.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data11.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . Optimise tree topology : yes . Tree topology search : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : yes . Number of random starting trees : 5 . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 459 patterns found. (out of a total of 500 sites) . 37 sites without polymorphism (7.40%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -23996.7609] [GTR parameters ] . ( 2 sec) [ -23502.9010] [Alpha ][ 0.500960] . ( 2 sec) [ -23291.0918] [ 5536] [depth= 8] . ( 2 sec) [ -22661.0551] [ 5534] [depth= 13] . ( 2 sec) [ -22270.5115] [ 5510] [depth= 5] . ( 2 sec) [ -22003.7556] [ 5470] [depth= 7] . ( 2 sec) [ -21939.1252] [ 5335] [depth= 3] . ( 2 sec) [ -21643.4961] [ 5307] [depth= 7] . ( 2 sec) [ -21456.6438] [ 5263] [depth= 9] . ( 2 sec) [ -20959.8267] [ 5248] [depth= 1] . ( 2 sec) [ -20343.1518] [ 5173] [depth= 14] . ( 2 sec) [ -19800.7921] [ 5071] [depth= 5] . ( 2 sec) [ -19259.4145] [ 4916] [depth= 1] . ( 2 sec) [ -19169.3161] [ 4841] [depth= 5] . ( 2 sec) [ -19134.5981] [ 4837] [depth= 2] . ( 2 sec) [ -19087.5111] [ 4838] [depth= 1] . ( 2 sec) [ -19045.5210] [ 4802] [depth= 5] . ( 2 sec) [ -18989.5508] [ 4783] [depth= 3] . ( 2 sec) [ -18946.8338] [ 4762] [depth= 9] . ( 2 sec) [ -18815.3154] [ 4746] [depth= 4] . ( 2 sec) [ -18696.7173] [ 4669] [depth= 3] . ( 3 sec) [ -18581.2349] [ 4633] [depth= 9] . ( 3 sec) [ -18555.1364] [ 4625] [depth= 1] . ( 3 sec) [ -18548.5691] [ 4563] [depth= 3] . ( 3 sec) [ -18419.8734] [ 4552] [depth= 5] . ( 3 sec) [ -18224.4443] [ 4555] [depth= 1] . ( 3 sec) [ -17967.3474] [ 4491] [depth= 1] . ( 3 sec) [ -17954.1865] [ 4468] [depth= 1] . ( 3 sec) [ -17702.6736] [ 4375] [depth= 3] . ( 3 sec) [ -17524.7361] [ 4294] [depth= 13] . ( 3 sec) [ -17423.6109] [ 4281] [depth= 1] . ( 3 sec) [ -16940.3748] [ 4199] [depth= 2] . ( 3 sec) [ -16586.5973] [ 4103] [depth= 5] . ( 3 sec) [ -16222.9018] [ 4009] [depth= 7] . ( 3 sec) [ -16131.0362] [ 4004] [depth= 1] . ( 3 sec) [ -16005.5347] [ 3960] [depth= 1] . ( 3 sec) [ -15977.5842] [ 3961] [depth= 1] . ( 4 sec) [ -15817.7024] [ 3889] [depth= 1] . ( 4 sec) [ -15813.9821] [ 3888] [depth= 1] . ( 4 sec) [ -15751.6473] [ 3890] [depth= 1] . ( 4 sec) [ -15402.8788] [ 3857] [depth= 13] . ( 4 sec) [ -15295.7100] [ 3843] [depth= 1] . ( 4 sec) [ -15229.8586] [ 3809] [depth= 5] . ( 4 sec) [ -15205.4185] [ 3745] [depth= 9] . ( 4 sec) [ -15057.1098] [ 3713] [depth= 6] . ( 4 sec) [ -14986.0045] [ 3709] [depth= 2] . ( 4 sec) [ -14648.5291] [ 3694] [depth= 2] . ( 4 sec) [ -14573.7667] [ 3658] [depth= 9] . ( 4 sec) [ -14438.6334] [ 3599] [depth= 4] . ( 4 sec) [ -14340.7269] [ 3554] [depth= 3] . ( 5 sec) [ -13984.9759] [ 3484] [depth= 3] . ( 5 sec) [ -13751.2732] [ 3368] [depth= 9] . ( 5 sec) [ -13748.1854] [ 3348] [depth= 1] . ( 5 sec) [ -13727.5877] [ 3347] [depth= 1] . ( 5 sec) [ -13449.1007] [ 3205] [depth= 8] . ( 5 sec) [ -13446.8975] [ 3205] [depth= 2] . ( 5 sec) [ -13170.2011] [ 3092] [depth= 5] . ( 5 sec) [ -13087.4776] [ 3073] [depth= 2] . ( 5 sec) [ -13041.7064] [ 3043] [depth= 1] . ( 5 sec) [ -13031.7897] [ 3032] [depth= 1] . ( 5 sec) [ -13005.9816] [ 3026] [depth= 3] . ( 5 sec) [ -12887.1657] [ 2962] [depth= 2] . ( 5 sec) [ -12632.7069] [ 2843] [depth= 10] . ( 5 sec) [ -12611.1494] [ 2844] [depth= 1] . ( 5 sec) [ -12603.2298] [ 2841] [depth= 1] . ( 6 sec) [ -12551.6898] [ 2841] [depth= 1] . ( 6 sec) [ -12550.9169] [ 2841] [depth= 1] . ( 6 sec) [ -12376.7084] [ 2772] [depth= 1] . ( 6 sec) [ -12376.6228] [ 2772] [depth= 1] . ( 6 sec) [ -12342.8229] [ 2753] [depth= 1] . ( 6 sec) [ -12340.6542] [ 2754] [depth= 1] . ( 6 sec) [ -12339.8659] [ 2754] [depth= 1] . ( 6 sec) [ -12304.3932] [ 2741] [depth= 1] . ( 6 sec) [ -12290.2134] [ 2809] [depth= 9] . ( 6 sec) [ -12188.6605] [ 2811] [depth= 1] . ( 6 sec) [ -12182.1262] [ 2809] [depth= 4] . ( 6 sec) [ -11726.8912] [ 2788] [depth= 1] . ( 6 sec) [ -11669.7403] [ 2790] [depth= 2] . ( 6 sec) [ -11641.6389] [ 2782] [depth= 1] . ( 6 sec) [ -11616.6146] [ 2779] [depth= 1] . ( 6 sec) [ -11571.9323] [ 2771] [depth= 1] . ( 7 sec) [ -11570.5145] [ 2774] [depth= 1] . ( 7 sec) [ -11545.8282] [ 2819] [depth= 2] . ( 7 sec) [ -11449.3817] [ 2818] [depth= 1] . ( 7 sec) [ -11421.0185] [ 2804] [depth= 3] . ( 7 sec) [ -11357.8643] [ 2806] [depth= 1] . ( 7 sec) [ -11355.2763] [ 2808] [depth= 1] . ( 7 sec) [ -11154.4137] [Branch lengths ] . ( 8 sec) [ -11151.2490] [GTR parameters ] . ( 8 sec) [ -11109.1659] [Alpha ][ 0.919498] . ( 8 sec) [ -11087.0288] [ 2778] [depth= 2] . ( 8 sec) [ -11064.1643] [ 2715] [depth= 5] . ( 8 sec) [ -11056.9309] [ 2700] [depth= 1] . ( 8 sec) [ -11044.4146] [ 2708] [depth= 1] . ( 8 sec) [ -11013.0248] [ 2705] [depth= 1] . ( 8 sec) [ -10842.4689] [ 2593] [depth= 8] . ( 8 sec) [ -10839.1939] [ 2591] [depth= 1] . ( 8 sec) [ -10837.8310] [ 2592] [depth= 1] . ( 8 sec) [ -10837.3708] [ 2592] [depth= 2] . ( 8 sec) [ -10836.8880] [ 2585] [depth= 1] . ( 8 sec) [ -10835.3928] [ 2581] [depth= 1] . ( 9 sec) [ -10738.4738] [ 2555] [depth= 1] . ( 9 sec) [ -10725.4385] [ 2547] [depth= 2] . ( 9 sec) [ -10716.2244] [ 2535] [depth= 1] . ( 9 sec) [ -10714.0549] [ 2530] [depth= 1] . ( 9 sec) [ -10713.9822] [ 2530] [depth= 1] . ( 9 sec) [ -10711.9857] [ 2535] [depth= 1] . ( 9 sec) [ -10710.6008] [ 2543] [depth= 1] . ( 9 sec) [ -10709.2740] [ 2548] [depth= 2] . ( 9 sec) [ -10702.4219] [ 2545] [depth= 2] . ( 9 sec) [ -10678.6847] [ 2513] [depth= 3] . ( 9 sec) [ -10677.4976] [ 2515] [depth= 1] . ( 10 sec) [ -10677.4492] [ 2519] [depth= 1] . ( 10 sec) [ -10675.5577] [ 2520] [depth= 1] . ( 10 sec) [ -10675.1137] [ 2524] [depth= 1] . ( 10 sec) [ -10673.9296] [ 2518] [depth= 1] . ( 10 sec) [ -10671.3353] [ 2530] [depth= 1] . ( 10 sec) [ -10670.8954] [ 2533] [depth= 1] . ( 10 sec) [ -10670.8360] [ 2533] [depth= 1] . ( 10 sec) [ -10649.8376] [ 2529] [depth= 2] . ( 11 sec) [ -10648.2024] [ 2529] [depth= 1] . ( 11 sec) [ -10647.8808] [ 2529] [depth= 1] . ( 11 sec) [ -10642.4315] [ 2522] [depth= 1] . ( 12 sec) [ -10611.1496] [Branch lengths ] . ( 12 sec) [ -10610.8080] [GTR parameters ] . ( 12 sec) [ -10608.3726] [Alpha ][ 1.070186] . ( 12 sec) [ -10605.1940] [ 2510] [depth= 1] . ( 13 sec) [ -10605.1534] [ 2510] [depth= 1] . ( 13 sec) [ -10604.8427] [ 2504] [depth= 1] . ( 13 sec) [ -10604.4454] [ 2503] [depth= 1] . ( 13 sec) [ -10604.4349] [ 2503] [depth= 1] . ( 13 sec) [ -10604.2447] [ 2508] [depth= 1] . ( 17 sec) [ -10594.5672] [Branch lengths ] . ( 17 sec) [ -10594.5605] [GTR parameters ] . ( 17 sec) [ -10594.5602] [Alpha ][ 1.072146] . ( 17 sec) [ -10594.4949] [ 2505] [depth= 1] . ( 21 sec) [ -10592.8054] [Branch lengths ] . ( 21 sec) [ -10592.8040] [GTR parameters ] . ( 21 sec) [ -10592.8001] [Alpha ][ 1.065551] . ( 26 sec) [ -10592.5066] [Branch lengths ] . ( 48 sec) [ -10592.4285] [Branch lengths ] . ( 48 sec) [ -10592.4285] [Topology ] . ( 49 sec) [ -10592.4142] [Topology ] . ( 50 sec) [ -10592.4070] [Topology ] . ( 51 sec) [ -10592.4027] [Topology ] . ( 52 sec) [ -10592.4000] [Topology ] . ( 53 sec) [ -10592.3983] [Topology ] . ( 53 sec) [ -10592.3973] [Topology ] . ( 54 sec) [ -10592.3965] [GTR parameters ] . ( 54 sec) [ -10592.3948] [Alpha ][ 1.061176] . ( 54 sec) [ -10592.3948] [Topology ] . ( 54 sec) [ -10592.3939] [Topology ] . ( 55 sec) [ -10592.3939] [GTR parameters ] . ( 55 sec) [ -10592.3939] [Alpha ][ 1.061176] . Checking for NNIs, optimizing five branches... . ( 61 sec) [ -10592.2440] [Topology ] . Checking for NNIs, optimizing five branches... . ( 67 sec) [ -10592.2320] [Topology ] . Checking for NNIs, optimizing five branches... . ( 73 sec) [ -10592.2242] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10592.224156. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22847.5919] [GTR parameters ] . ( 1 sec) [ -22418.7665] [Alpha ][ 0.500960] . ( 1 sec) [ -22147.2403] [ 5433] [depth= 3] . ( 1 sec) [ -21928.6130] [ 5397] [depth= 11] . ( 1 sec) [ -21808.6672] [ 5378] [depth= 3] . ( 1 sec) [ -21653.5633] [ 5361] [depth= 7] . ( 1 sec) [ -21130.9314] [ 5229] [depth= 5] . ( 1 sec) [ -21018.6557] [ 5194] [depth= 4] . ( 1 sec) [ -20871.1442] [ 5148] [depth= 1] . ( 1 sec) [ -20600.4110] [ 5135] [depth= 4] . ( 1 sec) [ -20003.5538] [ 4994] [depth= 1] . ( 1 sec) [ -19952.6456] [ 4989] [depth= 3] . ( 1 sec) [ -19445.7457] [ 4869] [depth= 3] . ( 1 sec) [ -19401.6924] [ 4851] [depth= 1] . ( 1 sec) [ -19318.4863] [ 4751] [depth= 1] . ( 2 sec) [ -19310.2145] [ 4746] [depth= 2] . ( 2 sec) [ -18923.1248] [ 4649] [depth= 9] . ( 2 sec) [ -18894.1239] [ 4632] [depth= 1] . ( 2 sec) [ -18891.7589] [ 4637] [depth= 1] . ( 2 sec) [ -18453.4407] [ 4627] [depth= 1] . ( 2 sec) [ -17801.0304] [ 4617] [depth= 1] . ( 2 sec) [ -17800.6278] [ 4618] [depth= 1] . ( 2 sec) [ -17440.8987] [ 4627] [depth= 1] . ( 2 sec) [ -17415.6773] [ 4618] [depth= 1] . ( 2 sec) [ -17261.0137] [ 4501] [depth= 10] . ( 2 sec) [ -17258.7215] [ 4501] [depth= 1] . ( 2 sec) [ -17113.6534] [ 4469] [depth= 8] . ( 2 sec) [ -17024.5998] [ 4451] [depth= 2] . ( 2 sec) [ -16917.6402] [ 4401] [depth= 9] . ( 2 sec) [ -16730.3497] [ 4332] [depth= 10] . ( 2 sec) [ -16343.0703] [ 4211] [depth= 11] . ( 2 sec) [ -16281.6315] [ 4144] [depth= 5] . ( 2 sec) [ -16102.5974] [ 4113] [depth= 1] . ( 3 sec) [ -15913.6825] [ 4090] [depth= 15] . ( 3 sec) [ -15838.2455] [ 4058] [depth= 1] . ( 3 sec) [ -15571.4661] [ 3923] [depth= 8] . ( 3 sec) [ -15562.5561] [ 3956] [depth= 1] . ( 3 sec) [ -15093.4531] [ 3879] [depth= 11] . ( 3 sec) [ -14815.0854] [ 3752] [depth= 9] . ( 3 sec) [ -14669.0839] [ 3705] [depth= 10] . ( 3 sec) [ -14621.7383] [ 3676] [depth= 7] . ( 3 sec) [ -14492.7377] [ 3595] [depth= 2] . ( 3 sec) [ -14361.5063] [ 3565] [depth= 3] . ( 3 sec) [ -14041.9621] [ 3536] [depth= 7] . ( 3 sec) [ -13773.6761] [ 3433] [depth= 4] . ( 3 sec) [ -13752.1942] [ 3437] [depth= 1] . ( 3 sec) [ -13699.4512] [ 3409] [depth= 11] . ( 3 sec) [ -13554.5347] [ 3405] [depth= 3] . ( 3 sec) [ -13431.6555] [ 3403] [depth= 3] . ( 3 sec) [ -13217.1053] [ 3368] [depth= 1] . ( 3 sec) [ -12973.7795] [ 3325] [depth= 6] . ( 3 sec) [ -12744.1267] [ 3304] [depth= 9] . ( 3 sec) [ -12718.2119] [ 3291] [depth= 2] . ( 3 sec) [ -12577.2498] [ 3285] [depth= 1] . ( 4 sec) [ -12468.6800] [ 3068] [depth= 1] . ( 4 sec) [ -12416.0772] [ 3068] [depth= 1] . ( 4 sec) [ -12344.9212] [ 3061] [depth= 3] . ( 4 sec) [ -12244.5371] [ 3062] [depth= 1] . ( 4 sec) [ -12244.1882] [ 3064] [depth= 1] . ( 4 sec) [ -12153.3329] [ 3064] [depth= 1] . ( 4 sec) [ -11996.0997] [ 2979] [depth= 5] . ( 4 sec) [ -11910.1993] [ 2964] [depth= 1] . ( 4 sec) [ -11904.8540] [ 2963] [depth= 1] . ( 4 sec) [ -11792.8714] [ 2920] [depth= 2] . ( 4 sec) [ -11783.7607] [ 2929] [depth= 1] . ( 4 sec) [ -11710.4478] [ 2929] [depth= 1] . ( 4 sec) [ -11631.6946] [ 2934] [depth= 1] . ( 4 sec) [ -11631.5329] [ 2931] [depth= 1] . ( 4 sec) [ -11620.2356] [ 2916] [depth= 2] . ( 5 sec) [ -11599.0782] [ 2907] [depth= 1] . ( 5 sec) [ -11568.2879] [ 2886] [depth= 1] . ( 5 sec) [ -11568.1429] [ 2890] [depth= 1] . ( 5 sec) [ -11564.4100] [ 2892] [depth= 1] . ( 5 sec) [ -11558.9966] [ 2886] [depth= 1] . ( 5 sec) [ -11558.5819] [ 2885] [depth= 1] . ( 5 sec) [ -11404.9223] [ 2798] [depth= 14] . ( 5 sec) [ -11363.3394] [ 2760] [depth= 3] . ( 5 sec) [ -11358.6606] [ 2759] [depth= 1] . ( 5 sec) [ -11205.4513] [ 2694] [depth= 1] . ( 5 sec) [ -11187.4042] [ 2682] [depth= 1] . ( 5 sec) [ -11160.5131] [ 2677] [depth= 1] . ( 5 sec) [ -11090.0933] [ 2646] [depth= 1] . ( 6 sec) [ -10822.3150] [Branch lengths ] . ( 6 sec) [ -10819.0862] [GTR parameters ] . ( 6 sec) [ -10766.4541] [Alpha ][ 1.000575] . ( 6 sec) [ -10757.8845] [ 2641] [depth= 1] . ( 7 sec) [ -10757.6750] [ 2641] [depth= 1] . ( 7 sec) [ -10757.3961] [ 2644] [depth= 1] . ( 7 sec) [ -10756.0000] [ 2649] [depth= 1] . ( 7 sec) [ -10748.7235] [ 2652] [depth= 1] . ( 7 sec) [ -10725.8832] [ 2626] [depth= 2] . ( 7 sec) [ -10725.3715] [ 2621] [depth= 1] . ( 7 sec) [ -10725.3343] [ 2624] [depth= 1] . ( 8 sec) [ -10723.8442] [ 2625] [depth= 1] . ( 8 sec) [ -10723.6664] [ 2625] [depth= 1] . ( 8 sec) [ -10713.7826] [ 2590] [depth= 6] . ( 8 sec) [ -10639.6382] [ 2499] [depth= 10] . ( 9 sec) [ -10639.5000] [ 2506] [depth= 1] . ( 9 sec) [ -10639.4826] [ 2505] [depth= 1] . ( 9 sec) [ -10639.4332] [ 2506] [depth= 1] . ( 10 sec) [ -10639.3881] [ 2507] [depth= 1] . ( 10 sec) [ -10630.8071] [ 2499] [depth= 1] . ( 10 sec) [ -10598.5297] [Branch lengths ] . ( 11 sec) [ -10598.3505] [GTR parameters ] . ( 11 sec) [ -10597.9279] [Alpha ][ 1.065103] . ( 11 sec) [ -10597.8198] [ 2496] [depth= 1] . ( 15 sec) [ -10592.9168] [Branch lengths ] . ( 15 sec) [ -10592.9110] [GTR parameters ] . ( 15 sec) [ -10592.9098] [Alpha ][ 1.068594] . ( 19 sec) [ -10592.3373] [Branch lengths ] . ( 39 sec) [ -10592.1779] [ 2496] [depth= 1] . ( 41 sec) [ -10592.0279] [Branch lengths ] . ( 41 sec) [ -10592.0271] [GTR parameters ] . ( 41 sec) [ -10592.0242] [Alpha ][ 1.062870] . ( 41 sec) [ -10592.0242] [Topology ] . ( 42 sec) [ -10591.9995] [Topology ] . ( 43 sec) [ -10591.9874] [Topology ] . ( 44 sec) [ -10591.9802] [Topology ] . ( 44 sec) [ -10591.9757] [Topology ] . ( 45 sec) [ -10591.9730] [Topology ] . ( 46 sec) [ -10591.9712] [Topology ] . ( 46 sec) [ -10591.9712] [GTR parameters ] . ( 46 sec) [ -10591.9710] [Alpha ][ 1.061716] . ( 46 sec) [ -10591.9710] [Topology ] . ( 47 sec) [ -10591.9699] [Topology ] . ( 48 sec) [ -10591.9692] [Topology ] . ( 48 sec) [ -10591.9692] [GTR parameters ] . ( 48 sec) [ -10591.9692] [Alpha ][ 1.061716] . ( 48 sec) [ -10591.9692] [Topology ] . ( 49 sec) [ -10591.9687] [Topology ] . ( 49 sec) [ -10591.9687] [GTR parameters ] . ( 49 sec) [ -10591.9687] [Alpha ][ 1.061716] . Checking for NNIs, optimizing five branches... . ( 56 sec) [ -10591.9571] [Topology ] . Checking for NNIs, optimizing five branches... . ( 62 sec) [ -10591.9567] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10591.956670. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -24986.8431] [GTR parameters ] . ( 1 sec) [ -24462.4804] [Alpha ][ 0.500960] . ( 1 sec) [ -23851.6101] [ 5770] [depth= 8] . ( 1 sec) [ -23251.0150] [ 5746] [depth= 10] . ( 1 sec) [ -23188.5536] [ 5730] [depth= 4] . ( 1 sec) [ -23085.6247] [ 5722] [depth= 3] . ( 1 sec) [ -23040.0931] [ 5621] [depth= 10] . ( 1 sec) [ -22965.5556] [ 5620] [depth= 5] . ( 1 sec) [ -22646.2571] [ 5514] [depth= 6] . ( 1 sec) [ -22303.3377] [ 5471] [depth= 16] . ( 1 sec) [ -21992.9925] [ 5251] [depth= 3] . ( 1 sec) [ -21631.7748] [ 5258] [depth= 18] . ( 1 sec) [ -21253.5250] [ 5151] [depth= 10] . ( 1 sec) [ -20874.2484] [ 5039] [depth= 17] . ( 1 sec) [ -20099.5162] [ 5007] [depth= 1] . ( 1 sec) [ -19943.7527] [ 4992] [depth= 1] . ( 1 sec) [ -19801.4859] [ 4882] [depth= 2] . ( 1 sec) [ -19688.2759] [ 4864] [depth= 9] . ( 1 sec) [ -19395.4811] [ 4813] [depth= 6] . ( 1 sec) [ -19375.9460] [ 4818] [depth= 1] . ( 1 sec) [ -19198.5334] [ 4795] [depth= 7] . ( 2 sec) [ -18664.3896] [ 4686] [depth= 6] . ( 2 sec) [ -18661.3689] [ 4686] [depth= 1] . ( 2 sec) [ -18551.9799] [ 4638] [depth= 1] . ( 2 sec) [ -18530.9644] [ 4615] [depth= 5] . ( 2 sec) [ -18301.6060] [ 4468] [depth= 3] . ( 2 sec) [ -18255.4606] [ 4452] [depth= 9] . ( 2 sec) [ -17220.7078] [ 4273] [depth= 12] . ( 2 sec) [ -17172.4217] [ 4278] [depth= 2] . ( 2 sec) [ -16755.8560] [ 4101] [depth= 5] . ( 2 sec) [ -16633.5992] [ 4004] [depth= 3] . ( 2 sec) [ -16616.6656] [ 3989] [depth= 3] . ( 2 sec) [ -16193.1831] [ 3933] [depth= 3] . ( 2 sec) [ -15616.9547] [ 3806] [depth= 4] . ( 2 sec) [ -15596.4825] [ 3830] [depth= 1] . ( 2 sec) [ -15282.4017] [ 3677] [depth= 8] . ( 2 sec) [ -15263.2331] [ 3672] [depth= 2] . ( 2 sec) [ -15032.4022] [ 3590] [depth= 7] . ( 2 sec) [ -14964.2088] [ 3584] [depth= 2] . ( 2 sec) [ -14937.7858] [ 3622] [depth= 1] . ( 2 sec) [ -14726.8568] [ 3582] [depth= 4] . ( 3 sec) [ -14695.7243] [ 3528] [depth= 1] . ( 3 sec) [ -14538.1793] [ 3463] [depth= 3] . ( 3 sec) [ -14353.4116] [ 3387] [depth= 2] . ( 3 sec) [ -14324.5656] [ 3353] [depth= 5] . ( 3 sec) [ -14322.6167] [ 3351] [depth= 8] . ( 3 sec) [ -14312.4616] [ 3329] [depth= 1] . ( 3 sec) [ -13991.4296] [ 3298] [depth= 6] . ( 3 sec) [ -13937.7108] [ 3272] [depth= 4] . ( 3 sec) [ -13920.6003] [ 3261] [depth= 2] . ( 3 sec) [ -13893.5229] [ 3264] [depth= 1] . ( 3 sec) [ -13642.5126] [ 3177] [depth= 5] . ( 3 sec) [ -13514.9893] [ 3127] [depth= 1] . ( 3 sec) [ -13494.0406] [ 3122] [depth= 2] . ( 3 sec) [ -13318.3767] [ 3130] [depth= 1] . ( 3 sec) [ -13043.2769] [ 3061] [depth= 9] . ( 3 sec) [ -12979.4916] [ 3064] [depth= 1] . ( 3 sec) [ -12966.5358] [ 3089] [depth= 1] . ( 3 sec) [ -12838.7162] [ 3049] [depth= 2] . ( 3 sec) [ -12640.5537] [ 3000] [depth= 5] . ( 3 sec) [ -12333.0780] [ 2846] [depth= 7] . ( 3 sec) [ -12255.3765] [ 2874] [depth= 1] . ( 4 sec) [ -12232.3080] [ 2876] [depth= 1] . ( 4 sec) [ -12223.5391] [ 2866] [depth= 1] . ( 4 sec) [ -12207.7887] [ 2863] [depth= 1] . ( 4 sec) [ -11918.5466] [ 2787] [depth= 7] . ( 4 sec) [ -11875.3259] [ 2792] [depth= 1] . ( 4 sec) [ -11843.8671] [ 2836] [depth= 2] . ( 4 sec) [ -11791.2163] [ 2818] [depth= 3] . ( 4 sec) [ -11785.4141] [ 2821] [depth= 2] . ( 4 sec) [ -11777.2673] [ 2818] [depth= 1] . ( 4 sec) [ -11776.6737] [ 2826] [depth= 1] . ( 4 sec) [ -11758.9210] [ 2831] [depth= 1] . ( 4 sec) [ -11717.3247] [ 2775] [depth= 1] . ( 4 sec) [ -11705.0270] [ 2764] [depth= 1] . ( 4 sec) [ -11669.4271] [ 2760] [depth= 3] . ( 4 sec) [ -11661.8733] [ 2757] [depth= 1] . ( 4 sec) [ -11644.3314] [ 2764] [depth= 1] . ( 5 sec) [ -11592.9232] [ 2753] [depth= 4] . ( 5 sec) [ -11592.7205] [ 2749] [depth= 1] . ( 5 sec) [ -11564.3144] [ 2740] [depth= 1] . ( 5 sec) [ -11403.6099] [ 2736] [depth= 3] . ( 5 sec) [ -11346.3277] [ 2707] [depth= 2] . ( 5 sec) [ -11343.1011] [ 2710] [depth= 1] . ( 5 sec) [ -11163.3480] [ 2684] [depth= 4] . ( 5 sec) [ -11148.5849] [ 2680] [depth= 1] . ( 5 sec) [ -11089.3521] [ 2658] [depth= 1] . ( 5 sec) [ -11080.9634] [ 2652] [depth= 1] . ( 5 sec) [ -11078.1045] [ 2652] [depth= 1] . ( 5 sec) [ -11059.9983] [ 2651] [depth= 1] . ( 5 sec) [ -10976.8868] [ 2526] [depth= 8] . ( 5 sec) [ -10703.8503] [Branch lengths ] . ( 6 sec) [ -10700.3306] [GTR parameters ] . ( 6 sec) [ -10646.6197] [Alpha ][ 1.000306] . ( 6 sec) [ -10646.5104] [ 2527] [depth= 1] . ( 7 sec) [ -10643.3982] [ 2527] [depth= 1] . ( 7 sec) [ -10642.9452] [ 2526] [depth= 1] . ( 7 sec) [ -10613.2252] [ 2495] [depth= 2] . ( 7 sec) [ -10611.4769] [ 2499] [depth= 3] . ( 7 sec) [ -10609.6736] [ 2499] [depth= 1] . ( 7 sec) [ -10609.6594] [ 2500] [depth= 1] . ( 7 sec) [ -10607.5121] [ 2496] [depth= 1] . ( 8 sec) [ -10606.1052] [ 2499] [depth= 1] . ( 8 sec) [ -10606.0744] [ 2499] [depth= 1] . ( 9 sec) [ -10605.9416] [ 2498] [depth= 1] . ( 9 sec) [ -10605.8698] [ 2502] [depth= 1] . ( 10 sec) [ -10594.4958] [Branch lengths ] . ( 10 sec) [ -10594.4633] [GTR parameters ] . ( 10 sec) [ -10594.0205] [Alpha ][ 1.066175] . ( 11 sec) [ -10593.9309] [ 2506] [depth= 2] . ( 11 sec) [ -10593.8623] [ 2502] [depth= 1] . ( 12 sec) [ -10593.6974] [ 2500] [depth= 1] . ( 12 sec) [ -10593.6164] [ 2502] [depth= 1] . ( 15 sec) [ -10592.5055] [Branch lengths ] . ( 15 sec) [ -10592.5028] [GTR parameters ] . ( 15 sec) [ -10592.5027] [Alpha ][ 1.064960] . ( 19 sec) [ -10592.3133] [Branch lengths ] . ( 41 sec) [ -10592.2633] [Branch lengths ] . ( 41 sec) [ -10592.2633] [Topology ] . ( 42 sec) [ -10592.2542] [Topology ] . ( 43 sec) [ -10592.2495] [Topology ] . ( 44 sec) [ -10592.2468] [Topology ] . ( 45 sec) [ -10592.2450] [Topology ] . ( 46 sec) [ -10592.2440] [Topology ] . ( 46 sec) [ -10592.2433] [Topology ] . ( 47 sec) [ -10592.2429] [GTR parameters ] . ( 47 sec) [ -10592.2418] [Alpha ][ 1.061465] . ( 47 sec) [ -10592.2418] [Topology ] . ( 48 sec) [ -10592.2412] [Topology ] . ( 48 sec) [ -10592.2412] [GTR parameters ] . ( 48 sec) [ -10592.2412] [Alpha ][ 1.061465] . Checking for NNIs, optimizing five branches... . ( 54 sec) [ -10592.2290] [Topology ] . Checking for NNIs, optimizing five branches... . ( 60 sec) [ -10592.2207] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10592.220652. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22898.6995] [GTR parameters ] . ( 1 sec) [ -22476.4078] [Alpha ][ 0.500960] . ( 1 sec) [ -22298.9911] [ 5642] [depth= 8] . ( 1 sec) [ -22029.3881] [ 5584] [depth= 7] . ( 1 sec) [ -21561.8328] [ 5505] [depth= 8] . ( 1 sec) [ -21433.1854] [ 5340] [depth= 1] . ( 1 sec) [ -21102.8651] [ 5301] [depth= 9] . ( 1 sec) [ -20970.6638] [ 5277] [depth= 3] . ( 1 sec) [ -20477.0870] [ 5267] [depth= 5] . ( 1 sec) [ -20120.4621] [ 5112] [depth= 3] . ( 1 sec) [ -19986.2323] [ 5108] [depth= 1] . ( 1 sec) [ -19862.4799] [ 5085] [depth= 6] . ( 2 sec) [ -19432.1812] [ 5021] [depth= 16] . ( 2 sec) [ -19238.2318] [ 4983] [depth= 12] . ( 2 sec) [ -19209.1438] [ 4973] [depth= 2] . ( 2 sec) [ -19096.2096] [ 4938] [depth= 13] . ( 2 sec) [ -19045.3979] [ 4941] [depth= 5] . ( 2 sec) [ -18866.5477] [ 4893] [depth= 8] . ( 2 sec) [ -18620.7652] [ 4871] [depth= 1] . ( 2 sec) [ -18455.2989] [ 4709] [depth= 16] . ( 2 sec) [ -18232.6815] [ 4702] [depth= 12] . ( 2 sec) [ -18154.6516] [ 4667] [depth= 1] . ( 2 sec) [ -18113.2868] [ 4640] [depth= 14] . ( 2 sec) [ -17772.8515] [ 4539] [depth= 14] . ( 2 sec) [ -17297.8699] [ 4520] [depth= 3] . ( 2 sec) [ -17044.9445] [ 4492] [depth= 9] . ( 2 sec) [ -16763.8324] [ 4366] [depth= 4] . ( 2 sec) [ -16555.8760] [ 4353] [depth= 5] . ( 2 sec) [ -16295.7301] [ 4374] [depth= 1] . ( 2 sec) [ -15853.6160] [ 4193] [depth= 12] . ( 2 sec) [ -15619.2596] [ 4157] [depth= 16] . ( 2 sec) [ -15507.1482] [ 4140] [depth= 7] . ( 2 sec) [ -15467.3158] [ 4107] [depth= 2] . ( 3 sec) [ -15387.0262] [ 4111] [depth= 2] . ( 3 sec) [ -15184.0824] [ 4059] [depth= 15] . ( 3 sec) [ -15044.8274] [ 4059] [depth= 1] . ( 3 sec) [ -14927.4963] [ 3952] [depth= 7] . ( 3 sec) [ -14917.9252] [ 3945] [depth= 3] . ( 3 sec) [ -14591.6915] [ 3855] [depth= 1] . ( 3 sec) [ -14521.0779] [ 3841] [depth= 1] . ( 3 sec) [ -14401.1187] [ 3832] [depth= 8] . ( 3 sec) [ -14352.1841] [ 3819] [depth= 1] . ( 3 sec) [ -13911.7049] [ 3687] [depth= 9] . ( 3 sec) [ -13850.2011] [ 3669] [depth= 9] . ( 3 sec) [ -13832.8603] [ 3655] [depth= 2] . ( 3 sec) [ -13764.4051] [ 3637] [depth= 6] . ( 3 sec) [ -13741.3518] [ 3637] [depth= 1] . ( 3 sec) [ -13662.9835] [ 3637] [depth= 1] . ( 3 sec) [ -13644.4135] [ 3643] [depth= 2] . ( 3 sec) [ -13455.6774] [ 3529] [depth= 2] . ( 3 sec) [ -13413.3984] [ 3487] [depth= 1] . ( 3 sec) [ -13361.3262] [ 3476] [depth= 2] . ( 3 sec) [ -13297.1707] [ 3472] [depth= 3] . ( 3 sec) [ -13244.5192] [ 3474] [depth= 1] . ( 4 sec) [ -13229.6828] [ 3472] [depth= 1] . ( 4 sec) [ -13186.4850] [ 3447] [depth= 1] . ( 4 sec) [ -13063.8598] [ 3333] [depth= 11] . ( 4 sec) [ -12914.3826] [ 3321] [depth= 5] . ( 4 sec) [ -12621.7610] [ 3237] [depth= 9] . ( 4 sec) [ -12425.8058] [ 3095] [depth= 7] . ( 4 sec) [ -12365.2961] [ 3087] [depth= 1] . ( 4 sec) [ -12356.0846] [ 3072] [depth= 1] . ( 4 sec) [ -12345.3013] [ 3070] [depth= 1] . ( 4 sec) [ -12344.5352] [ 3078] [depth= 1] . ( 4 sec) [ -12096.3239] [ 3027] [depth= 7] . ( 4 sec) [ -11974.6931] [ 3005] [depth= 8] . ( 4 sec) [ -11905.3655] [ 2971] [depth= 4] . ( 4 sec) [ -11875.3734] [ 2970] [depth= 2] . ( 4 sec) [ -11800.0928] [ 2948] [depth= 1] . ( 4 sec) [ -11729.6701] [ 2943] [depth= 9] . ( 4 sec) [ -11716.5328] [ 2952] [depth= 1] . ( 5 sec) [ -11646.3148] [ 2928] [depth= 4] . ( 5 sec) [ -11520.3301] [ 2846] [depth= 5] . ( 5 sec) [ -11507.0460] [ 2839] [depth= 1] . ( 5 sec) [ -11483.5925] [ 2843] [depth= 1] . ( 5 sec) [ -11417.0880] [ 2807] [depth= 2] . ( 5 sec) [ -11369.0648] [ 2805] [depth= 2] . ( 5 sec) [ -11360.2657] [ 2796] [depth= 2] . ( 5 sec) [ -11304.5694] [ 2758] [depth= 1] . ( 5 sec) [ -11281.8972] [ 2752] [depth= 1] . ( 5 sec) [ -11239.8310] [ 2733] [depth= 2] . ( 5 sec) [ -11226.9537] [ 2735] [depth= 1] . ( 5 sec) [ -11214.5058] [ 2718] [depth= 1] . ( 5 sec) [ -11196.0811] [ 2706] [depth= 1] . ( 5 sec) [ -11180.3551] [ 2680] [depth= 7] . ( 5 sec) [ -11171.4693] [ 2675] [depth= 1] . ( 5 sec) [ -11117.1980] [ 2658] [depth= 2] . ( 6 sec) [ -11062.8729] [ 2644] [depth= 1] . ( 6 sec) [ -10952.9780] [Branch lengths ] . ( 6 sec) [ -10948.5817] [GTR parameters ] . ( 6 sec) [ -10902.1157] [Alpha ][ 0.973809] . ( 7 sec) [ -10890.2412] [ 2619] [depth= 2] . ( 7 sec) [ -10885.6860] [ 2582] [depth= 2] . ( 7 sec) [ -10885.3934] [ 2581] [depth= 1] . ( 7 sec) [ -10878.0836] [ 2570] [depth= 1] . ( 7 sec) [ -10873.8739] [ 2571] [depth= 1] . ( 7 sec) [ -10872.2500] [ 2570] [depth= 1] . ( 8 sec) [ -10872.2301] [ 2571] [depth= 1] . ( 8 sec) [ -10871.9652] [ 2571] [depth= 1] . ( 8 sec) [ -10838.3246] [ 2545] [depth= 1] . ( 8 sec) [ -10802.3551] [ 2546] [depth= 2] . ( 8 sec) [ -10733.1279] [ 2510] [depth= 3] . ( 8 sec) [ -10703.6862] [ 2507] [depth= 1] . ( 8 sec) [ -10700.2684] [ 2512] [depth= 1] . ( 8 sec) [ -10700.1917] [ 2511] [depth= 1] . ( 9 sec) [ -10699.6730] [ 2508] [depth= 1] . ( 9 sec) [ -10690.0243] [ 2503] [depth= 1] . ( 9 sec) [ -10641.7636] [ 2509] [depth= 1] . ( 9 sec) [ -10640.1422] [ 2510] [depth= 1] . ( 9 sec) [ -10639.6717] [ 2511] [depth= 1] . ( 9 sec) [ -10636.9102] [ 2508] [depth= 1] . ( 9 sec) [ -10635.4643] [ 2512] [depth= 1] . ( 9 sec) [ -10635.4508] [ 2513] [depth= 1] . ( 10 sec) [ -10634.7548] [ 2520] [depth= 1] . ( 10 sec) [ -10632.8920] [ 2514] [depth= 1] . ( 10 sec) [ -10624.3895] [ 2511] [depth= 1] . ( 10 sec) [ -10623.9163] [ 2512] [depth= 1] . ( 10 sec) [ -10623.3474] [ 2516] [depth= 1] . ( 11 sec) [ -10598.3431] [Branch lengths ] . ( 11 sec) [ -10597.9512] [GTR parameters ] . ( 11 sec) [ -10597.1026] [Alpha ][ 1.064022] . ( 12 sec) [ -10596.1763] [ 2516] [depth= 1] . ( 13 sec) [ -10596.1660] [ 2515] [depth= 1] . ( 14 sec) [ -10596.1518] [ 2516] [depth= 1] . ( 15 sec) [ -10593.1844] [Branch lengths ] . ( 16 sec) [ -10593.1823] [GTR parameters ] . ( 16 sec) [ -10593.1814] [Alpha ][ 1.067048] . ( 20 sec) [ -10592.5424] [Branch lengths ] . ( 42 sec) [ -10592.3958] [Branch lengths ] . ( 42 sec) [ -10592.3958] [Topology ] . ( 43 sec) [ -10592.2281] [Topology ] . ( 44 sec) [ -10592.1966] [Topology ] . ( 44 sec) [ -10592.1867] [Topology ] . ( 45 sec) [ -10592.1816] [Topology ] . ( 46 sec) [ -10592.1786] [Topology ] . ( 47 sec) [ -10592.1768] [Topology ] . ( 48 sec) [ -10592.1756] [Topology ] . ( 48 sec) [ -10592.1743] [GTR parameters ] . ( 48 sec) [ -10592.1718] [Alpha ][ 1.061748] . ( 48 sec) [ -10592.1718] [Topology ] . ( 49 sec) [ -10592.1708] [Topology ] . ( 49 sec) [ -10592.1708] [GTR parameters ] . ( 49 sec) [ -10592.1708] [Alpha ][ 1.061748] . ( 49 sec) [ -10592.1708] [Topology ] . ( 50 sec) [ -10592.1702] [Topology ] . ( 50 sec) [ -10592.1702] [GTR parameters ] . ( 50 sec) [ -10592.1702] [Alpha ][ 1.061748] . Checking for NNIs, optimizing five branches... . ( 56 sec) [ -10592.0210] [Topology ] . Checking for NNIs, optimizing five branches... . ( 63 sec) [ -10591.9217] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10591.921676. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -23260.8312] [GTR parameters ] . ( 0 sec) [ -22782.1513] [Alpha ][ 0.500960] . ( 0 sec) [ -22462.4837] [ 5738] [depth= 6] . ( 0 sec) [ -22298.5334] [ 5697] [depth= 13] . ( 0 sec) [ -22159.8324] [ 5680] [depth= 5] . ( 0 sec) [ -22041.8279] [ 5665] [depth= 7] . ( 1 sec) [ -21647.5669] [ 5532] [depth= 3] . ( 1 sec) [ -21620.6855] [ 5529] [depth= 7] . ( 1 sec) [ -21449.7577] [ 5491] [depth= 6] . ( 1 sec) [ -21300.6152] [ 5493] [depth= 10] . ( 1 sec) [ -21237.7328] [ 5431] [depth= 13] . ( 1 sec) [ -20874.1236] [ 5309] [depth= 4] . ( 1 sec) [ -20457.5035] [ 5279] [depth= 12] . ( 1 sec) [ -20270.6022] [ 5276] [depth= 8] . ( 1 sec) [ -20266.0095] [ 5223] [depth= 9] . ( 1 sec) [ -20191.2316] [ 5205] [depth= 1] . ( 1 sec) [ -20139.7882] [ 5192] [depth= 1] . ( 1 sec) [ -19921.2726] [ 5146] [depth= 2] . ( 1 sec) [ -19829.7813] [ 5144] [depth= 1] . ( 1 sec) [ -19678.3792] [ 5120] [depth= 2] . ( 1 sec) [ -19498.2629] [ 5037] [depth= 3] . ( 1 sec) [ -19137.3339] [ 5006] [depth= 11] . ( 1 sec) [ -18707.6832] [ 4902] [depth= 3] . ( 1 sec) [ -18577.5827] [ 4896] [depth= 1] . ( 1 sec) [ -18416.7931] [ 4854] [depth= 8] . ( 1 sec) [ -18168.2125] [ 4768] [depth= 5] . ( 1 sec) [ -18071.9346] [ 4623] [depth= 5] . ( 2 sec) [ -17912.8391] [ 4599] [depth= 2] . ( 2 sec) [ -17663.3908] [ 4540] [depth= 1] . ( 2 sec) [ -17385.0431] [ 4443] [depth= 7] . ( 2 sec) [ -17122.3844] [ 4393] [depth= 13] . ( 2 sec) [ -17121.9145] [ 4395] [depth= 1] . ( 2 sec) [ -16906.9183] [ 4336] [depth= 8] . ( 2 sec) [ -16750.4080] [ 4334] [depth= 1] . ( 2 sec) [ -16684.7189] [ 4291] [depth= 2] . ( 2 sec) [ -16603.3159] [ 4198] [depth= 8] . ( 2 sec) [ -15897.2828] [ 4077] [depth= 9] . ( 2 sec) [ -15771.6306] [ 4019] [depth= 1] . ( 2 sec) [ -15690.8189] [ 3943] [depth= 4] . ( 2 sec) [ -15287.6694] [ 3944] [depth= 1] . ( 2 sec) [ -15155.5156] [ 3816] [depth= 8] . ( 2 sec) [ -15118.7038] [ 3816] [depth= 1] . ( 2 sec) [ -15096.6518] [ 3816] [depth= 1] . ( 2 sec) [ -14714.1728] [ 3693] [depth= 2] . ( 2 sec) [ -14520.8233] [ 3620] [depth= 2] . ( 2 sec) [ -14443.3977] [ 3590] [depth= 7] . ( 3 sec) [ -14176.0287] [ 3464] [depth= 5] . ( 3 sec) [ -13984.1485] [ 3419] [depth= 1] . ( 3 sec) [ -13568.9815] [ 3310] [depth= 6] . ( 3 sec) [ -13391.9490] [ 3277] [depth= 8] . ( 3 sec) [ -13344.6936] [ 3274] [depth= 1] . ( 3 sec) [ -13097.0605] [ 3165] [depth= 7] . ( 3 sec) [ -13073.7382] [ 3145] [depth= 3] . ( 3 sec) [ -12986.8311] [ 3145] [depth= 1] . ( 3 sec) [ -12971.9291] [ 3145] [depth= 1] . ( 3 sec) [ -12953.8077] [ 3109] [depth= 7] . ( 3 sec) [ -12891.1645] [ 3109] [depth= 1] . ( 3 sec) [ -12847.9231] [ 3097] [depth= 3] . ( 3 sec) [ -12738.1201] [ 3028] [depth= 4] . ( 3 sec) [ -12734.1227] [ 3029] [depth= 1] . ( 3 sec) [ -12731.9760] [ 3031] [depth= 1] . ( 3 sec) [ -12551.5228] [ 3014] [depth= 1] . ( 3 sec) [ -12512.0429] [ 3014] [depth= 1] . ( 3 sec) [ -12510.9903] [ 3012] [depth= 1] . ( 3 sec) [ -12500.0320] [ 3020] [depth= 2] . ( 4 sec) [ -12427.2294] [ 2985] [depth= 1] . ( 4 sec) [ -12383.7702] [ 2989] [depth= 3] . ( 4 sec) [ -12377.0085] [ 2995] [depth= 1] . ( 4 sec) [ -12370.7261] [ 2992] [depth= 1] . ( 4 sec) [ -12359.8324] [ 2993] [depth= 2] . ( 4 sec) [ -12340.4503] [ 2960] [depth= 3] . ( 4 sec) [ -12005.2449] [ 2962] [depth= 1] . ( 4 sec) [ -11882.2171] [ 2934] [depth= 6] . ( 4 sec) [ -11817.4058] [ 2907] [depth= 2] . ( 4 sec) [ -11816.6263] [ 2879] [depth= 2] . ( 4 sec) [ -11778.9513] [ 2865] [depth= 2] . ( 4 sec) [ -11568.0042] [ 2772] [depth= 8] . ( 4 sec) [ -11438.9782] [ 2767] [depth= 1] . ( 4 sec) [ -11430.2427] [ 2750] [depth= 3] . ( 4 sec) [ -11359.0432] [ 2727] [depth= 1] . ( 4 sec) [ -11353.0507] [ 2756] [depth= 1] . ( 4 sec) [ -11264.5048] [ 2727] [depth= 1] . ( 4 sec) [ -11180.3535] [ 2696] [depth= 2] . ( 4 sec) [ -11175.4607] [ 2695] [depth= 1] . ( 5 sec) [ -11165.0245] [ 2698] [depth= 1] . ( 5 sec) [ -11160.5174] [ 2698] [depth= 1] . ( 5 sec) [ -10978.4763] [Branch lengths ] . ( 6 sec) [ -10975.2926] [GTR parameters ] . ( 6 sec) [ -10932.2243] [Alpha ][ 0.933735] . ( 6 sec) [ -10925.1894] [ 2695] [depth= 1] . ( 6 sec) [ -10902.6639] [ 2652] [depth= 4] . ( 6 sec) [ -10876.5173] [ 2580] [depth= 5] . ( 6 sec) [ -10876.3452] [ 2579] [depth= 1] . ( 6 sec) [ -10876.2252] [ 2580] [depth= 1] . ( 6 sec) [ -10875.4687] [ 2555] [depth= 1] . ( 7 sec) [ -10875.3825] [ 2556] [depth= 1] . ( 7 sec) [ -10866.7877] [ 2558] [depth= 2] . ( 7 sec) [ -10833.0527] [ 2555] [depth= 1] . ( 7 sec) [ -10823.5267] [ 2555] [depth= 1] . ( 7 sec) [ -10705.6737] [ 2520] [depth= 3] . ( 7 sec) [ -10705.4839] [ 2521] [depth= 1] . ( 7 sec) [ -10696.3393] [ 2513] [depth= 2] . ( 8 sec) [ -10696.2825] [ 2511] [depth= 1] . ( 8 sec) [ -10695.6787] [ 2512] [depth= 1] . ( 8 sec) [ -10692.1641] [ 2509] [depth= 1] . ( 8 sec) [ -10690.8480] [ 2508] [depth= 1] . ( 8 sec) [ -10690.3484] [ 2507] [depth= 1] . ( 8 sec) [ -10688.4538] [ 2506] [depth= 1] . ( 9 sec) [ -10686.2574] [ 2509] [depth= 1] . ( 9 sec) [ -10686.0703] [ 2507] [depth= 1] . ( 9 sec) [ -10685.8048] [ 2509] [depth= 1] . ( 9 sec) [ -10684.9542] [ 2533] [depth= 1] . ( 9 sec) [ -10684.6063] [ 2533] [depth= 1] . ( 10 sec) [ -10682.0501] [ 2537] [depth= 1] . ( 10 sec) [ -10681.8903] [ 2539] [depth= 1] . ( 10 sec) [ -10651.2381] [Branch lengths ] . ( 10 sec) [ -10651.0853] [GTR parameters ] . ( 10 sec) [ -10649.5989] [Alpha ][ 1.048743] . ( 11 sec) [ -10649.5642] [ 2514] [depth= 1] . ( 12 sec) [ -10648.4110] [ 2507] [depth= 1] . ( 12 sec) [ -10648.3876] [ 2508] [depth= 1] . ( 12 sec) [ -10647.5286] [ 2509] [depth= 1] . ( 12 sec) [ -10647.3633] [ 2511] [depth= 1] . ( 15 sec) [ -10638.9964] [Branch lengths ] . ( 15 sec) [ -10638.9839] [GTR parameters ] . ( 15 sec) [ -10638.9753] [Alpha ][ 1.058186] . ( 19 sec) [ -10627.4325] [Branch lengths ] . ( 33 sec) [ -10627.2935] [ 2510] [depth= 1] . ( 41 sec) [ -10619.4462] [Branch lengths ] . ( 41 sec) [ -10619.4254] [GTR parameters ] . ( 41 sec) [ -10619.4241] [Alpha ][ 1.054512] . ( 63 sec) [ -10617.1809] [Branch lengths ] . ( 63 sec) [ -10617.1809] [Topology ] . ( 64 sec) [ -10608.0027] [Topology ] . ( 65 sec) [ -10596.5175] [Topology ] . ( 66 sec) [ -10592.9448] [Topology ] . ( 66 sec) [ -10592.2225] [Topology ] . ( 67 sec) [ -10592.0941] [Topology ] . ( 68 sec) [ -10592.0672] [Topology ] . ( 68 sec) [ -10592.0424] [GTR parameters ] . ( 68 sec) [ -10592.0404] [Alpha ][ 1.059070] . ( 68 sec) [ -10592.0404] [Topology ] . ( 69 sec) [ -10592.0314] [Topology ] . ( 70 sec) [ -10592.0281] [Topology ] . ( 71 sec) [ -10592.0267] [Topology ] . ( 72 sec) [ -10592.0260] [Topology ] . ( 72 sec) [ -10592.0259] [GTR parameters ] . ( 72 sec) [ -10592.0259] [Alpha ][ 1.060130] . ( 72 sec) [ -10592.0259] [Topology ] . ( 73 sec) [ -10592.0255] [Topology ] . ( 73 sec) [ -10592.0255] [GTR parameters ] . ( 73 sec) [ -10592.0255] [Alpha ][ 1.060130] . Checking for NNIs, optimizing five branches... . ( 79 sec) [ -10591.9589] [Topology ] . Checking for NNIs, optimizing five branches... . ( 86 sec) [ -10591.9584] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10591.958387. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-10696.571610 . ( 1 sec) [ -10694.6353] [GTR parameters ] . ( 1 sec) [ -10693.9844] [Alpha ][ 1.087154] . ( 1 sec) [ -10693.9844] [Topology ] . ( 2 sec) [ -10617.6895] [Topology ] . ( 3 sec) [ -10603.4090] [Topology ] . ( 4 sec) [ -10598.1320] [Topology ] . ( 4 sec) [ -10595.6592] [Topology ] . ( 5 sec) [ -10594.3258] [Topology ] . ( 6 sec) [ -10593.6099] [Topology ] . ( 7 sec) [ -10593.2291] [Topology ] . ( 8 sec) [ -10593.0135] [Topology ] . ( 9 sec) [ -10592.8883] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10592.814399 . ( 16 sec) [ -10592.7141] [GTR parameters ] . ( 16 sec) [ -10592.6699] [Alpha ][ 1.066035] . ( 16 sec) [ -10592.6699] [Topology ] . ( 17 sec) [ -10592.6165] [Topology ] . ( 18 sec) [ -10592.5856] [Topology ] . ( 19 sec) [ -10592.5669] [Topology ] . ( 20 sec) [ -10592.5554] [Topology ] . ( 21 sec) [ -10592.5483] [Topology ] . ( 21 sec) [ -10592.5439] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10592.543867 . ( 28 sec) [ -10592.5435] [GTR parameters ] . ( 28 sec) [ -10592.5422] [Alpha ][ 1.062217] . ( 28 sec) [ -10592.5422] [Topology ] . ( 29 sec) [ -10592.5391] [Topology ] . ( 30 sec) [ -10592.5372] [Topology ] . ( 30 sec) [ -10592.5360] [Topology ] . ( 31 sec) [ -10592.5353] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10592.535251 . ( 38 sec) [ -10592.5352] [GTR parameters ] . ( 38 sec) [ -10592.5352] [Alpha ][ 1.062217] . ( 38 sec) [ -10592.5352] [Topology ] . ( 39 sec) [ -10592.5347] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 52 sec) [ -10694.6353] [GTR parameters ] . ( 52 sec) [ -10693.9844] [Alpha ][ 1.087154] . ( 52 sec) [ -10692.5984] [ 2491] [depth= 1] . ( 52 sec) [ -10692.4701] [ 2490] [depth= 1] . ( 52 sec) [ -10692.1352] [ 2491] [depth= 1] . ( 52 sec) [ -10690.2151] [ 2492] [depth= 2] . ( 52 sec) [ -10688.6342] [ 2492] [depth= 1] . ( 53 sec) [ -10685.3503] [ 2497] [depth= 1] . ( 53 sec) [ -10672.2878] [ 2498] [depth= 1] . ( 53 sec) [ -10671.1974] [ 2497] [depth= 1] . ( 53 sec) [ -10665.1161] [ 2502] [depth= 1] . ( 53 sec) [ -10661.0885] [ 2514] [depth= 1] . ( 53 sec) [ -10658.8661] [ 2511] [depth= 1] . ( 53 sec) [ -10657.3290] [ 2511] [depth= 1] . ( 54 sec) [ -10657.3187] [ 2511] [depth= 1] . ( 54 sec) [ -10656.8438] [ 2511] [depth= 1] . ( 54 sec) [ -10652.9075] [ 2502] [depth= 1] . ( 54 sec) [ -10649.8132] [ 2505] [depth= 1] . ( 54 sec) [ -10648.2321] [ 2505] [depth= 1] . ( 54 sec) [ -10645.8625] [ 2505] [depth= 1] . ( 55 sec) [ -10645.7963] [ 2509] [depth= 1] . ( 55 sec) [ -10645.6961] [ 2511] [depth= 1] . ( 56 sec) [ -10598.2174] [Branch lengths ] . ( 56 sec) [ -10598.1359] [GTR parameters ] . ( 56 sec) [ -10598.1269] [Alpha ][ 1.076709] . ( 57 sec) [ -10597.7301] [ 2513] [depth= 1] . ( 58 sec) [ -10597.7137] [ 2514] [depth= 1] . ( 58 sec) [ -10597.5528] [ 2516] [depth= 1] . ( 60 sec) [ -10593.5177] [Branch lengths ] . ( 61 sec) [ -10593.5111] [GTR parameters ] . ( 61 sec) [ -10593.5060] [Alpha ][ 1.069079] . ( 65 sec) [ -10592.7190] [Branch lengths ] . ( 75 sec) [ -10592.5598] [ 2516] [depth= 1] . ( 87 sec) [ -10592.3160] [Branch lengths ] . ( 87 sec) [ -10592.3146] [GTR parameters ] . ( 87 sec) [ -10592.3103] [Alpha ][ 1.062209] . ( 87 sec) [ -10592.3103] [Topology ] . ( 88 sec) [ -10592.2693] [Topology ] . ( 89 sec) [ -10592.2493] [Topology ] . ( 90 sec) [ -10592.2374] [Topology ] . ( 90 sec) [ -10592.2301] [Topology ] . ( 91 sec) [ -10592.2256] [Topology ] . ( 92 sec) [ -10592.2227] [Topology ] . ( 92 sec) [ -10592.2227] [GTR parameters ] . ( 92 sec) [ -10592.2224] [Alpha ][ 1.060463] . ( 92 sec) [ -10592.2224] [Topology ] . ( 93 sec) [ -10592.2205] [Topology ] . ( 94 sec) [ -10592.2193] [Topology ] . ( 95 sec) [ -10592.2186] [Topology ] . ( 95 sec) [ -10592.2186] [GTR parameters ] . ( 95 sec) [ -10592.2186] [Alpha ][ 1.060463] . ( 95 sec) [ -10592.2186] [Topology ] . ( 96 sec) [ -10592.2181] [Topology ] . ( 96 sec) [ -10592.2181] [GTR parameters ] . ( 96 sec) [ -10592.2181] [Alpha ][ 1.060463] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10592.534732 . Log likelihood obtained after SPR moves : -10592.218086 . Log likelihood of the current tree: -10592.218086. . Printing the most likely tree in file 'data11.phy_phyml_tree.txt'... . Best log likelihood : -10591.921676 . Time used 0h1m42s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo