . ( 5 sec) [ -7252.1969] [ 708] [depth= 16] . ( 5 sec) [ -7244.9479] [ 708] [depth= 1] . ( 5 sec) [ -7243.0642] [ 708] [depth= 4] . ( 5 sec) [ -7233.8789] [ 707] [depth= 16] . ( 5 sec) [ -7146.2230] [ 700] [depth= 5] . ( 5 sec) [ -7146.0137] [ 700] [depth= 25] . ( 6 sec) [ -6997.8057] [ 681] [depth= 11] . ( 6 sec) [ -6941.1026] [ 667] [depth= 15] . ( 6 sec) [ -6931.9098] [ 664] [depth= 4] . ( 6 sec) [ -6761.5265] [ 647] [depth= 12] . ( 6 sec) [ -6758.5405] [ 647] [depth= 1] . ( 6 sec) [ -6708.5328] [ 637] [depth= 3] . ( 6 sec) [ -6592.5667] [ 637] [depth= 1] . ( 6 sec) [ -6582.5967] [ 635] [depth= 1] . ( 6 sec) [ -5936.2709] [ 635] [depth= 13] . ( 6 sec) [ -5923.0843] [ 632] [depth= 1] . ( 6 sec) [ -5864.9268] [ 630] [depth= 12] . ( 7 sec) [ -5864.3490] [ 630] [depth= 5] . ( 7 sec) [ -5863.9209] [ 630] [depth= 6] . ( 7 sec) [ -5859.8598] [ 630] [depth= 19] . ( 7 sec) [ -5803.0532] [ 618] [depth= 14] . ( 7 sec) [ -5760.4462] [ 618] [depth= 1] . ( 7 sec) [ -5757.3550] [ 623] [depth= 7] . ( 7 sec) [ -5613.0273] [ 611] [depth= 6] . ( 7 sec) [ -5572.0732] [ 608] [depth= 1] . ( 7 sec) [ -5562.4562] [ 607] [depth= 4] . ( 7 sec) [ -5559.1853] [ 607] [depth= 1] . ( 7 sec) [ -5538.8317] [ 603] [depth= 14] . ( 8 sec) [ -5537.4896] [ 604] [depth= 7] . ( 8 sec) [ -5531.4513] [ 603] [depth= 11] . ( 8 sec) [ -5287.6783] [ 593] [depth= 6] . ( 8 sec) [ -5269.6268] [ 592] [depth= 7] . ( 8 sec) [ -5254.7121] [ 590] [depth= 7] . ( 8 sec) [ -5254.2144] [ 590] [depth= 3] . ( 8 sec) [ -5231.2483] [ 586] [depth= 7] . ( 8 sec) [ -5228.2754] [ 586] [depth= 5] . ( 8 sec) [ -5220.2833] [ 586] [depth= 1] . ( 8 sec) [ -5215.0498] [ 586] [depth= 2] . ( 8 sec) [ -5180.3906] [ 581] [depth= 15] . ( 8 sec) [ -5168.5218] [ 580] [depth= 19] . ( 9 sec) [ -5055.5523] [ 559] [depth= 8] . ( 9 sec) [ -5046.0103] [ 559] [depth= 5] . ( 9 sec) [ -5043.1070] [ 559] [depth= 3] . ( 9 sec) [ -5043.0953] [ 559] [depth= 3] . ( 9 sec) [ -5042.6282] [ 559] [depth= 4] . ( 9 sec) [ -4915.8145] [ 559] [depth= 12] . ( 9 sec) [ -4910.3916] [ 559] [depth= 13] . ( 9 sec) [ -4901.7482] [ 559] [depth= 1] . ( 9 sec) [ -4877.4873] [ 554] [depth= 18] . ( 9 sec) [ -4871.3324] [ 553] [depth= 12] . ( 9 sec) [ -4863.2056] [ 553] [depth= 6] . ( 9 sec) [ -4852.7070] [ 552] [depth= 12] . ( 10 sec) [ -4776.5550] [ 538] [depth= 16] . ( 10 sec) [ -4767.3124] [ 538] [depth= 12] . ( 10 sec) [ -4756.0719] [ 537] [depth= 7] . ( 10 sec) [ -4741.2146] [ 538] [depth= 11] . ( 10 sec) [ -4737.5537] [ 537] [depth= 2] . ( 10 sec) [ -4730.0092] [ 537] [depth= 15] . ( 10 sec) [ -4714.7408] [ 539] [depth= 1] . ( 10 sec) [ -4553.0588] [ 527] [depth= 11] . ( 11 sec) [ -4552.8349] [ 527] [depth= 2] . ( 11 sec) [ -4552.5731] [ 527] [depth= 3] . ( 11 sec) [ -4552.3431] [ 523] [depth= 17] . ( 11 sec) [ -4518.8708] [ 513] [depth= 8] . ( 11 sec) [ -4518.6258] [ 513] [depth= 2] . ( 11 sec) [ -4517.8391] [ 513] [depth= 1] . ( 11 sec) [ -4517.3998] [ 513] [depth= 4] . ( 11 sec) [ -4516.5253] [ 513] [depth= 2] . ( 11 sec) [ -4510.7132] [ 513] [depth= 17] . ( 11 sec) [ -4509.7987] [ 513] [depth= 10] . ( 11 sec) [ -4508.7450] [ 513] [depth= 7] . ( 11 sec) [ -4499.2436] [ 511] [depth= 9] . ( 11 sec) [ -4497.5846] [ 511] [depth= 7] . ( 11 sec) [ -4496.4913] [ 511] [depth= 2] . ( 11 sec) [ -4496.3703] [ 511] [depth= 3] . ( 11 sec) [ -4486.5646] [ 511] [depth= 1] . ( 11 sec) [ -4481.5136] [ 510] [depth= 2] . ( 11 sec) [ -4393.1208] [ 489] [depth= 7] . ( 12 sec) [ -4390.7028] [ 489] [depth= 4] . ( 12 sec) [ -4390.5900] [ 489] [depth= 11] . ( 12 sec) [ -4389.6148] [ 489] [depth= 8] . ( 12 sec) [ -4388.0112] [ 489] [depth= 4] . ( 12 sec) [ -4386.9371] [ 489] [depth= 6] . ( 12 sec) [ -4363.5179] [ 483] [depth= 4] . ( 12 sec) [ -4359.6944] [ 483] [depth= 4] . ( 12 sec) [ -4357.4389] [ 483] [depth= 1] . ( 12 sec) [ -4293.0660] [ 475] [depth= 13] . ( 12 sec) [ -4291.5635] [ 475] [depth= 2] . ( 12 sec) [ -4290.3852] [ 475] [depth= 2] . ( 12 sec) [ -4224.8072] [ 461] [depth= 7] . ( 12 sec) [ -4222.5611] [ 461] [depth= 7] . ( 12 sec) [ -4222.1529] [ 462] [depth= 17] . ( 13 sec) [ -4220.7610] [ 462] [depth= 14] . ( 13 sec) [ -4170.5854] [ 456] [depth= 8] . ( 13 sec) [ -4116.0188] [ 449] [depth= 7] . ( 13 sec) [ -4096.8752] [ 445] [depth= 17] . ( 13 sec) [ -4096.5904] [ 445] [depth= 2] . ( 13 sec) [ -4087.1309] [ 445] [depth= 9] . ( 13 sec) [ -4056.8048] [ 445] [depth= 4] . ( 13 sec) [ -4056.7906] [ 445] [depth= 8] . ( 13 sec) [ -4056.2012] [ 445] [depth= 1] . ( 13 sec) [ -4056.1851] [ 445] [depth= 1] . ( 13 sec) [ -4055.5625] [ 445] [depth= 6] . ( 14 sec) [ -4051.6372] [ 443] [depth= 3] . ( 14 sec) [ -4029.1800] [ 443] [depth= 1] . ( 14 sec) [ -4003.3802] [ 438] [depth= 3] . ( 14 sec) [ -4001.9233] [ 438] [depth= 6] . ( 14 sec) [ -4000.7056] [ 438] [depth= 8] . ( 14 sec) [ -4000.6653] [ 438] [depth= 3] . ( 14 sec) [ -4000.1999] [ 438] [depth= 2] . ( 14 sec) [ -3926.5717] [ 429] [depth= 3] . ( 14 sec) [ -3911.6717] [ 424] [depth= 4] . ( 14 sec) [ -3911.6522] [ 424] [depth= 4] . ( 14 sec) [ -3882.2235] [ 420] [depth= 13] . ( 14 sec) [ -3877.5280] [ 416] [depth= 4] . ( 14 sec) [ -3876.1099] [ 416] [depth= 1] . ( 14 sec) [ -3845.1575] [ 416] [depth= 1] . ( 15 sec) [ -3838.9514] [ 416] [depth= 2] . ( 15 sec) [ -3826.7432] [ 412] [depth= 5] . ( 15 sec) [ -3824.7902] [ 412] [depth= 1] . ( 15 sec) [ -3818.0634] [ 411] [depth= 8] . ( 15 sec) [ -3817.3583] [ 411] [depth= 9] . ( 15 sec) [ -3813.8598] [ 411] [depth= 1] . ( 15 sec) [ -3813.2540] [ 411] [depth= 1] . ( 15 sec) [ -3811.2635] [ 411] [depth= 11] . ( 15 sec) [ -3791.6275] [ 407] [depth= 2] . ( 15 sec) [ -3785.2597] [ 406] [depth= 8] . ( 15 sec) [ -3785.2205] [ 406] [depth= 11] . ( 15 sec) [ -3738.3457] [ 391] [depth= 22] . ( 15 sec) [ -3738.3032] [ 391] [depth= 2] . ( 15 sec) [ -3737.5116] [ 391] [depth= 8] . ( 16 sec) [ -3717.3322] [ 382] [depth= 13] . ( 16 sec) [ -3714.7709] [ 382] [depth= 4] . ( 16 sec) [ -3714.3217] [ 382] [depth= 3] . ( 16 sec) [ -3705.2444] [ 379] [depth= 15] . ( 16 sec) [ -3704.4618] [ 380] [depth= 2] . ( 16 sec) [ -3701.1854] [ 380] [depth= 1] . ( 16 sec) [ -3699.1608] [ 379] [depth= 2] . ( 16 sec) [ -3699.1341] [ 379] [depth= 10] . ( 16 sec) [ -3699.1093] [ 379] [depth= 3] . ( 16 sec) [ -3690.0435] [ 379] [depth= 8] . ( 16 sec) [ -3688.2128] [ 379] [depth= 5] . ( 17 sec) [ -3684.2861] [ 379] [depth= 4] . ( 17 sec) [ -3684.1857] [ 379] [depth= 4] . ( 17 sec) [ -3684.0134] [ 379] [depth= 10] . ( 17 sec) [ -3676.4767] [ 378] [depth= 3] . ( 17 sec) [ -3675.5494] [ 378] [depth= 5] . ( 18 sec) [ -3630.4075] [Branch lengths ] . ( 21 sec) [ -3597.0179] [GTR parameters ] . ( 22 sec) [ -3579.2064] [Alpha ][ 0.250961] . ( 22 sec) [ -3578.3233] [ 378] [depth= 4] . ( 22 sec) [ -3577.8429] [ 378] [depth= 1] . ( 22 sec) [ -3577.7196] [ 378] [depth= 6] . ( 22 sec) [ -3577.6572] [ 378] [depth= 4] . ( 22 sec) [ -3556.9936] [ 374] [depth= 6] . ( 22 sec) [ -3554.3120] [ 373] [depth= 6] . ( 25 sec) [ -3549.2520] [ 373] [depth= 2] . ( 25 sec) [ -3549.2369] [ 373] [depth= 3] . ( 25 sec) [ -3548.8639] [ 373] [depth= 1] . ( 25 sec) [ -3548.7551] [ 373] [depth= 4] . ( 25 sec) [ -3548.6714] [ 373] [depth= 3] . ( 25 sec) [ -3537.5949] [ 370] [depth= 1] . ( 26 sec) [ -3535.0450] [ 370] [depth= 11] . ( 26 sec) [ -3534.9256] [ 370] [depth= 18] . ( 27 sec) [ -3534.7821] [ 370] [depth= 6] . ( 27 sec) [ -3534.7459] [ 370] [depth= 1] . ( 27 sec) [ -3520.7596] [ 366] [depth= 9] . ( 28 sec) [ -3520.5225] [ 366] [depth= 2] . ( 28 sec) [ -3520.4491] [ 366] [depth= 1] . ( 29 sec) [ -3520.0238] [ 366] [depth= 2] . ( 29 sec) [ -3519.9842] [ 366] [depth= 8] . ( 30 sec) [ -3519.9535] [ 366] [depth= 2] . ( 30 sec) [ -3519.9311] [ 366] [depth= 3] . ( 31 sec) [ -3516.0938] [ 365] [depth= 4] . ( 32 sec) [ -3509.0193] [ 364] [depth= 9] . ( 32 sec) [ -3509.0092] [ 364] [depth= 9] . ( 33 sec) [ -3508.9955] [ 364] [depth= 1] . ( 33 sec) [ -3484.7676] [ 359] [depth= 19] . ( 33 sec) [ -3483.7908] [ 359] [depth= 4] . ( 34 sec) [ -3473.7130] [ 357] [depth= 4] . ( 34 sec) [ -3469.5695] [ 357] [depth= 2] . ( 35 sec) [ -3469.4927] [ 357] [depth= 1] . ( 36 sec) [ -3469.1117] [ 357] [depth= 6] . ( 36 sec) [ -3467.2950] [ 357] [depth= 3] . ( 37 sec) [ -3457.3615] [ 355] [depth= 1] . ( 37 sec) [ -3455.8543] [ 355] [depth= 1] . ( 37 sec) [ -3455.8393] [ 355] [depth= 10] . ( 37 sec) [ -3455.7785] [ 355] [depth= 1] . ( 37 sec) [ -3455.7307] [ 355] [depth= 1] . ( 38 sec) [ -3455.6855] [ 355] [depth= 2] . ( 38 sec) [ -3453.1497] [ 355] [depth= 2] . ( 39 sec) [ -3452.5543] [ 355] [depth= 3] . ( 39 sec) [ -3452.3412] [ 355] [depth= 1] . ( 39 sec) [ -3452.2241] [ 355] [depth= 6] . ( 39 sec) [ -3398.9592] [ 346] [depth= 11] . ( 39 sec) [ -3388.4792] [ 346] [depth= 2] . ( 40 sec) [ -3388.2719] [ 346] [depth= 6] . ( 40 sec) [ -3388.0903] [ 346] [depth= 7] . ( 40 sec) [ -3388.0329] [ 346] [depth= 2] . ( 41 sec) [ -3383.1466] [ 346] [depth= 1] . ( 41 sec) [ -3379.3530] [ 345] [depth= 10] . ( 41 sec) [ -3379.2244] [ 345] [depth= 6] . ( 41 sec) [ -3378.9519] [ 345] [depth= 7] . ( 41 sec) [ -3378.9130] [ 345] [depth= 4] . ( 41 sec) [ -3372.7795] [ 337] [depth= 8] . ( 42 sec) [ -3372.5020] [ 337] [depth= 3] . ( 42 sec) [ -3372.4475] [ 337] [depth= 1] . ( 42 sec) [ -3372.3900] [ 337] [depth= 1] . ( 42 sec) [ -3372.1546] [ 337] [depth= 1] . ( 42 sec) [ -3372.0148] [ 337] [depth= 2] . ( 42 sec) [ -3370.9702] [ 337] [depth= 2] . ( 42 sec) [ -3370.1775] [ 335] [depth= 2] . ( 42 sec) [ -3370.1657] [ 335] [depth= 3] . ( 42 sec) [ -3370.1241] [ 335] [depth= 8] . ( 43 sec) [ -3369.4457] [ 335] [depth= 1] . ( 43 sec) [ -3369.0077] [ 335] [depth= 6] . ( 43 sec) [ -3368.9974] [ 335] [depth= 2] . ( 43 sec) [ -3367.9224] [ 335] [depth= 1] . ( 43 sec) [ -3367.8404] [ 335] [depth= 4] . ( 43 sec) [ -3367.5651] [ 335] [depth= 3] . ( 43 sec) [ -3367.3562] [ 335] [depth= 3] . ( 43 sec) [ -3367.0896] [ 335] [depth= 3] . ( 43 sec) [ -3362.6069] [ 332] [depth= 7] . ( 43 sec) [ -3359.9136] [ 331] [depth= 1] . ( 45 sec) [ -3359.8834] [ 331] [depth= 2] . ( 45 sec) [ -3359.7620] [ 331] [depth= 3] . ( 45 sec) [ -3359.5776] [ 331] [depth= 4] . ( 46 sec) [ -3359.4883] [ 331] [depth= 7] . ( 46 sec) [ -3359.3975] [ 331] [depth= 7] . ( 47 sec) [ -3358.3271] [ 331] [depth= 8] . ( 47 sec) [ -3358.2595] [ 331] [depth= 5] . ( 47 sec) [ -3357.9520] [ 332] [depth= 1] . ( 47 sec) [ -3357.9206] [ 332] [depth= 7] . ( 47 sec) [ -3357.8833] [ 332] [depth= 7] . ( 48 sec) [ -3357.7950] [ 332] [depth= 7] . ( 48 sec) [ -3357.7182] [ 332] [depth= 10] . ( 49 sec) [ -3357.6850] [ 332] [depth= 1] . ( 49 sec) [ -3357.6249] [ 332] [depth= 2] . ( 49 sec) [ -3357.1196] [ 333] [depth= 1] . ( 49 sec) [ -3357.0810] [ 333] [depth= 1] . ( 49 sec) [ -3357.0489] [ 333] [depth= 6] . ( 50 sec) [ -3357.0263] [ 333] [depth= 4] . ( 50 sec) [ -3357.0140] [ 333] [depth= 2] . ( 51 sec) [ -3351.0685] [ 333] [depth= 3] . ( 51 sec) [ -3351.0578] [ 333] [depth= 4] . ( 51 sec) [ -3350.9343] [ 333] [depth= 8] . ( 51 sec) [ -3350.9120] [ 333] [depth= 8] . ( 52 sec) [ -3350.8915] [ 333] [depth= 1] . ( 53 sec) [ -3350.8810] [ 333] [depth= 3] . ( 53 sec) [ -3350.8473] [ 333] [depth= 13] . ( 53 sec) [ -3350.5058] [ 332] [depth= 4] . ( 53 sec) [ -3350.4292] [ 332] [depth= 2] . ( 54 sec) [ -3350.3620] [ 332] [depth= 5] . ( 54 sec) [ -3349.9683] [ 332] [depth= 2] . ( 54 sec) [ -3349.5850] [ 332] [depth= 2] . ( 55 sec) [ -3349.4350] [ 332] [depth= 2] . ( 55 sec) [ -3346.3134] [Branch lengths ] . ( 57 sec) [ -3345.8674] [GTR parameters ] . ( 57 sec) [ -3345.8487] [Alpha ][ 0.242904] . ( 63 sec) [ -3345.8318] [ 332] [depth= 1] . ( 78 sec) [ -3345.0566] [ 331] [depth= 1] . ( 79 sec) [ -3345.0291] [ 331] [depth= 1] . ( 108 sec) [ -3345.0145] [ 331] [depth= 2] . ( 116 sec) [ -3344.9960] [ 331] [depth= 11] . ( 118 sec) [ -3344.8182] [Branch lengths ] . ( 119 sec) [ -3344.8129] [GTR parameters ] . ( 119 sec) [ -3344.8093] [Alpha ][ 0.246530] . ( 181 sec) [ -3344.7853] [Branch lengths ] . ( 225 sec) [ -3344.7818] [Branch lengths ] . ( 225 sec) [ -3344.7818] [Topology ] . ( 226 sec) [ -3344.7815] [Topology ] . ( 227 sec) [ -3344.7792] [GTR parameters ] . ( 227 sec) [ -3344.7791] [Alpha ][ 0.247052] . ( 227 sec) [ -3344.7791] [Topology ] . ( 227 sec) [ -3344.7789] [Topology ] . ( 228 sec) [ -3344.7789] [GTR parameters ] . ( 228 sec) [ -3344.7789] [Alpha ][ 0.247299] . Checking for NNIs, optimizing five branches... . ( 232 sec) [ -3344.7768] [Topology ] . Checking for NNIs, optimizing five branches... . ( 237 sec) [ -3344.7767] [Topology ] . Checking for NNIs, optimizing five branches... . ( 241 sec) [ -3344.7766] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3344.776568. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -10863.6834] [GTR parameters ] . ( 0 sec) [ -10679.8780] [Alpha ][ 0.500960] . ( 1 sec) [ -10588.8205] [ 1021] [depth= 6] . ( 1 sec) [ -10200.0883] [ 995] [depth= 11] . ( 1 sec) [ -10186.6079] [ 992] [depth= 1] . ( 1 sec) [ -10178.3730] [ 992] [depth= 3] . ( 1 sec) [ -10145.8730] [ 988] [depth= 1] . ( 1 sec) [ -10104.3961] [ 988] [depth= 2] . ( 1 sec) [ -9745.7619] [ 981] [depth= 4] . ( 1 sec) [ -9725.4900] [ 981] [depth= 5] . ( 1 sec) [ -9714.9545] [ 977] [depth= 12] . ( 1 sec) [ -9689.0090] [ 977] [depth= 2] . ( 1 sec) [ -9528.2568] [ 972] [depth= 2] . ( 1 sec) [ -9269.8296] [ 972] [depth= 1] . ( 1 sec) [ -9239.6687] [ 948] [depth= 2] . ( 1 sec) [ -8989.3257] [ 948] [depth= 4] . ( 1 sec) [ -8834.0154] [ 922] [depth= 6] . ( 1 sec) [ -8781.1269] [ 918] [depth= 2] . ( 1 sec) [ -8731.8323] [ 917] [depth= 10] . ( 1 sec) [ -8726.6442] [ 917] [depth= 1] . ( 1 sec) [ -8672.4630] [ 914] [depth= 2] . ( 2 sec) [ -8617.9763] [ 901] [depth= 9] . ( 2 sec) [ -8602.0539] [ 901] [depth= 2] . ( 2 sec) [ -8600.9930] [ 901] [depth= 20] . ( 2 sec) [ -8596.4718] [ 901] [depth= 18] . ( 2 sec) [ -8596.1098] [ 901] [depth= 7] . ( 2 sec) [ -8527.9871] [ 890] [depth= 4] . ( 2 sec) [ -8507.8282] [ 887] [depth= 3] . ( 2 sec) [ -8506.0672] [ 887] [depth= 1] . ( 2 sec) [ -8477.4883] [ 886] [depth= 1] . ( 2 sec) [ -8452.7983] [ 883] [depth= 9] . ( 2 sec) [ -8423.0863] [ 883] [depth= 7] . ( 2 sec) [ -8173.5261] [ 863] [depth= 5] . ( 2 sec) [ -8150.8360] [ 864] [depth= 1] . ( 2 sec) [ -8147.8428] [ 864] [depth= 2] . ( 2 sec) [ -8023.8353] [ 838] [depth= 9] . ( 3 sec) [ -8003.1150] [ 839] [depth= 2] . ( 3 sec) [ -7882.8452] [ 819] [depth= 12] . ( 3 sec) [ -7866.2991] [ 815] [depth= 10] . ( 3 sec) [ -7610.3445] [ 782] [depth= 8] . ( 3 sec) [ -7591.6885] [ 782] [depth= 20] . ( 3 sec) [ -7591.3995] [ 782] [depth= 2] . ( 3 sec) [ -7558.2721] [ 777] [depth= 21] . ( 3 sec) [ -7552.6096] [ 777] [depth= 1] . ( 3 sec) [ -7499.5361] [ 759] [depth= 16] . ( 3 sec) [ -7491.9333] [ 759] [depth= 1] . ( 3 sec) [ -7417.2384] [ 747] [depth= 9] . ( 3 sec) [ -7400.7246] [ 747] [depth= 2] . ( 3 sec) [ -7350.1828] [ 744] [depth= 20] . ( 3 sec) [ -7318.4789] [ 740] [depth= 24] . ( 3 sec) [ -7314.8360] [ 740] [depth= 3] . ( 3 sec) [ -7306.6031] [ 740] [depth= 3] . ( 3 sec) [ -7233.2452] [ 728] [depth= 10] . ( 4 sec) [ -7228.5694] [ 728] [depth= 4] . ( 4 sec) [ -7171.4504] [ 716] [depth= 13] . ( 4 sec) [ -7128.1578] [ 711] [depth= 3] . ( 4 sec) [ -7125.0266] [ 711] [depth= 2] . ( 4 sec) [ -7059.1515] [ 699] [depth= 1] . ( 4 sec) [ -7049.0606] [ 699] [depth= 1] . ( 4 sec) [ -6857.7772] [ 692] [depth= 7] . ( 4 sec) [ -6806.4859] [ 692] [depth= 8] . ( 4 sec) [ -6697.6561] [ 686] [depth= 5] . ( 4 sec) [ -6687.7578] [ 686] [depth= 2] . ( 4 sec) [ -6671.2970] [ 678] [depth= 3] . ( 4 sec) [ -6645.6328] [ 676] [depth= 15] . ( 4 sec) [ -6543.8311] [ 675] [depth= 3] . ( 4 sec) [ -6540.6470] [ 675] [depth= 1] . ( 4 sec) [ -6540.6348] [ 675] [depth= 2] . ( 4 sec) [ -6535.5782] [ 675] [depth= 4] . ( 4 sec) [ -6535.5566] [ 675] [depth= 5] . ( 5 sec) [ -6529.1086] [ 675] [depth= 2] . ( 5 sec) [ -6522.3909] [ 674] [depth= 14] . ( 5 sec) [ -6511.7358] [ 674] [depth= 5] . ( 5 sec) [ -6510.5789] [ 674] [depth= 2] . ( 5 sec) [ -6510.0941] [ 674] [depth= 1] . ( 5 sec) [ -6509.8517] [ 674] [depth= 1] . ( 5 sec) [ -6456.1762] [ 674] [depth= 1] . ( 5 sec) [ -6426.1471] [ 668] [depth= 7] . ( 5 sec) [ -6406.2500] [ 671] [depth= 2] . ( 5 sec) [ -6325.3913] [ 656] [depth= 18] . ( 5 sec) [ -6321.7444] [ 656] [depth= 3] . ( 5 sec) [ -6256.3536] [ 642] [depth= 5] . ( 5 sec) [ -6219.0491] [ 641] [depth= 12] . ( 5 sec) [ -6217.6935] [ 641] [depth= 8] . ( 5 sec) [ -6183.5774] [ 631] [depth= 3] . ( 6 sec) [ -6183.2943] [ 631] [depth= 7] . ( 6 sec) [ -6181.2670] [ 631] [depth= 1] . ( 6 sec) [ -6174.1218] [ 628] [depth= 2] . ( 6 sec) [ -6172.9333] [ 627] [depth= 2] . ( 6 sec) [ -6097.9776] [ 609] [depth= 12] . ( 6 sec) [ -6072.7129] [ 605] [depth= 1] . ( 6 sec) [ -6057.4942] [ 605] [depth= 1] . ( 6 sec) [ -5992.5041] [ 595] [depth= 5] . ( 6 sec) [ -5986.3884] [ 595] [depth= 1] . ( 6 sec) [ -5930.5270] [ 595] [depth= 3] . ( 6 sec) [ -5929.9154] [ 595] [depth= 1] . ( 6 sec) [ -5929.6011] [ 595] [depth= 3] . ( 6 sec) [ -5916.6608] [ 595] [depth= 1] . ( 6 sec) [ -5908.2358] [ 595] [depth= 10] . ( 6 sec) [ -5871.1678] [ 595] [depth= 1] . ( 6 sec) [ -5826.6428] [ 587] [depth= 7] . ( 7 sec) [ -5768.5596] [ 587] [depth= 4] . ( 7 sec) [ -5761.4536] [ 585] [depth= 9] . ( 7 sec) [ -5749.7986] [ 585] [depth= 1] . ( 7 sec) [ -5741.6897] [ 582] [depth= 6] . ( 7 sec) [ -5740.6422] [ 582] [depth= 1] . ( 7 sec) [ -5733.1553] [ 582] [depth= 1] . ( 7 sec) [ -5711.3169] [ 577] [depth= 5] . ( 7 sec) [ -5706.8199] [ 577] [depth= 4] . ( 7 sec) [ -5581.2236] [ 552] [depth= 6] . ( 7 sec) [ -5572.4660] [ 551] [depth= 5] . ( 7 sec) [ -5571.8803] [ 551] [depth= 5] . ( 7 sec) [ -5571.6608] [ 551] [depth= 4] . ( 7 sec) [ -5542.4651] [ 546] [depth= 7] . ( 7 sec) [ -5524.3216] [ 546] [depth= 3] . ( 7 sec) [ -5463.5780] [ 541] [depth= 9] . ( 7 sec) [ -5453.1296] [ 541] [depth= 1] . ( 7 sec) [ -5377.8781] [ 536] [depth= 2] . ( 7 sec) [ -5318.9307] [ 536] [depth= 1] . ( 8 sec) [ -5153.0540] [ 520] [depth= 16] . ( 8 sec) [ -5152.2825] [ 520] [depth= 1] . ( 8 sec) [ -5061.6244] [ 499] [depth= 8] . ( 8 sec) [ -5050.8911] [ 499] [depth= 1] . ( 8 sec) [ -5049.0113] [ 499] [depth= 2] . ( 8 sec) [ -4895.8001] [ 503] [depth= 16] . ( 8 sec) [ -4878.1617] [ 501] [depth= 16] . ( 8 sec) [ -4874.3608] [ 501] [depth= 1] . ( 8 sec) [ -4861.3188] [ 504] [depth= 5] . ( 8 sec) [ -4348.9022] [ 499] [depth= 19] . ( 8 sec) [ -4348.0307] [ 499] [depth= 1] . ( 8 sec) [ -4342.9852] [ 493] [depth= 15] . ( 8 sec) [ -4336.3465] [ 493] [depth= 21] . ( 8 sec) [ -4334.5707] [ 492] [depth= 9] . ( 9 sec) [ -4331.0841] [ 492] [depth= 5] . ( 9 sec) [ -4290.5593] [ 484] [depth= 1] . ( 9 sec) [ -4290.0658] [ 483] [depth= 5] . ( 9 sec) [ -4242.9903] [ 465] [depth= 5] . ( 9 sec) [ -4232.7304] [ 465] [depth= 1] . ( 9 sec) [ -4111.9074] [ 465] [depth= 2] . ( 9 sec) [ -4091.1773] [ 462] [depth= 6] . ( 9 sec) [ -4090.3855] [ 462] [depth= 3] . ( 9 sec) [ -4088.3911] [ 462] [depth= 15] . ( 9 sec) [ -4086.2287] [ 462] [depth= 1] . ( 9 sec) [ -3978.2212] [ 436] [depth= 16] . ( 9 sec) [ -3973.1483] [ 436] [depth= 1] . ( 10 sec) [ -3971.8989] [ 436] [depth= 2] . ( 10 sec) [ -3971.8818] [ 436] [depth= 2] . ( 10 sec) [ -3969.0502] [ 434] [depth= 5] . ( 10 sec) [ -3968.4967] [ 434] [depth= 1] . ( 10 sec) [ -3968.2817] [ 434] [depth= 6] . ( 10 sec) [ -3921.8131] [ 419] [depth= 15] . ( 10 sec) [ -3861.5641] [ 405] [depth= 9] . ( 10 sec) [ -3860.5235] [ 407] [depth= 9] . ( 10 sec) [ -3858.7849] [ 407] [depth= 5] . ( 10 sec) [ -3855.0466] [ 407] [depth= 1] . ( 10 sec) [ -3853.7032] [ 407] [depth= 1] . ( 11 sec) [ -3853.6798] [ 407] [depth= 21] . ( 11 sec) [ -3853.5978] [ 407] [depth= 2] . ( 11 sec) [ -3853.5809] [ 407] [depth= 1] . ( 11 sec) [ -3847.1221] [ 407] [depth= 5] . ( 11 sec) [ -3827.2501] [ 407] [depth= 4] . ( 11 sec) [ -3827.2033] [ 407] [depth= 1] . ( 11 sec) [ -3827.1837] [ 407] [depth= 2] . ( 11 sec) [ -3815.7547] [ 407] [depth= 2] . ( 11 sec) [ -3815.5460] [ 407] [depth= 1] . ( 11 sec) [ -3815.0499] [ 407] [depth= 2] . ( 12 sec) [ -3814.8123] [ 407] [depth= 1] . ( 12 sec) [ -3812.9165] [ 407] [depth= 1] . ( 12 sec) [ -3811.1884] [ 407] [depth= 4] . ( 12 sec) [ -3807.3749] [ 405] [depth= 11] . ( 12 sec) [ -3807.3632] [ 405] [depth= 6] . ( 12 sec) [ -3807.2856] [ 405] [depth= 12] . ( 12 sec) [ -3806.9311] [ 405] [depth= 9] . ( 12 sec) [ -3805.9464] [ 405] [depth= 3] . ( 12 sec) [ -3805.2693] [ 405] [depth= 2] . ( 13 sec) [ -3804.8515] [ 405] [depth= 7] . ( 13 sec) [ -3802.9006] [ 405] [depth= 2] . ( 13 sec) [ -3799.3208] [ 403] [depth= 9] . ( 13 sec) [ -3799.2915] [ 403] [depth= 1] . ( 13 sec) [ -3799.2777] [ 403] [depth= 6] . ( 13 sec) [ -3798.1201] [ 403] [depth= 3] . ( 13 sec) [ -3794.3427] [ 403] [depth= 4] . ( 13 sec) [ -3794.0155] [ 403] [depth= 2] . ( 13 sec) [ -3775.0086] [ 396] [depth= 4] . ( 13 sec) [ -3774.4600] [ 396] [depth= 3] . ( 13 sec) [ -3773.9224] [ 396] [depth= 6] . ( 13 sec) [ -3772.4596] [ 396] [depth= 12] . ( 14 sec) [ -3772.4479] [ 396] [depth= 5] . ( 14 sec) [ -3772.0897] [ 396] [depth= 1] . ( 14 sec) [ -3771.9962] [ 396] [depth= 4] . ( 14 sec) [ -3709.3301] [ 382] [depth= 10] . ( 14 sec) [ -3709.3084] [ 382] [depth= 3] . ( 14 sec) [ -3646.7244] [Branch lengths ] . ( 17 sec) [ -3608.4730] [GTR parameters ] . ( 18 sec) [ -3591.5231] [Alpha ][ 0.250961] . ( 18 sec) [ -3591.5112] [ 382] [depth= 5] . ( 18 sec) [ -3587.8652] [ 382] [depth= 8] . ( 18 sec) [ -3584.2466] [ 380] [depth= 14] . ( 19 sec) [ -3584.2069] [ 380] [depth= 1] . ( 19 sec) [ -3584.0523] [ 380] [depth= 2] . ( 20 sec) [ -3584.0110] [ 380] [depth= 19] . ( 20 sec) [ -3583.6937] [ 380] [depth= 3] . ( 20 sec) [ -3583.6732] [ 380] [depth= 2] . ( 20 sec) [ -3583.6263] [ 380] [depth= 1] . ( 20 sec) [ -3583.1484] [ 380] [depth= 2] . ( 20 sec) [ -3583.1206] [ 380] [depth= 1] . ( 21 sec) [ -3583.1039] [ 380] [depth= 7] . ( 21 sec) [ -3582.9735] [ 380] [depth= 4] . ( 21 sec) [ -3582.8728] [ 380] [depth= 6] . ( 21 sec) [ -3582.7881] [ 380] [depth= 11] . ( 21 sec) [ -3582.7757] [ 380] [depth= 5] . ( 22 sec) [ -3581.9877] [ 380] [depth= 1] . ( 23 sec) [ -3581.4705] [ 380] [depth= 4] . ( 24 sec) [ -3581.4576] [ 380] [depth= 2] . ( 24 sec) [ -3483.1736] [ 364] [depth= 22] . ( 24 sec) [ -3483.1346] [ 364] [depth= 1] . ( 25 sec) [ -3482.7387] [ 364] [depth= 1] . ( 25 sec) [ -3482.6356] [ 364] [depth= 5] . ( 25 sec) [ -3482.6234] [ 364] [depth= 3] . ( 25 sec) [ -3448.4162] [ 361] [depth= 5] . ( 26 sec) [ -3447.3911] [ 361] [depth= 6] . ( 26 sec) [ -3446.9150] [ 361] [depth= 1] . ( 26 sec) [ -3446.4776] [ 361] [depth= 9] . ( 26 sec) [ -3446.4178] [ 361] [depth= 3] . ( 26 sec) [ -3446.4063] [ 361] [depth= 1] . ( 26 sec) [ -3445.2520] [ 361] [depth= 1] . ( 27 sec) [ -3445.2359] [ 361] [depth= 2] . ( 27 sec) [ -3445.1168] [ 361] [depth= 2] . ( 27 sec) [ -3445.0394] [ 361] [depth= 3] . ( 27 sec) [ -3444.9391] [ 361] [depth= 6] . ( 27 sec) [ -3444.8189] [ 361] [depth= 4] . ( 27 sec) [ -3444.7621] [ 361] [depth= 3] . ( 27 sec) [ -3444.7503] [ 361] [depth= 2] . ( 27 sec) [ -3444.5304] [ 361] [depth= 5] . ( 28 sec) [ -3444.2996] [ 361] [depth= 6] . ( 28 sec) [ -3444.2026] [ 361] [depth= 1] . ( 28 sec) [ -3443.8464] [ 361] [depth= 2] . ( 28 sec) [ -3443.8346] [ 361] [depth= 1] . ( 28 sec) [ -3443.8200] [ 361] [depth= 3] . ( 29 sec) [ -3443.8067] [ 361] [depth= 1] . ( 29 sec) [ -3443.6770] [ 361] [depth= 3] . ( 30 sec) [ -3443.6233] [ 361] [depth= 6] . ( 30 sec) [ -3443.5961] [ 361] [depth= 1] . ( 30 sec) [ -3443.2404] [ 361] [depth= 1] . ( 30 sec) [ -3443.2216] [ 361] [depth= 7] . ( 31 sec) [ -3443.1623] [ 361] [depth= 6] . ( 31 sec) [ -3443.1463] [ 361] [depth= 8] . ( 31 sec) [ -3443.1290] [ 361] [depth= 1] . ( 31 sec) [ -3421.1778] [ 355] [depth= 2] . ( 32 sec) [ -3421.1333] [ 355] [depth= 4] . ( 32 sec) [ -3391.0970] [ 344] [depth= 1] . ( 32 sec) [ -3390.9989] [ 344] [depth= 4] . ( 32 sec) [ -3390.9261] [ 344] [depth= 1] . ( 32 sec) [ -3390.7412] [ 344] [depth= 4] . ( 32 sec) [ -3390.3477] [ 344] [depth= 5] . ( 32 sec) [ -3390.3312] [ 344] [depth= 6] . ( 33 sec) [ -3390.3208] [ 344] [depth= 2] . ( 33 sec) [ -3390.3029] [ 344] [depth= 1] . ( 33 sec) [ -3390.2170] [ 344] [depth= 15] . ( 33 sec) [ -3388.0643] [ 344] [depth= 1] . ( 34 sec) [ -3388.0443] [ 344] [depth= 3] . ( 34 sec) [ -3388.0328] [ 344] [depth= 2] . ( 34 sec) [ -3387.9969] [ 344] [depth= 4] . ( 35 sec) [ -3383.2951] [ 340] [depth= 18] . ( 35 sec) [ -3382.8665] [ 340] [depth= 14] . ( 36 sec) [ -3377.9888] [ 339] [depth= 11] . ( 36 sec) [ -3377.7063] [ 339] [depth= 5] . ( 37 sec) [ -3377.6929] [ 339] [depth= 11] . ( 38 sec) [ -3377.6572] [ 339] [depth= 5] . ( 39 sec) [ -3377.4496] [ 339] [depth= 2] . ( 39 sec) [ -3377.4079] [ 339] [depth= 3] . ( 40 sec) [ -3377.3858] [ 339] [depth= 4] . ( 40 sec) [ -3377.2647] [ 339] [depth= 2] . ( 42 sec) [ -3377.2434] [ 339] [depth= 5] . ( 46 sec) [ -3377.0168] [ 339] [depth= 15] . ( 46 sec) [ -3376.9982] [ 339] [depth= 1] . ( 47 sec) [ -3375.9367] [ 339] [depth= 14] . ( 48 sec) [ -3373.6203] [ 337] [depth= 11] . ( 48 sec) [ -3373.5725] [ 337] [depth= 6] . ( 48 sec) [ -3373.5299] [ 337] [depth= 6] . ( 48 sec) [ -3373.5105] [ 337] [depth= 6] . ( 48 sec) [ -3373.4864] [ 337] [depth= 8] . ( 49 sec) [ -3373.4546] [ 337] [depth= 5] . ( 49 sec) [ -3369.2707] [Branch lengths ] . ( 49 sec) [ -3369.2705] [GTR parameters ] . ( 49 sec) [ -3369.1978] [Alpha ][ 0.235248] . ( 50 sec) [ -3369.1877] [ 337] [depth= 2] . ( 50 sec) [ -3367.9211] [ 337] [depth= 6] . ( 50 sec) [ -3367.7145] [ 337] [depth= 1] . ( 50 sec) [ -3367.6671] [ 337] [depth= 3] . ( 51 sec) [ -3366.8281] [ 338] [depth= 1] . ( 51 sec) [ -3364.8645] [ 337] [depth= 4] . ( 51 sec) [ -3364.8214] [ 337] [depth= 7] . ( 53 sec) [ -3364.7416] [ 337] [depth= 3] . ( 54 sec) [ -3364.6544] [ 337] [depth= 9] . ( 55 sec) [ -3364.5798] [ 337] [depth= 2] . ( 56 sec) [ -3364.5632] [ 337] [depth= 4] . ( 56 sec) [ -3364.5068] [ 337] [depth= 4] . ( 59 sec) [ -3364.4801] [ 337] [depth= 3] . ( 59 sec) [ -3364.4545] [ 337] [depth= 1] . ( 60 sec) [ -3364.4291] [ 337] [depth= 6] . ( 63 sec) [ -3364.4162] [ 337] [depth= 8] . ( 63 sec) [ -3364.4033] [ 337] [depth= 2] . ( 65 sec) [ -3364.3908] [ 337] [depth= 1] . ( 67 sec) [ -3364.3617] [ 337] [depth= 1] . ( 69 sec) [ -3364.2946] [ 337] [depth= 2] . ( 79 sec) [ -3363.4308] [ 337] [depth= 4] . ( 79 sec) [ -3362.6975] [ 337] [depth= 1] . ( 79 sec) [ -3362.6132] [ 336] [depth= 1] . ( 79 sec) [ -3362.5944] [ 339] [depth= 1] . ( 80 sec) [ -3362.4855] [ 337] [depth= 1] . ( 81 sec) [ -3362.4725] [ 337] [depth= 7] . ( 82 sec) [ -3362.2879] [ 337] [depth= 10] . ( 87 sec) [ -3352.6718] [ 337] [depth= 18] . ( 90 sec) [ -3352.6426] [ 337] [depth= 1] . ( 90 sec) [ -3352.3839] [ 337] [depth= 1] . ( 91 sec) [ -3350.0991] [ 337] [depth= 6] . ( 92 sec) [ -3349.6896] [ 337] [depth= 9] . ( 94 sec) [ -3349.6632] [ 337] [depth= 11] . ( 94 sec) [ -3349.5839] [ 337] [depth= 9] . ( 94 sec) [ -3349.5697] [ 337] [depth= 9] . ( 96 sec) [ -3349.5555] [ 337] [depth= 8] . ( 97 sec) [ -3349.4247] [ 337] [depth= 1] . ( 97 sec) [ -3349.3817] [ 337] [depth= 2] . ( 100 sec) [ -3346.5291] [Branch lengths ] . ( 100 sec) [ -3346.5290] [GTR parameters ] . ( 101 sec) [ -3346.5279] [Alpha ][ 0.237139] . ( 104 sec) [ -3346.5172] [ 337] [depth= 2] . ( 113 sec) [ -3346.4602] [ 337] [depth= 2] . ( 115 sec) [ -3346.4241] [ 337] [depth= 1] . ( 115 sec) [ -3346.4052] [ 337] [depth= 7] . ( 117 sec) [ -3346.3745] [ 337] [depth= 2] . ( 123 sec) [ -3346.2449] [ 337] [depth= 3] . ( 137 sec) [ -3346.2174] [ 337] [depth= 1] . ( 165 sec) [ -3346.0127] [Branch lengths ] . ( 166 sec) [ -3345.9477] [GTR parameters ] . ( 166 sec) [ -3345.9467] [Alpha ][ 0.235282] . ( 212 sec) [ -3345.9138] [Branch lengths ] . ( 212 sec) [ -3345.9138] [Topology ] . ( 213 sec) [ -3345.9111] [Topology ] . ( 214 sec) [ -3345.9101] [Topology ] . ( 215 sec) [ -3345.8993] [GTR parameters ] . ( 215 sec) [ -3345.8985] [Alpha ][ 0.233636] . ( 215 sec) [ -3345.8985] [Topology ] . ( 216 sec) [ -3345.8982] [Topology ] . ( 217 sec) [ -3345.8978] [GTR parameters ] . ( 217 sec) [ -3345.8978] [Alpha ][ 0.233402] . Checking for NNIs, optimizing five branches... . ( 222 sec) [ -3345.8959] [Topology ] . Checking for NNIs, optimizing five branches... . ( 227 sec) [ -3345.8887] [Topology ] . Checking for NNIs, optimizing five branches... . ( 232 sec) [ -3345.8871] [Topology ] . Checking for NNIs, optimizing five branches... . ( 237 sec) [ -3345.8861] [Topology ] . Checking for NNIs, optimizing five branches... . ( 242 sec) [ -3345.8860] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3345.885956. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 2 sec) [ -3429.4082] [GTR parameters ] . ( 2 sec) [ -3418.4507] [Alpha ][ 0.500960] . ( 2 sec) [ -3418.4507] [Topology ] . ( 4 sec) [ -3383.7580] [Topology ] . ( 4 sec) [ -3375.4885] [Topology ] . ( 5 sec) [ -3373.8574] [Topology ] . ( 6 sec) [ -3375.5743] [Topology ] . Moving backward . ( 6 sec) [ -3372.6560] [Topology ] . ( 7 sec) [ -3373.0305] [Topology ] . Moving backward . ( 7 sec) [ -3371.8967] [Topology ] . ( 8 sec) [ -3371.9248] [Topology ] . Moving backward . ( 8 sec) [ -3371.5939] [Topology ] . ( 10 sec) [ -3371.1516] [GTR parameters ] . ( 10 sec) [ -3365.0485] [Alpha ][ 0.259276] . ( 10 sec) [ -3365.0485] [Topology ] . ( 11 sec) [ -3364.5439] [Topology ] . ( 11 sec) [ -3364.9588] [Topology ] . Moving backward . ( 11 sec) [ -3363.9789] [Topology ] . ( 12 sec) [ -3364.1521] [Topology ] . Moving backward . ( 12 sec) [ -3363.9097] [Topology ] . ( 13 sec) [ -3363.9390] [Topology ] . Moving backward . ( 13 sec) [ -3363.8773] [Topology ] . ( 14 sec) [ -3363.9045] [Topology ] . Moving backward . ( 14 sec) [ -3363.8521] [Topology ] . Checking for NNIs, optimizing five branches... . ( 20 sec) [ -3363.8103] [Topology ] . ( 21 sec) [ -3363.6958] [GTR parameters ] . ( 21 sec) [ -3363.6179] [Alpha ][ 0.242419] . ( 21 sec) [ -3363.6179] [Topology ] . ( 21 sec) [ -3363.5719] [Topology ] . ( 22 sec) [ -3363.5643] [Topology ] . ( 23 sec) [ -3363.6368] [Topology ] . Moving backward . ( 23 sec) [ -3363.5567] [Topology ] . ( 23 sec) [ -3363.5928] [Topology ] . Moving backward . ( 24 sec) [ -3363.5488] [Topology ] . ( 24 sec) [ -3363.5884] [Topology ] . Moving backward . ( 24 sec) [ -3363.5425] [Topology ] . ( 25 sec) [ -3363.5619] [Topology ] . Checking for NNIs, optimizing five branches... . ( 30 sec) [ -3363.5617] [Topology ] . ( 30 sec) [ -3363.5577] [GTR parameters ] . ( 30 sec) [ -3363.5548] [Alpha ][ 0.239253] . ( 30 sec) [ -3363.5548] [Topology ] . ( 31 sec) [ -3363.9067] [Topology ] . Moving backward . ( 31 sec) [ -3363.5441] [Topology ] . ( 32 sec) [ -3363.6769] [Topology ] . Moving backward . ( 32 sec) [ -3363.5300] [Topology ] . ( 32 sec) [ -3363.7362] [Topology ] . Moving backward . ( 33 sec) [ -3363.5250] [Topology ] . ( 33 sec) [ -3363.6144] [Topology ] . Moving backward . ( 33 sec) [ -3363.5137] [Topology ] . ( 34 sec) [ -3363.6283] [Topology ] . Moving backward . Checking for NNIs, optimizing five branches... . ( 39 sec) [ -3363.4943] [Topology ] . ( 39 sec) [ -3363.4941] [GTR parameters ] . ( 39 sec) [ -3363.4939] [Alpha ][ 0.238325] . ( 39 sec) [ -3363.4939] [Topology ] . ( 40 sec) [ -3363.4851] [Topology ] . ( 41 sec) [ -3363.4793] [Topology ] . ( 41 sec) [ -3363.4779] [Topology ] . ( 42 sec) [ -3363.4819] [Topology ] . Moving backward . ( 42 sec) [ -3363.4758] [Topology ] . ( 43 sec) [ -3363.4760] [Topology ] . Checking for NNIs, optimizing five branches... . ( 47 sec) [ -3363.4729] [Topology ] . ( 48 sec) [ -3363.4729] [GTR parameters ] . ( 48 sec) [ -3363.4729] [Alpha ][ 0.238087] . ( 48 sec) [ -3363.4729] [Topology ] . ( 49 sec) [ -3363.4717] [Topology ] . ( 49 sec) [ -3363.4707] [Topology ] . ( 50 sec) [ -3363.4697] [Topology ] . ( 51 sec) [ -3363.4687] [Topology ] . Checking for NNIs, optimizing five branches... . ( 56 sec) [ -3363.4497] [Topology ] . ( 56 sec) [ -3363.4497] [GTR parameters ] . ( 56 sec) [ -3363.4497] [Alpha ][ 0.238087] . ( 56 sec) [ -3363.4497] [Topology ] . ( 56 sec) [ -3363.4489] [Topology ] . Checking for NNIs, optimizing five branches... . ( 61 sec) [ -3363.4487] [Topology ] . Checking for NNIs, optimizing five branches... . ( 66 sec) [ -3363.4294] [Topology ] . Checking for NNIs, optimizing five branches... . ( 71 sec) [ -3363.4235] [Topology ] . Checking for NNIs, optimizing five branches... . ( 76 sec) [ -3363.4219] [Topology ] . Checking for NNIs, optimizing five branches... . ( 81 sec) [ -3363.4203] [Topology ] . Checking for NNIs, optimizing five branches... . ( 85 sec) [ -3363.3839] [Topology ] . Checking for NNIs, optimizing five branches... . ( 90 sec) [ -3363.3837] [Topology ] . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 97 sec) [ -3429.4082] [GTR parameters ] . ( 97 sec) [ -3418.4507] [Alpha ][ 0.500960] . ( 97 sec) [ -3418.0700] [ 336] [depth= 1] . ( 97 sec) [ -3417.9931] [ 336] [depth= 1] . ( 98 sec) [ -3417.0232] [ 340] [depth= 1] . ( 98 sec) [ -3414.9815] [ 340] [depth= 1] . ( 98 sec) [ -3414.6607] [ 340] [depth= 1] . ( 98 sec) [ -3413.6439] [ 340] [depth= 1] . ( 99 sec) [ -3413.6013] [ 340] [depth= 1] . ( 99 sec) [ -3413.5823] [ 340] [depth= 2] . ( 99 sec) [ -3413.5625] [ 340] [depth= 2] . ( 100 sec) [ -3413.4774] [ 340] [depth= 2] . ( 100 sec) [ -3413.2737] [ 340] [depth= 3] . ( 100 sec) [ -3413.1917] [ 340] [depth= 1] . ( 100 sec) [ -3412.8933] [ 340] [depth= 1] . ( 101 sec) [ -3412.5965] [ 340] [depth= 1] . ( 101 sec) [ -3412.5584] [ 340] [depth= 3] . ( 101 sec) [ -3410.8766] [ 340] [depth= 8] . ( 101 sec) [ -3406.7619] [ 339] [depth= 8] . ( 101 sec) [ -3406.6175] [ 339] [depth= 1] . ( 101 sec) [ -3402.2669] [ 335] [depth= 1] . ( 101 sec) [ -3399.0047] [ 333] [depth= 1] . ( 102 sec) [ -3398.9267] [ 333] [depth= 2] . ( 104 sec) [ -3397.9709] [ 333] [depth= 1] . ( 104 sec) [ -3397.1404] [ 333] [depth= 1] . ( 105 sec) [ -3397.1210] [ 333] [depth= 1] . ( 105 sec) [ -3396.9412] [ 333] [depth= 1] . ( 106 sec) [ -3396.8891] [ 333] [depth= 1] . ( 106 sec) [ -3396.8753] [ 333] [depth= 2] . ( 106 sec) [ -3396.1252] [ 333] [depth= 1] . ( 106 sec) [ -3396.0723] [ 333] [depth= 1] . ( 106 sec) [ -3395.9211] [ 333] [depth= 3] . ( 106 sec) [ -3395.8836] [ 333] [depth= 1] . ( 107 sec) [ -3395.8563] [ 333] [depth= 1] . ( 107 sec) [ -3395.8398] [ 333] [depth= 9] . ( 107 sec) [ -3395.8258] [ 333] [depth= 1] . ( 107 sec) [ -3395.7835] [ 333] [depth= 6] . ( 107 sec) [ -3395.2384] [ 333] [depth= 1] . ( 107 sec) [ -3395.1397] [ 333] [depth= 4] . ( 107 sec) [ -3394.7715] [ 333] [depth= 1] . ( 108 sec) [ -3394.5784] [ 333] [depth= 2] . ( 108 sec) [ -3394.5632] [ 333] [depth= 1] . ( 108 sec) [ -3394.5504] [ 333] [depth= 3] . ( 109 sec) [ -3394.5376] [ 333] [depth= 2] . ( 110 sec) [ -3386.5760] [ 332] [depth= 4] . ( 111 sec) [ -3386.5168] [ 333] [depth= 1] . ( 111 sec) [ -3381.5448] [ 333] [depth= 2] . ( 111 sec) [ -3381.3991] [ 333] [depth= 1] . ( 112 sec) [ -3380.8694] [ 332] [depth= 1] . ( 112 sec) [ -3378.2572] [ 331] [depth= 1] . ( 113 sec) [ -3377.5295] [ 331] [depth= 1] . ( 113 sec) [ -3376.7550] [ 331] [depth= 1] . ( 113 sec) [ -3376.0843] [ 332] [depth= 5] . ( 114 sec) [ -3376.0700] [ 332] [depth= 2] . ( 114 sec) [ -3375.9891] [ 332] [depth= 1] . ( 114 sec) [ -3375.6208] [ 332] [depth= 4] . ( 114 sec) [ -3375.3710] [ 332] [depth= 1] . ( 114 sec) [ -3374.9783] [ 332] [depth= 1] . ( 114 sec) [ -3373.1937] [ 332] [depth= 4] . ( 114 sec) [ -3372.6258] [ 332] [depth= 1] . ( 114 sec) [ -3372.3898] [ 332] [depth= 1] . ( 114 sec) [ -3372.1519] [ 332] [depth= 2] . ( 115 sec) [ -3371.9848] [ 332] [depth= 4] . ( 115 sec) [ -3371.7360] [ 332] [depth= 3] . ( 115 sec) [ -3371.7198] [ 332] [depth= 4] . ( 116 sec) [ -3371.6999] [ 332] [depth= 1] . ( 116 sec) [ -3371.5829] [ 332] [depth= 3] . ( 116 sec) [ -3371.4835] [ 332] [depth= 3] . ( 118 sec) [ -3368.4015] [ 331] [depth= 1] . ( 119 sec) [ -3368.0489] [ 331] [depth= 3] . ( 119 sec) [ -3367.9113] [ 331] [depth= 6] . ( 119 sec) [ -3367.7666] [ 331] [depth= 4] . ( 119 sec) [ -3367.7274] [ 331] [depth= 2] . ( 119 sec) [ -3367.6900] [ 331] [depth= 2] . ( 119 sec) [ -3367.6727] [ 331] [depth= 3] . ( 119 sec) [ -3367.6524] [ 331] [depth= 1] . ( 119 sec) [ -3364.9507] [ 331] [depth= 1] . ( 119 sec) [ -3364.8801] [ 331] [depth= 6] . ( 119 sec) [ -3364.8181] [ 331] [depth= 1] . ( 119 sec) [ -3364.7366] [ 331] [depth= 3] . ( 121 sec) [ -3361.9486] [ 330] [depth= 1] . ( 121 sec) [ -3361.9264] [ 330] [depth= 5] . ( 122 sec) [ -3361.9098] [ 330] [depth= 2] . ( 122 sec) [ -3360.4111] [ 330] [depth= 1] . ( 123 sec) [ -3360.3954] [ 330] [depth= 5] . ( 123 sec) [ -3359.6347] [ 330] [depth= 1] . ( 123 sec) [ -3359.5920] [ 330] [depth= 3] . ( 123 sec) [ -3359.1840] [ 330] [depth= 1] . ( 124 sec) [ -3359.1667] [ 330] [depth= 4] . ( 124 sec) [ -3359.1552] [ 330] [depth= 1] . ( 124 sec) [ -3359.1345] [ 330] [depth= 1] . ( 137 sec) [ -3351.5540] [Branch lengths ] . ( 137 sec) [ -3351.3432] [GTR parameters ] . ( 137 sec) [ -3346.1094] [Alpha ][ 0.269884] . ( 139 sec) [ -3346.0945] [ 330] [depth= 1] . ( 139 sec) [ -3346.0798] [ 330] [depth= 3] . ( 142 sec) [ -3345.9716] [ 330] [depth= 2] . ( 143 sec) [ -3345.9603] [ 330] [depth= 2] . ( 145 sec) [ -3345.9380] [ 330] [depth= 1] . ( 199 sec) [ -3345.1355] [Branch lengths ] . ( 199 sec) [ -3345.0529] [GTR parameters ] . ( 199 sec) [ -3344.9773] [Alpha ][ 0.252061] . ( 204 sec) [ -3344.9610] [ 330] [depth= 2] . ( 259 sec) [ -3344.8643] [Branch lengths ] . ( 259 sec) [ -3344.8610] [GTR parameters ] . ( 259 sec) [ -3344.8585] [Alpha ][ 0.248914] . ( 303 sec) [ -3344.8441] [Branch lengths ] . ( 303 sec) [ -3344.8441] [Topology ] . ( 304 sec) [ -3344.7927] [Topology ] . ( 304 sec) [ -3344.7677] [Topology ] . ( 305 sec) [ -3344.7626] [Topology ] . ( 305 sec) [ -3344.7608] [Topology ] . ( 306 sec) [ -3344.7602] [Topology ] . ( 306 sec) [ -3344.7595] [GTR parameters ] . ( 306 sec) [ -3344.7589] [Alpha ][ 0.247340] . ( 307 sec) [ -3344.7589] [Topology ] . ( 307 sec) [ -3344.7585] [Topology ] . ( 307 sec) [ -3344.7584] [GTR parameters ] . ( 307 sec) [ -3344.7584] [Alpha ][ 0.247092] . Checking for NNIs, optimizing five branches... . ( 312 sec) [ -3344.7583] [Topology ] . Checking for NNIs, optimizing five branches... . ( 317 sec) [ -3344.7582] [Topology ] . Checking for NNIs, optimizing five branches... . ( 321 sec) [ -3344.7500] [Topology ] . Checking for NNIs, optimizing five branches... . ( 326 sec) [ -3344.7479] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -3363.383651 . Log likelihood obtained after SPR moves : -3344.747935 . Log likelihood of the current tree: -3344.747935. . Printing the most likely tree in file 'nucleic_M2716_79x1252_2006.phy_phyml_tree.txt'... . Best log likelihood : -3344.747935 . Time used 0h5m31s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1827.11user 0.00system 33:58.77elapsed 89%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps