.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2975_93x982_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 . Compressing sequences... . 725 patterns found. (out of a total of 982 sites) . 454 sites without polymorphism (46.23%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 36Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -28108.1978] [GTR parameters ] . ( 4 sec) [ -27421.1155] [Alpha ][ 0.500960] . ( 4 sec) [ -27294.2586] [ 4733] [depth= 11] . ( 4 sec) [ -27116.5000] [ 4716] [depth= 10] . ( 4 sec) [ -27096.4597] [ 4709] [depth= 3] . ( 5 sec) [ -27086.9316] [ 4707] [depth= 6] . ( 5 sec) [ -26908.9738] [ 4693] [depth= 3] . ( 5 sec) [ -26809.8403] [ 4685] [depth= 8] . ( 5 sec) [ -26756.2972] [ 4669] [depth= 3] . ( 5 sec) [ -26726.2296] [ 4668] [depth= 2] . ( 5 sec) [ -26723.6454] [ 4668] [depth= 1] . ( 5 sec) [ -26723.5096] [ 4665] [depth= 2] . ( 6 sec) [ -26679.6625] [ 4659] [depth= 1] . ( 6 sec) [ -26208.2818] [ 4657] [depth= 5] . ( 6 sec) [ -25842.3611] [ 4599] [depth= 10] . ( 6 sec) [ -25812.1561] [ 4597] [depth= 2] . ( 6 sec) [ -25770.4914] [ 4588] [depth= 7] . ( 6 sec) [ -25564.5536] [ 4582] [depth= 3] . ( 6 sec) [ -25393.5198] [ 4528] [depth= 6] . ( 7 sec) [ -25387.5152] [ 4528] [depth= 2] . ( 7 sec) [ -25373.2580] [ 4516] [depth= 4] . ( 7 sec) [ -25265.9564] [ 4502] [depth= 20] . ( 7 sec) [ -25065.7895] [ 4498] [depth= 1] . ( 8 sec) [ -24758.7672] [ 4480] [depth= 14] . ( 8 sec) [ -24753.1650] [ 4480] [depth= 1] . ( 8 sec) [ -24654.3003] [ 4480] [depth= 1] . ( 8 sec) [ -24612.5058] [ 4472] [depth= 7] . ( 8 sec) [ -24571.6636] [ 4471] [depth= 8] . ( 9 sec) [ -24495.3014] [ 4454] [depth= 13] . ( 9 sec) [ -24383.5843] [ 4455] [depth= 16] . ( 9 sec) [ -24306.8381] [ 4432] [depth= 6] . ( 9 sec) [ -24297.1739] [ 4430] [depth= 2] . ( 9 sec) [ -24274.9515] [ 4425] [depth= 3] . ( 10 sec) [ -24059.3017] [ 4400] [depth= 12] . ( 10 sec) [ -23797.2657] [ 4331] [depth= 8] . ( 10 sec) [ -23465.0897] [ 4310] [depth= 7] . ( 10 sec) [ -23264.5112] [ 4243] [depth= 10] . ( 10 sec) [ -23161.9681] [ 4216] [depth= 24] . ( 10 sec) [ -23100.2166] [ 4202] [depth= 20] . ( 11 sec) [ -22972.7555] [ 4165] [depth= 6] . ( 11 sec) [ -22937.5819] [ 4162] [depth= 1] . ( 11 sec) [ -22847.4894] [ 4165] [depth= 1] . ( 11 sec) [ -22820.9647] [ 4152] [depth= 1] . ( 11 sec) [ -22746.3245] [ 4126] [depth= 4] . ( 12 sec) [ -22731.0516] [ 4120] [depth= 1] . ( 12 sec) [ -21933.5006] [ 4053] [depth= 9] . ( 12 sec) [ -21871.5739] [ 4055] [depth= 1] . ( 12 sec) [ -21425.1391] [ 3988] [depth= 16] . ( 13 sec) [ -21373.6695] [ 3986] [depth= 2] . ( 13 sec) [ -21152.4864] [ 3935] [depth= 18] . ( 13 sec) [ -21129.9841] [ 3927] [depth= 5] . ( 13 sec) [ -21119.5785] [ 3927] [depth= 1] . ( 14 sec) [ -21046.4890] [ 3899] [depth= 7] . ( 14 sec) [ -20887.3178] [ 3890] [depth= 1] . ( 14 sec) [ -20802.2593] [ 3857] [depth= 17] . ( 14 sec) [ -20746.7310] [ 3840] [depth= 9] . ( 14 sec) [ -20631.2325] [ 3794] [depth= 7] . ( 14 sec) [ -20540.5758] [ 3793] [depth= 1] . ( 15 sec) [ -20385.1590] [ 3764] [depth= 12] . ( 15 sec) [ -20167.6574] [ 3748] [depth= 1] . ( 15 sec) [ -20090.7190] [ 3717] [depth= 11] . ( 15 sec) [ -19974.0371] [ 3714] [depth= 2] . ( 15 sec) [ -19805.0884] [ 3655] [depth= 13] . ( 15 sec) [ -19747.2494] [ 3635] [depth= 1] . ( 16 sec) [ -19452.4871] [ 3592] [depth= 9] . ( 16 sec) [ -19389.3425] [ 3588] [depth= 12] . ( 16 sec) [ -19240.0500] [ 3570] [depth= 6] . ( 16 sec) [ -19149.7624] [ 3551] [depth= 13] . ( 16 sec) [ -19095.0840] [ 3543] [depth= 17] . ( 17 sec) [ -19086.7956] [ 3531] [depth= 13] . ( 17 sec) [ -19079.0444] [ 3529] [depth= 1] . ( 17 sec) [ -18900.4281] [ 3472] [depth= 8] . ( 17 sec) [ -18864.4289] [ 3466] [depth= 15] . ( 17 sec) [ -18853.1652] [ 3461] [depth= 3] . ( 17 sec) [ -18371.3173] [ 3448] [depth= 17] . ( 18 sec) [ -18294.8785] [ 3393] [depth= 18] . ( 18 sec) [ -18287.0671] [ 3394] [depth= 15] . ( 18 sec) [ -17996.7531] [ 3352] [depth= 14] . ( 18 sec) [ -17846.9722] [ 3346] [depth= 1] . ( 18 sec) [ -17751.6140] [ 3324] [depth= 23] . ( 18 sec) [ -17568.2636] [ 3292] [depth= 8] . ( 19 sec) [ -17527.5008] [ 3287] [depth= 1] . ( 19 sec) [ -17431.2655] [ 3280] [depth= 26] . ( 19 sec) [ -17370.0912] [ 3266] [depth= 1] . ( 19 sec) [ -17220.2103] [ 3212] [depth= 20] . ( 19 sec) [ -17211.9249] [ 3213] [depth= 1] . ( 19 sec) [ -17176.0760] [ 3210] [depth= 1] . ( 20 sec) [ -16919.6439] [ 3156] [depth= 5] . ( 20 sec) [ -16900.2888] [ 3151] [depth= 1] . ( 20 sec) [ -16878.4797] [ 3167] [depth= 12] . ( 20 sec) [ -16709.3590] [ 3117] [depth= 11] . ( 20 sec) [ -16671.8261] [ 3107] [depth= 15] . ( 20 sec) [ -16627.7522] [ 3104] [depth= 1] . ( 21 sec) [ -16583.2810] [ 3102] [depth= 1] . ( 21 sec) [ -15953.1362] [ 3085] [depth= 11] . ( 21 sec) [ -15868.9755] [ 3063] [depth= 3] . ( 21 sec) [ -15816.2117] [ 3046] [depth= 16] . ( 21 sec) [ -15701.6424] [ 3028] [depth= 1] . ( 22 sec) [ -15467.1648] [ 3016] [depth= 8] . ( 22 sec) [ -15317.5490] [ 2982] [depth= 20] . ( 22 sec) [ -15236.6011] [ 2970] [depth= 19] . ( 22 sec) [ -15227.4345] [ 2970] [depth= 1] . ( 22 sec) [ -15207.5260] [ 2963] [depth= 1] . ( 22 sec) [ -15191.0338] [ 2964] [depth= 1] . ( 23 sec) [ -15164.1242] [ 2964] [depth= 1] . ( 23 sec) [ -15083.0054] [ 2929] [depth= 7] . ( 23 sec) [ -15082.6271] [ 2929] [depth= 1] . ( 23 sec) [ -15063.1399] [ 2927] [depth= 2] . ( 24 sec) [ -15010.3782] [ 2917] [depth= 2] . ( 24 sec) [ -14956.2719] [ 2898] [depth= 3] . ( 24 sec) [ -14951.4602] [ 2889] [depth= 2] . ( 24 sec) [ -14885.6655] [ 2877] [depth= 16] . ( 25 sec) [ -14871.8454] [ 2864] [depth= 3] . ( 25 sec) [ -14774.5104] [ 2854] [depth= 2] . ( 25 sec) [ -14748.8101] [ 2838] [depth= 2] . ( 25 sec) [ -14636.0084] [ 2815] [depth= 2] . ( 25 sec) [ -14611.6629] [ 2810] [depth= 1] . ( 26 sec) [ -14574.6585] [ 2811] [depth= 1] . ( 26 sec) [ -14548.1288] [ 2801] [depth= 14] . ( 26 sec) [ -14333.1439] [ 2748] [depth= 3] . ( 26 sec) [ -14323.8268] [ 2743] [depth= 16] . ( 27 sec) [ -14307.0187] [ 2743] [depth= 1] . ( 27 sec) [ -14306.5223] [ 2743] [depth= 1] . ( 27 sec) [ -14265.9531] [ 2734] [depth= 1] . ( 27 sec) [ -14265.4533] [ 2734] [depth= 1] . ( 28 sec) [ -14199.3458] [ 2721] [depth= 15] . ( 28 sec) [ -14191.9720] [ 2720] [depth= 1] . ( 28 sec) [ -14171.2470] [ 2704] [depth= 11] . ( 28 sec) [ -14144.3173] [ 2700] [depth= 1] . ( 28 sec) [ -14085.9012] [ 2672] [depth= 11] . ( 29 sec) [ -14065.3757] [ 2671] [depth= 2] . ( 29 sec) [ -14040.9926] [ 2671] [depth= 2] . ( 29 sec) [ -14026.7167] [ 2675] [depth= 2] . ( 29 sec) [ -13996.0475] [ 2670] [depth= 3] . ( 29 sec) [ -13989.9421] [ 2661] [depth= 5] . ( 30 sec) [ -13971.2326] [ 2654] [depth= 5] . ( 30 sec) [ -13962.5938] [ 2651] [depth= 1] . ( 30 sec) [ -13952.2557] [ 2649] [depth= 1] . ( 30 sec) [ -13932.9459] [ 2639] [depth= 3] . ( 31 sec) [ -13837.8401] [ 2620] [depth= 7] . ( 31 sec) [ -13736.6129] [ 2618] [depth= 1] . ( 32 sec) [ -13721.0739] [ 2607] [depth= 13] . ( 32 sec) [ -13679.5659] [ 2601] [depth= 8] . ( 32 sec) [ -13647.2550] [ 2591] [depth= 2] . ( 33 sec) [ -13638.0271] [ 2589] [depth= 1] . ( 33 sec) [ -13633.8241] [ 2595] [depth= 1] . ( 33 sec) [ -13632.7647] [ 2597] [depth= 8] . ( 33 sec) [ -13632.0813] [ 2598] [depth= 1] . ( 34 sec) [ -13625.0217] [ 2602] [depth= 2] . ( 34 sec) [ -13580.3354] [ 2584] [depth= 5] . ( 34 sec) [ -13578.3964] [ 2584] [depth= 1] . ( 34 sec) [ -13570.9593] [ 2584] [depth= 1] . ( 34 sec) [ -13534.5151] [ 2571] [depth= 1] . ( 35 sec) [ -13532.1059] [ 2575] [depth= 5] . ( 35 sec) [ -13480.2517] [ 2559] [depth= 2] . ( 35 sec) [ -13438.4151] [ 2552] [depth= 3] . ( 35 sec) [ -13431.1368] [ 2551] [depth= 2] . ( 35 sec) [ -13428.6905] [ 2551] [depth= 1] . ( 36 sec) [ -13403.9339] [ 2550] [depth= 2] . ( 36 sec) [ -13396.6080] [ 2546] [depth= 2] . ( 36 sec) [ -13387.5580] [ 2541] [depth= 7] . ( 36 sec) [ -13379.3289] [ 2535] [depth= 2] . ( 36 sec) [ -13372.1668] [ 2523] [depth= 3] . ( 37 sec) [ -13356.7782] [ 2514] [depth= 5] . ( 37 sec) [ -13353.2376] [ 2512] [depth= 5] . ( 37 sec) [ -13353.0101] [ 2514] [depth= 1] . ( 37 sec) [ -13275.2751] [ 2515] [depth= 3] . ( 38 sec) [ -13271.7536] [ 2515] [depth= 2] . ( 38 sec) [ -13264.5837] [ 2515] [depth= 3] . ( 38 sec) [ -13258.4962] [ 2516] [depth= 1] . ( 39 sec) [ -13258.1673] [ 2520] [depth= 3] . ( 39 sec) [ -13257.2154] [ 2527] [depth= 1] . ( 39 sec) [ -13256.7158] [ 2523] [depth= 1] . ( 39 sec) [ -13252.5682] [ 2521] [depth= 1] . ( 40 sec) [ -13251.1937] [ 2521] [depth= 1] . ( 40 sec) [ -13248.2639] [ 2522] [depth= 1] . ( 40 sec) [ -13237.7807] [ 2521] [depth= 3] . ( 40 sec) [ -13228.5457] [ 2521] [depth= 2] . ( 40 sec) [ -13221.3950] [ 2514] [depth= 1] . ( 41 sec) [ -13219.6668] [ 2514] [depth= 1] . ( 41 sec) [ -13215.1853] [ 2515] [depth= 1] . ( 41 sec) [ -13177.8013] [ 2515] [depth= 1] . ( 42 sec) [ -13111.8946] [ 2498] [depth= 2] . ( 42 sec) [ -13103.2514] [ 2494] [depth= 2] . ( 42 sec) [ -13101.0790] [ 2495] [depth= 1] . ( 43 sec) [ -13084.2828] [ 2494] [depth= 4] . ( 43 sec) [ -13041.3175] [ 2483] [depth= 13] . ( 43 sec) [ -13032.6583] [ 2479] [depth= 4] . ( 44 sec) [ -13031.9888] [ 2478] [depth= 1] . ( 44 sec) [ -13030.1741] [ 2477] [depth= 2] . ( 45 sec) [ -12987.2360] [ 2455] [depth= 7] . ( 45 sec) [ -12983.6823] [ 2455] [depth= 1] . ( 45 sec) [ -12969.9381] [ 2455] [depth= 1] . ( 45 sec) [ -12965.2428] [ 2455] [depth= 1] . ( 45 sec) [ -12964.8528] [ 2455] [depth= 1] . ( 45 sec) [ -12964.5515] [ 2457] [depth= 1] . ( 46 sec) [ -12963.1584] [ 2459] [depth= 1] . ( 46 sec) [ -12963.1293] [ 2459] [depth= 1] . ( 46 sec) [ -12892.7588] [ 2451] [depth= 7] . ( 46 sec) [ -12875.7344] [ 2442] [depth= 5] . ( 47 sec) [ -12869.8253] [ 2441] [depth= 1] . ( 47 sec) [ -12869.3500] [ 2441] [depth= 1] . ( 48 sec) [ -12643.4463] [Branch lengths ] . ( 58 sec) [ -12629.1411] [GTR parameters ] . ( 58 sec) [ -12617.5342] [Alpha ][ 0.391977] . ( 58 sec) [ -12617.3625] [ 2438] [depth= 1] . ( 59 sec) [ -12616.4767] [ 2438] [depth= 1] . ( 59 sec) [ -12616.3703] [ 2439] [depth= 1] . ( 59 sec) [ -12614.2765] [ 2437] [depth= 1] . ( 60 sec) [ -12610.0689] [ 2437] [depth= 2] . ( 60 sec) [ -12608.5700] [ 2434] [depth= 1] . ( 60 sec) [ -12602.3991] [ 2435] [depth= 2] . ( 60 sec) [ -12599.7224] [ 2434] [depth= 1] . ( 61 sec) [ -12586.7923] [ 2429] [depth= 3] . ( 61 sec) [ -12572.0564] [ 2423] [depth= 1] . ( 61 sec) [ -12561.5591] [ 2420] [depth= 1] . ( 61 sec) [ -12561.5240] [ 2420] [depth= 1] . ( 62 sec) [ -12560.8788] [ 2421] [depth= 1] . ( 65 sec) [ -12559.9249] [ 2422] [depth= 1] . ( 65 sec) [ -12558.9023] [ 2422] [depth= 1] . ( 65 sec) [ -12553.6482] [ 2419] [depth= 5] . ( 65 sec) [ -12546.0314] [ 2419] [depth= 1] . ( 66 sec) [ -12538.8127] [ 2414] [depth= 2] . ( 66 sec) [ -12538.6168] [ 2413] [depth= 3] . ( 67 sec) [ -12537.5766] [ 2413] [depth= 1] . ( 68 sec) [ -12535.9018] [ 2411] [depth= 1] . ( 68 sec) [ -12534.0154] [ 2408] [depth= 2] . ( 68 sec) [ -12529.4576] [ 2406] [depth= 1] . ( 69 sec) [ -12524.9949] [ 2404] [depth= 2] . ( 70 sec) [ -12504.3126] [ 2394] [depth= 1] . ( 70 sec) [ -12498.9536] [ 2390] [depth= 2] . ( 71 sec) [ -12497.7994] [ 2392] [depth= 1] . ( 72 sec) [ -12497.7851] [ 2392] [depth= 1] . ( 73 sec) [ -12495.6682] [ 2381] [depth= 1] . ( 74 sec) [ -12495.5438] [ 2382] [depth= 1] . ( 74 sec) [ -12483.9253] [ 2380] [depth= 1] . ( 75 sec) [ -12483.3486] [ 2381] [depth= 2] . ( 75 sec) [ -12466.6071] [ 2374] [depth= 7] . ( 75 sec) [ -12465.2898] [ 2374] [depth= 7] . ( 76 sec) [ -12440.1247] [ 2363] [depth= 4] . ( 76 sec) [ -12439.6073] [ 2361] [depth= 2] . ( 77 sec) [ -12439.2583] [ 2361] [depth= 1] . ( 78 sec) [ -12439.2377] [ 2363] [depth= 1] . ( 78 sec) [ -12437.5069] [ 2364] [depth= 1] . ( 79 sec) [ -12425.1333] [ 2362] [depth= 2] . ( 79 sec) [ -12424.0004] [ 2363] [depth= 1] . ( 80 sec) [ -12418.3584] [ 2358] [depth= 8] . ( 81 sec) [ -12414.4472] [ 2355] [depth= 1] . ( 82 sec) [ -12350.3378] [ 2357] [depth= 6] . ( 83 sec) [ -12349.6145] [ 2357] [depth= 1] . ( 84 sec) [ -12349.5542] [ 2358] [depth= 1] . ( 87 sec) [ -12343.8345] [ 2356] [depth= 1] . ( 88 sec) [ -12341.8032] [ 2352] [depth= 5] . ( 89 sec) [ -12341.6435] [ 2351] [depth= 1] . ( 91 sec) [ -12341.6308] [ 2351] [depth= 1] . ( 92 sec) [ -12341.4645] [ 2353] [depth= 2] . ( 95 sec) [ -12340.8976] [ 2355] [depth= 1] . ( 96 sec) [ -12339.6244] [ 2353] [depth= 1] . ( 96 sec) [ -12339.5262] [ 2354] [depth= 1] . ( 96 sec) [ -12337.1908] [ 2353] [depth= 1] . ( 97 sec) [ -12336.9813] [ 2353] [depth= 1] . ( 98 sec) [ -12336.5287] [ 2356] [depth= 1] . ( 99 sec) [ -12336.4268] [ 2356] [depth= 1] . ( 102 sec) [ -12335.3693] [ 2355] [depth= 1] . ( 104 sec) [ -12335.3280] [ 2357] [depth= 2] . ( 105 sec) [ -12335.2015] [ 2358] [depth= 1] . ( 105 sec) [ -12335.0781] [ 2358] [depth= 1] . ( 106 sec) [ -12303.9709] [Branch lengths ] . ( 111 sec) [ -12303.6924] [GTR parameters ] . ( 112 sec) [ -12303.6853] [Alpha ][ 0.394384] . ( 114 sec) [ -12303.6308] [ 2358] [depth= 1] . ( 114 sec) [ -12303.3266] [ 2360] [depth= 1] . ( 116 sec) [ -12302.8154] [ 2362] [depth= 1] . ( 117 sec) [ -12301.9599] [ 2363] [depth= 1] . ( 127 sec) [ -12301.2062] [ 2367] [depth= 1] . ( 130 sec) [ -12299.9725] [ 2363] [depth= 1] . ( 132 sec) [ -12295.7224] [ 2360] [depth= 2] . ( 132 sec) [ -12295.5398] [ 2359] [depth= 1] . ( 133 sec) [ -12293.0695] [ 2360] [depth= 2] . ( 134 sec) [ -12293.0583] [ 2360] [depth= 1] . ( 142 sec) [ -12292.3482] [ 2360] [depth= 2] . ( 144 sec) [ -12291.7642] [ 2359] [depth= 1] . ( 168 sec) [ -12289.1062] [Branch lengths ] . ( 172 sec) [ -12289.0992] [GTR parameters ] . ( 172 sec) [ -12289.0990] [Alpha ][ 0.394779] . ( 179 sec) [ -12289.0836] [ 2359] [depth= 1] . ( 241 sec) [ -12288.4139] [Branch lengths ] . ( 245 sec) [ -12288.4131] [GTR parameters ] . ( 245 sec) [ -12288.4131] [Alpha ][ 0.394779] . ( 387 sec) [ -12288.3491] [Branch lengths ] . ( 387 sec) [ -12288.3491] [Topology ] . ( 390 sec) [ -12288.3466] [Topology ] . ( 393 sec) [ -12288.3459] [Topology ] . ( 394 sec) [ -12288.3459] [GTR parameters ] . ( 394 sec) [ -12288.3458] [Alpha ][ 0.394384] . ( 394 sec) [ -12288.3458] [Topology ] . ( 397 sec) [ -12288.3455] [Topology ] . ( 398 sec) [ -12288.3455] [GTR parameters ] . ( 398 sec) [ -12288.3455] [Alpha ][ 0.394384] . Checking for NNIs, optimizing five branches... . ( 419 sec) [ -12288.3453] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12288.345335. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 5 sec) [ -27755.9721] [GTR parameters ] . ( 5 sec) [ -27082.7609] [Alpha ][ 0.500960] . ( 6 sec) [ -26792.3468] [ 4731] [depth= 15] . ( 6 sec) [ -26301.0415] [ 4714] [depth= 9] . ( 6 sec) [ -26297.2674] [ 4711] [depth= 2] . ( 6 sec) [ -26082.5621] [ 4708] [depth= 11] . ( 6 sec) [ -25534.8924] [ 4689] [depth= 2] . ( 6 sec) [ -25527.7872] [ 4687] [depth= 4] . ( 6 sec) [ -25436.8248] [ 4685] [depth= 9] . ( 7 sec) [ -25314.5228] [ 4641] [depth= 4] . ( 7 sec) [ -25304.3453] [ 4637] [depth= 1] . ( 7 sec) [ -25161.6196] [ 4627] [depth= 4] . ( 7 sec) [ -25160.4435] [ 4626] [depth= 1] . ( 7 sec) [ -25104.9113] [ 4619] [depth= 5] . ( 7 sec) [ -25039.8286] [ 4615] [depth= 8] . ( 7 sec) [ -24868.3311] [ 4614] [depth= 1] . ( 8 sec) [ -24723.3803] [ 4608] [depth= 5] . ( 8 sec) [ -24565.0667] [ 4579] [depth= 3] . ( 8 sec) [ -24483.7777] [ 4575] [depth= 10] . ( 8 sec) [ -24437.1815] [ 4573] [depth= 1] . ( 8 sec) [ -24337.3567] [ 4570] [depth= 8] . ( 8 sec) [ -24299.4495] [ 4558] [depth= 4] . ( 8 sec) [ -24268.4690] [ 4554] [depth= 1] . ( 9 sec) [ -24262.1772] [ 4546] [depth= 3] . ( 9 sec) [ -24234.2632] [ 4546] [depth= 1] . ( 9 sec) [ -23960.4839] [ 4533] [depth= 11] . ( 9 sec) [ -23853.2584] [ 4521] [depth= 10] . ( 10 sec) [ -23755.3059] [ 4471] [depth= 14] . ( 10 sec) [ -23502.0468] [ 4448] [depth= 10] . ( 10 sec) [ -23368.3770] [ 4448] [depth= 1] . ( 10 sec) [ -23228.5127] [ 4437] [depth= 11] . ( 10 sec) [ -23033.1901] [ 4390] [depth= 31] . ( 11 sec) [ -22947.0912] [ 4371] [depth= 1] . ( 11 sec) [ -22911.5172] [ 4360] [depth= 29] . ( 11 sec) [ -22901.9749] [ 4356] [depth= 1] . ( 11 sec) [ -22848.6751] [ 4342] [depth= 1] . ( 11 sec) [ -22800.2255] [ 4355] [depth= 33] . ( 12 sec) [ -22796.8336] [ 4359] [depth= 27] . ( 12 sec) [ -22630.7726] [ 4315] [depth= 32] . ( 12 sec) [ -22340.7347] [ 4304] [depth= 5] . ( 12 sec) [ -22285.0907] [ 4296] [depth= 2] . ( 12 sec) [ -22214.8641] [ 4265] [depth= 11] . ( 13 sec) [ -22135.8867] [ 4260] [depth= 1] . ( 13 sec) [ -22053.4178] [ 4236] [depth= 13] . ( 13 sec) [ -21979.1803] [ 4235] [depth= 12] . ( 13 sec) [ -21960.8032] [ 4229] [depth= 1] . ( 14 sec) [ -21932.9936] [ 4225] [depth= 2] . ( 14 sec) [ -21854.1066] [ 4204] [depth= 1] . ( 14 sec) [ -21746.7348] [ 4174] [depth= 18] . ( 14 sec) [ -21719.0380] [ 4166] [depth= 30] . ( 14 sec) [ -21674.9466] [ 4165] [depth= 1] . ( 15 sec) [ -21530.9843] [ 4157] [depth= 5] . ( 15 sec) [ -21420.5679] [ 4128] [depth= 11] . ( 15 sec) [ -21378.9312] [ 4120] [depth= 5] . ( 15 sec) [ -21289.2090] [ 4121] [depth= 7] . ( 16 sec) [ -20988.2806] [ 4080] [depth= 3] . ( 16 sec) [ -20956.4844] [ 4071] [depth= 6] . ( 16 sec) [ -20617.3603] [ 4064] [depth= 1] . ( 16 sec) [ -20532.4432] [ 4038] [depth= 11] . ( 17 sec) [ -20425.3822] [ 4023] [depth= 17] . ( 17 sec) [ -20319.3392] [ 3994] [depth= 1] . ( 17 sec) [ -20263.4218] [ 3988] [depth= 11] . ( 17 sec) [ -20194.1086] [ 3965] [depth= 12] . ( 17 sec) [ -20180.3101] [ 3965] [depth= 1] . ( 18 sec) [ -20039.8764] [ 3926] [depth= 9] . ( 18 sec) [ -20010.4347] [ 3911] [depth= 4] . ( 18 sec) [ -19877.5493] [ 3895] [depth= 14] . ( 18 sec) [ -19829.7049] [ 3885] [depth= 3] . ( 18 sec) [ -19594.9828] [ 3834] [depth= 6] . ( 18 sec) [ -19563.6432] [ 3837] [depth= 1] . ( 19 sec) [ -19477.8421] [ 3802] [depth= 1] . ( 19 sec) [ -19469.3535] [ 3803] [depth= 3] . ( 19 sec) [ -19350.5530] [ 3754] [depth= 14] . ( 19 sec) [ -19345.3775] [ 3750] [depth= 1] . ( 19 sec) [ -19334.2133] [ 3746] [depth= 1] . ( 20 sec) [ -19314.5351] [ 3745] [depth= 1] . ( 20 sec) [ -19192.0136] [ 3718] [depth= 17] . ( 20 sec) [ -19057.5740] [ 3702] [depth= 13] . ( 20 sec) [ -18788.9926] [ 3673] [depth= 1] . ( 20 sec) [ -18722.1854] [ 3651] [depth= 19] . ( 21 sec) [ -18546.6484] [ 3618] [depth= 13] . ( 21 sec) [ -18454.9763] [ 3614] [depth= 5] . ( 21 sec) [ -18333.6852] [ 3600] [depth= 12] . ( 21 sec) [ -18325.4541] [ 3590] [depth= 3] . ( 21 sec) [ -18287.9221] [ 3581] [depth= 12] . ( 21 sec) [ -18239.3164] [ 3568] [depth= 5] . ( 21 sec) [ -18113.3592] [ 3563] [depth= 9] . ( 22 sec) [ -18041.6784] [ 3556] [depth= 10] . ( 22 sec) [ -18040.1208] [ 3554] [depth= 1] . ( 22 sec) [ -18013.0510] [ 3548] [depth= 2] . ( 22 sec) [ -17907.0273] [ 3541] [depth= 14] . ( 22 sec) [ -17870.1250] [ 3541] [depth= 14] . ( 23 sec) [ -17849.3396] [ 3541] [depth= 1] . ( 23 sec) [ -17714.1424] [ 3537] [depth= 15] . ( 23 sec) [ -17661.0772] [ 3529] [depth= 9] . ( 23 sec) [ -17611.0633] [ 3509] [depth= 11] . ( 24 sec) [ -17532.6694] [ 3484] [depth= 20] . ( 24 sec) [ -17477.1989] [ 3477] [depth= 9] . ( 24 sec) [ -17258.3261] [ 3447] [depth= 2] . ( 24 sec) [ -17233.2107] [ 3434] [depth= 21] . ( 24 sec) [ -17226.1464] [ 3434] [depth= 1] . ( 24 sec) [ -17206.1673] [ 3431] [depth= 12] . ( 25 sec) [ -17194.7831] [ 3430] [depth= 1] . ( 25 sec) [ -17171.4080] [ 3422] [depth= 8] . ( 26 sec) [ -17066.2364] [ 3378] [depth= 4] . ( 26 sec) [ -16887.7048] [ 3352] [depth= 2] . ( 27 sec) [ -16774.1686] [ 3347] [depth= 18] . ( 27 sec) [ -16682.0661] [ 3343] [depth= 16] . ( 27 sec) [ -16593.6566] [ 3295] [depth= 15] . ( 27 sec) [ -16580.7070] [ 3294] [depth= 1] . ( 27 sec) [ -16540.1658] [ 3276] [depth= 18] . ( 27 sec) [ -16527.1671] [ 3270] [depth= 4] . ( 28 sec) [ -16428.4566] [ 3246] [depth= 13] . ( 28 sec) [ -16411.9902] [ 3244] [depth= 3] . ( 28 sec) [ -16411.3068] [ 3244] [depth= 3] . ( 28 sec) [ -16401.0288] [ 3239] [depth= 3] . ( 28 sec) [ -16372.1669] [ 3238] [depth= 1] . ( 28 sec) [ -16372.0588] [ 3238] [depth= 13] . ( 29 sec) [ -16215.9630] [ 3246] [depth= 1] . ( 29 sec) [ -16161.0886] [ 3221] [depth= 7] . ( 29 sec) [ -15891.9094] [ 3138] [depth= 15] . ( 29 sec) [ -15850.9047] [ 3136] [depth= 2] . ( 30 sec) [ -15845.1323] [ 3134] [depth= 4] . ( 30 sec) [ -15819.8505] [ 3125] [depth= 2] . ( 30 sec) [ -15799.1901] [ 3114] [depth= 2] . ( 30 sec) [ -15760.3683] [ 3105] [depth= 2] . ( 30 sec) [ -15748.0587] [ 3101] [depth= 2] . ( 30 sec) [ -15746.4147] [ 3100] [depth= 1] . ( 31 sec) [ -15669.8422] [ 3092] [depth= 9] . ( 31 sec) [ -15645.9620] [ 3068] [depth= 5] . ( 31 sec) [ -15618.7212] [ 3064] [depth= 1] . ( 31 sec) [ -15618.0614] [ 3064] [depth= 1] . ( 32 sec) [ -15598.9909] [ 3053] [depth= 8] . ( 32 sec) [ -15577.1742] [ 3051] [depth= 1] . ( 32 sec) [ -15524.7847] [ 3045] [depth= 15] . ( 32 sec) [ -15478.8783] [ 3033] [depth= 7] . ( 32 sec) [ -15453.4611] [ 3029] [depth= 1] . ( 32 sec) [ -15420.5584] [ 3022] [depth= 3] . ( 32 sec) [ -15416.7288] [ 3022] [depth= 1] . ( 33 sec) [ -15268.6978] [ 2972] [depth= 8] . ( 33 sec) [ -15238.6773] [ 2959] [depth= 12] . ( 33 sec) [ -15217.5664] [ 2952] [depth= 2] . ( 33 sec) [ -15106.3550] [ 2945] [depth= 2] . ( 34 sec) [ -14896.4193] [ 2936] [depth= 1] . ( 34 sec) [ -14796.4739] [ 2888] [depth= 10] . ( 34 sec) [ -14771.1256] [ 2884] [depth= 3] . ( 34 sec) [ -14750.7552] [ 2883] [depth= 1] . ( 34 sec) [ -14749.7504] [ 2887] [depth= 2] . ( 35 sec) [ -14724.3740] [ 2877] [depth= 1] . ( 35 sec) [ -14722.8527] [ 2877] [depth= 1] . ( 35 sec) [ -14694.2181] [ 2871] [depth= 2] . ( 35 sec) [ -14679.4679] [ 2871] [depth= 1] . ( 36 sec) [ -14664.7383] [ 2873] [depth= 3] . ( 36 sec) [ -14664.7035] [ 2877] [depth= 1] . ( 36 sec) [ -14664.0277] [ 2873] [depth= 1] . ( 36 sec) [ -14623.0752] [ 2867] [depth= 9] . ( 37 sec) [ -14620.5316] [ 2866] [depth= 2] . ( 37 sec) [ -14603.3303] [ 2861] [depth= 12] . ( 37 sec) [ -14548.4407] [ 2844] [depth= 2] . ( 37 sec) [ -14533.1984] [ 2840] [depth= 1] . ( 38 sec) [ -14529.6988] [ 2839] [depth= 2] . ( 38 sec) [ -14497.5499] [ 2839] [depth= 2] . ( 39 sec) [ -14457.9525] [ 2830] [depth= 8] . ( 39 sec) [ -14401.8194] [ 2808] [depth= 10] . ( 39 sec) [ -14278.8028] [ 2772] [depth= 8] . ( 39 sec) [ -14228.7817] [ 2764] [depth= 17] . ( 39 sec) [ -14196.1672] [ 2766] [depth= 1] . ( 39 sec) [ -14193.8337] [ 2764] [depth= 1] . ( 40 sec) [ -14148.6888] [ 2766] [depth= 2] . ( 40 sec) [ -14107.5439] [ 2764] [depth= 1] . ( 41 sec) [ -14083.4596] [ 2760] [depth= 1] . ( 41 sec) [ -14065.8714] [ 2752] [depth= 1] . ( 41 sec) [ -13991.6491] [ 2733] [depth= 17] . ( 41 sec) [ -13962.2437] [ 2719] [depth= 1] . ( 42 sec) [ -13938.4042] [ 2707] [depth= 3] . ( 42 sec) [ -13936.1931] [ 2707] [depth= 1] . ( 42 sec) [ -13883.7695] [ 2692] [depth= 17] . ( 42 sec) [ -13818.9717] [ 2673] [depth= 1] . ( 43 sec) [ -13766.7170] [ 2640] [depth= 13] . ( 43 sec) [ -13763.1254] [ 2640] [depth= 1] . ( 43 sec) [ -13697.5726] [ 2644] [depth= 1] . ( 43 sec) [ -13695.0835] [ 2649] [depth= 1] . ( 43 sec) [ -13693.6891] [ 2649] [depth= 1] . ( 44 sec) [ -13652.3740] [ 2634] [depth= 4] . ( 44 sec) [ -13630.5182] [ 2631] [depth= 1] . ( 44 sec) [ -13626.4986] [ 2629] [depth= 7] . ( 44 sec) [ -13623.1201] [ 2626] [depth= 1] . ( 45 sec) [ -13617.1389] [ 2638] [depth= 1] . ( 45 sec) [ -13592.0132] [ 2626] [depth= 1] . ( 46 sec) [ -13513.3144] [ 2604] [depth= 12] . ( 46 sec) [ -13512.8436] [ 2604] [depth= 1] . ( 46 sec) [ -13493.6802] [ 2601] [depth= 1] . ( 46 sec) [ -13493.1887] [ 2605] [depth= 1] . ( 46 sec) [ -13473.9754] [ 2597] [depth= 6] . ( 46 sec) [ -13432.3450] [ 2574] [depth= 3] . ( 47 sec) [ -13391.8945] [ 2570] [depth= 2] . ( 47 sec) [ -13368.2872] [ 2570] [depth= 2] . ( 47 sec) [ -13367.5731] [ 2569] [depth= 5] . ( 47 sec) [ -13361.9734] [ 2572] [depth= 1] . ( 48 sec) [ -13352.5891] [ 2569] [depth= 9] . ( 48 sec) [ -13349.6483] [ 2566] [depth= 6] . ( 50 sec) [ -13093.2993] [Branch lengths ] . ( 56 sec) [ -13083.9950] [GTR parameters ] . ( 57 sec) [ -13068.9912] [Alpha ][ 0.382948] . ( 57 sec) [ -13060.3811] [ 2560] [depth= 2] . ( 58 sec) [ -13058.4122] [ 2559] [depth= 1] . ( 58 sec) [ -13018.4099] [ 2548] [depth= 2] . ( 58 sec) [ -13016.3493] [ 2543] [depth= 2] . ( 59 sec) [ -13014.1714] [ 2544] [depth= 2] . ( 59 sec) [ -12990.7495] [ 2535] [depth= 3] . ( 59 sec) [ -12990.3156] [ 2536] [depth= 1] . ( 59 sec) [ -12853.0445] [ 2535] [depth= 2] . ( 60 sec) [ -12852.5204] [ 2537] [depth= 2] . ( 60 sec) [ -12851.0892] [ 2536] [depth= 3] . ( 61 sec) [ -12847.8482] [ 2535] [depth= 1] . ( 61 sec) [ -12806.0521] [ 2507] [depth= 1] . ( 62 sec) [ -12797.6774] [ 2499] [depth= 10] . ( 62 sec) [ -12785.9756] [ 2501] [depth= 2] . ( 63 sec) [ -12779.1647] [ 2501] [depth= 4] . ( 63 sec) [ -12695.3155] [ 2477] [depth= 8] . ( 63 sec) [ -12687.8341] [ 2476] [depth= 6] . ( 65 sec) [ -12685.4263] [ 2471] [depth= 1] . ( 65 sec) [ -12678.0190] [ 2469] [depth= 1] . ( 66 sec) [ -12677.6481] [ 2471] [depth= 1] . ( 66 sec) [ -12654.5461] [ 2462] [depth= 19] . ( 67 sec) [ -12649.8820] [ 2464] [depth= 3] . ( 68 sec) [ -12646.3112] [ 2460] [depth= 1] . ( 68 sec) [ -12645.3967] [ 2462] [depth= 3] . ( 70 sec) [ -12637.7965] [ 2451] [depth= 5] . ( 71 sec) [ -12630.3218] [ 2447] [depth= 1] . ( 71 sec) [ -12626.0317] [ 2446] [depth= 2] . ( 72 sec) [ -12622.2841] [ 2440] [depth= 2] . ( 73 sec) [ -12619.0270] [ 2444] [depth= 4] . ( 74 sec) [ -12575.2827] [ 2422] [depth= 5] . ( 74 sec) [ -12516.8925] [ 2394] [depth= 10] . ( 74 sec) [ -12516.6855] [ 2397] [depth= 5] . ( 76 sec) [ -12514.6616] [ 2395] [depth= 1] . ( 76 sec) [ -12514.6439] [ 2395] [depth= 1] . ( 77 sec) [ -12513.9732] [ 2395] [depth= 1] . ( 77 sec) [ -12510.3642] [ 2397] [depth= 1] . ( 81 sec) [ -12507.5550] [ 2396] [depth= 2] . ( 81 sec) [ -12497.4895] [ 2389] [depth= 6] . ( 82 sec) [ -12493.6573] [ 2389] [depth= 7] . ( 82 sec) [ -12492.2069] [ 2394] [depth= 1] . ( 82 sec) [ -12491.8601] [ 2393] [depth= 1] . ( 83 sec) [ -12488.4700] [ 2396] [depth= 8] . ( 83 sec) [ -12488.4596] [ 2396] [depth= 1] . ( 84 sec) [ -12486.6923] [ 2395] [depth= 2] . ( 85 sec) [ -12480.5436] [ 2394] [depth= 2] . ( 85 sec) [ -12478.8373] [ 2397] [depth= 2] . ( 86 sec) [ -12477.3706] [ 2394] [depth= 4] . ( 89 sec) [ -12476.0178] [ 2394] [depth= 2] . ( 90 sec) [ -12445.9998] [ 2385] [depth= 7] . ( 90 sec) [ -12445.7640] [ 2388] [depth= 1] . ( 91 sec) [ -12445.6278] [ 2388] [depth= 1] . ( 92 sec) [ -12438.4091] [ 2385] [depth= 2] . ( 93 sec) [ -12437.0004] [ 2390] [depth= 1] . ( 93 sec) [ -12433.2202] [ 2385] [depth= 1] . ( 93 sec) [ -12431.5173] [ 2381] [depth= 1] . ( 93 sec) [ -12410.4565] [ 2376] [depth= 2] . ( 93 sec) [ -12406.6840] [ 2378] [depth= 1] . ( 94 sec) [ -12406.5631] [ 2378] [depth= 1] . ( 94 sec) [ -12405.1375] [ 2378] [depth= 1] . ( 94 sec) [ -12404.5985] [ 2378] [depth= 1] . ( 95 sec) [ -12404.5819] [ 2378] [depth= 1] . ( 96 sec) [ -12400.7986] [ 2375] [depth= 3] . ( 98 sec) [ -12398.4087] [ 2376] [depth= 2] . ( 99 sec) [ -12395.1637] [ 2381] [depth= 1] . ( 100 sec) [ -12393.1651] [ 2379] [depth= 1] . ( 102 sec) [ -12393.0903] [ 2379] [depth= 1] . ( 103 sec) [ -12387.1824] [ 2373] [depth= 2] . ( 103 sec) [ -12386.4997] [ 2373] [depth= 1] . ( 103 sec) [ -12386.3567] [ 2373] [depth= 1] . ( 104 sec) [ -12386.2979] [ 2372] [depth= 3] . ( 105 sec) [ -12386.1527] [ 2374] [depth= 1] . ( 105 sec) [ -12385.9378] [ 2372] [depth= 1] . ( 107 sec) [ -12385.5259] [ 2370] [depth= 2] . ( 107 sec) [ -12377.2500] [ 2371] [depth= 4] . ( 108 sec) [ -12376.0535] [ 2371] [depth= 2] . ( 109 sec) [ -12343.8754] [Branch lengths ] . ( 114 sec) [ -12343.4534] [GTR parameters ] . ( 115 sec) [ -12343.3060] [Alpha ][ 0.393534] . ( 115 sec) [ -12341.0158] [ 2366] [depth= 1] . ( 118 sec) [ -12339.9532] [ 2364] [depth= 1] . ( 121 sec) [ -12339.6982] [ 2366] [depth= 2] . ( 121 sec) [ -12339.5451] [ 2364] [depth= 1] . ( 122 sec) [ -12336.5826] [ 2363] [depth= 1] . ( 122 sec) [ -12331.7314] [ 2359] [depth= 3] . ( 122 sec) [ -12329.3745] [ 2358] [depth= 1] . ( 124 sec) [ -12328.8989] [ 2358] [depth= 1] . ( 126 sec) [ -12326.6668] [ 2357] [depth= 1] . ( 129 sec) [ -12325.7637] [ 2359] [depth= 4] . ( 130 sec) [ -12323.4826] [ 2355] [depth= 4] . ( 131 sec) [ -12322.4027] [ 2355] [depth= 1] . ( 132 sec) [ -12321.5167] [ 2358] [depth= 1] . ( 132 sec) [ -12320.0091] [ 2356] [depth= 1] . ( 133 sec) [ -12317.9084] [ 2357] [depth= 1] . ( 137 sec) [ -12316.5322] [ 2356] [depth= 1] . ( 137 sec) [ -12316.3807] [ 2356] [depth= 1] . ( 138 sec) [ -12316.3288] [ 2356] [depth= 1] . ( 138 sec) [ -12316.1431] [ 2357] [depth= 1] . ( 139 sec) [ -12310.4105] [ 2354] [depth= 1] . ( 140 sec) [ -12310.3245] [ 2353] [depth= 1] . ( 141 sec) [ -12308.0956] [ 2353] [depth= 1] . ( 143 sec) [ -12307.9396] [ 2348] [depth= 1] . ( 143 sec) [ -12307.8372] [ 2348] [depth= 1] . ( 144 sec) [ -12307.4659] [ 2349] [depth= 3] . ( 151 sec) [ -12307.2201] [ 2349] [depth= 1] . ( 153 sec) [ -12306.1128] [ 2351] [depth= 2] . ( 160 sec) [ -12305.9116] [ 2351] [depth= 1] . ( 162 sec) [ -12302.3091] [ 2348] [depth= 1] . ( 166 sec) [ -12301.8114] [ 2346] [depth= 1] . ( 168 sec) [ -12301.4480] [ 2345] [depth= 1] . ( 170 sec) [ -12301.4002] [ 2344] [depth= 1] . ( 171 sec) [ -12290.1067] [Branch lengths ] . ( 175 sec) [ -12290.0737] [GTR parameters ] . ( 175 sec) [ -12290.0717] [Alpha ][ 0.394797] . ( 185 sec) [ -12289.8696] [ 2344] [depth= 1] . ( 190 sec) [ -12287.6057] [ 2345] [depth= 4] . ( 209 sec) [ -12287.5754] [ 2346] [depth= 1] . ( 228 sec) [ -12286.4369] [Branch lengths ] . ( 231 sec) [ -12286.4113] [GTR parameters ] . ( 232 sec) [ -12286.4103] [Alpha ][ 0.395717] . ( 234 sec) [ -12286.3020] [ 2345] [depth= 1] . ( 272 sec) [ -12286.1653] [ 2344] [depth= 2] . ( 285 sec) [ -12285.8563] [Branch lengths ] . ( 286 sec) [ -12285.8557] [GTR parameters ] . ( 287 sec) [ -12285.8557] [Alpha ][ 0.395717] . ( 355 sec) [ -12285.6655] [ 2344] [depth= 1] . ( 429 sec) [ -12285.5915] [Branch lengths ] . ( 433 sec) [ -12285.5884] [GTR parameters ] . ( 433 sec) [ -12285.5884] [Alpha ][ 0.395717] . ( 433 sec) [ -12285.5884] [Topology ] . ( 436 sec) [ -12285.5825] [Topology ] . ( 439 sec) [ -12285.5805] [Topology ] . ( 442 sec) [ -12285.5796] [Topology ] . ( 443 sec) [ -12285.5796] [GTR parameters ] . ( 443 sec) [ -12285.5793] [Alpha ][ 0.395185] . ( 443 sec) [ -12285.5793] [Topology ] . ( 446 sec) [ -12285.5787] [Topology ] . ( 447 sec) [ -12285.5787] [GTR parameters ] . ( 447 sec) [ -12285.5787] [Alpha ][ 0.395185] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12285.578701. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -27410.2488] [GTR parameters ] . ( 2 sec) [ -26763.2603] [Alpha ][ 0.500960] . ( 3 sec) [ -26279.9124] [ 4656] [depth= 7] . ( 3 sec) [ -25997.4823] [ 4636] [depth= 12] . ( 3 sec) [ -25846.5589] [ 4604] [depth= 16] . ( 3 sec) [ -25799.6327] [ 4588] [depth= 1] . ( 4 sec) [ -25665.5187] [ 4559] [depth= 15] . ( 4 sec) [ -25468.4415] [ 4545] [depth= 2] . ( 4 sec) [ -25419.8867] [ 4541] [depth= 13] . ( 4 sec) [ -25290.2667] [ 4515] [depth= 1] . ( 4 sec) [ -25246.7581] [ 4509] [depth= 3] . ( 5 sec) [ -25233.5009] [ 4505] [depth= 1] . ( 5 sec) [ -25000.4094] [ 4504] [depth= 9] . ( 5 sec) [ -24970.7949] [ 4490] [depth= 1] . ( 5 sec) [ -24793.3005] [ 4469] [depth= 7] . ( 5 sec) [ -24788.9026] [ 4473] [depth= 2] . ( 6 sec) [ -24492.0732] [ 4453] [depth= 5] . ( 6 sec) [ -24284.9142] [ 4388] [depth= 3] . ( 6 sec) [ -24243.8129] [ 4374] [depth= 14] . ( 6 sec) [ -24199.7055] [ 4377] [depth= 5] . ( 6 sec) [ -24179.2086] [ 4372] [depth= 3] . ( 6 sec) [ -24160.4261] [ 4368] [depth= 1] . ( 6 sec) [ -24147.3553] [ 4365] [depth= 1] . ( 7 sec) [ -24102.8071] [ 4357] [depth= 4] . ( 7 sec) [ -24065.8867] [ 4356] [depth= 1] . ( 7 sec) [ -24000.6107] [ 4329] [depth= 11] . ( 7 sec) [ -23988.5235] [ 4329] [depth= 1] . ( 7 sec) [ -23961.2061] [ 4334] [depth= 7] . ( 7 sec) [ -23887.3001] [ 4313] [depth= 11] . ( 7 sec) [ -23726.9763] [ 4304] [depth= 2] . ( 8 sec) [ -23675.7745] [ 4298] [depth= 10] . ( 8 sec) [ -23651.9365] [ 4297] [depth= 1] . ( 8 sec) [ -23483.4682] [ 4278] [depth= 21] . ( 8 sec) [ -23414.5327] [ 4259] [depth= 13] . ( 9 sec) [ -23329.2850] [ 4251] [depth= 21] . ( 9 sec) [ -23156.9862] [ 4237] [depth= 17] . ( 9 sec) [ -23046.2356] [ 4224] [depth= 9] . ( 9 sec) [ -22981.0478] [ 4222] [depth= 22] . ( 9 sec) [ -22922.6379] [ 4190] [depth= 11] . ( 10 sec) [ -22452.7870] [ 4163] [depth= 9] . ( 10 sec) [ -22338.1220] [ 4158] [depth= 9] . ( 10 sec) [ -22190.2386] [ 4118] [depth= 10] . ( 10 sec) [ -22182.1742] [ 4120] [depth= 17] . ( 10 sec) [ -22033.9835] [ 4082] [depth= 6] . ( 10 sec) [ -22030.6313] [ 4083] [depth= 1] . ( 10 sec) [ -22016.9555] [ 4079] [depth= 3] . ( 11 sec) [ -21814.8224] [ 4010] [depth= 14] . ( 11 sec) [ -21682.4451] [ 3993] [depth= 7] . ( 11 sec) [ -21608.0267] [ 3972] [depth= 1] . ( 11 sec) [ -21583.8861] [ 3963] [depth= 8] . ( 11 sec) [ -21465.4760] [ 3954] [depth= 19] . ( 11 sec) [ -21444.3213] [ 3950] [depth= 1] . ( 12 sec) [ -21415.6968] [ 3949] [depth= 3] . ( 12 sec) [ -21373.1811] [ 3939] [depth= 1] . ( 12 sec) [ -21357.3054] [ 3933] [depth= 8] . ( 12 sec) [ -21338.2495] [ 3920] [depth= 6] . ( 12 sec) [ -21239.4232] [ 3905] [depth= 13] . ( 13 sec) [ -21221.7232] [ 3912] [depth= 5] . ( 13 sec) [ -21187.4704] [ 3911] [depth= 1] . ( 13 sec) [ -21139.2520] [ 3909] [depth= 1] . ( 13 sec) [ -21128.8679] [ 3906] [depth= 3] . ( 13 sec) [ -21112.3270] [ 3899] [depth= 19] . ( 14 sec) [ -21041.7535] [ 3896] [depth= 1] . ( 14 sec) [ -20967.6032] [ 3890] [depth= 9] . ( 14 sec) [ -20920.0150] [ 3883] [depth= 3] . ( 14 sec) [ -20877.7046] [ 3880] [depth= 19] . ( 14 sec) [ -20711.1664] [ 3853] [depth= 13] . ( 15 sec) [ -20661.1483] [ 3850] [depth= 1] . ( 15 sec) [ -20640.1910] [ 3848] [depth= 4] . ( 15 sec) [ -20553.9844] [ 3826] [depth= 1] . ( 16 sec) [ -20421.7824] [ 3800] [depth= 15] . ( 16 sec) [ -20372.9566] [ 3795] [depth= 1] . ( 16 sec) [ -20288.7932] [ 3784] [depth= 13] . ( 16 sec) [ -20243.3872] [ 3778] [depth= 2] . ( 16 sec) [ -20213.2068] [ 3769] [depth= 1] . ( 16 sec) [ -20137.9017] [ 3751] [depth= 18] . ( 17 sec) [ -19985.6907] [ 3706] [depth= 15] . ( 17 sec) [ -19921.3773] [ 3703] [depth= 1] . ( 17 sec) [ -19871.1184] [ 3691] [depth= 1] . ( 17 sec) [ -19698.3411] [ 3657] [depth= 18] . ( 17 sec) [ -19681.2915] [ 3639] [depth= 4] . ( 17 sec) [ -19565.5297] [ 3638] [depth= 3] . ( 18 sec) [ -19435.3721] [ 3605] [depth= 1] . ( 18 sec) [ -19415.6349] [ 3599] [depth= 11] . ( 18 sec) [ -19389.9253] [ 3596] [depth= 24] . ( 18 sec) [ -19319.0002] [ 3586] [depth= 1] . ( 18 sec) [ -19119.2507] [ 3577] [depth= 4] . ( 18 sec) [ -19109.7966] [ 3575] [depth= 1] . ( 19 sec) [ -19098.7057] [ 3569] [depth= 1] . ( 19 sec) [ -19087.0953] [ 3564] [depth= 9] . ( 19 sec) [ -19070.1606] [ 3550] [depth= 9] . ( 19 sec) [ -19056.5566] [ 3549] [depth= 1] . ( 19 sec) [ -18906.7159] [ 3537] [depth= 1] . ( 19 sec) [ -18895.1689] [ 3538] [depth= 1] . ( 20 sec) [ -18825.2281] [ 3502] [depth= 2] . ( 20 sec) [ -18817.3878] [ 3499] [depth= 2] . ( 20 sec) [ -18790.7617] [ 3497] [depth= 1] . ( 20 sec) [ -18720.5507] [ 3470] [depth= 3] . ( 20 sec) [ -18618.9695] [ 3456] [depth= 4] . ( 20 sec) [ -18577.9275] [ 3443] [depth= 9] . ( 21 sec) [ -18364.8763] [ 3394] [depth= 9] . ( 21 sec) [ -18157.7020] [ 3356] [depth= 7] . ( 21 sec) [ -17996.4486] [ 3294] [depth= 15] . ( 21 sec) [ -17731.4344] [ 3295] [depth= 1] . ( 21 sec) [ -17629.6104] [ 3263] [depth= 17] . ( 21 sec) [ -17473.8335] [ 3253] [depth= 17] . ( 22 sec) [ -17334.1483] [ 3235] [depth= 16] . ( 22 sec) [ -17322.2980] [ 3234] [depth= 2] . ( 22 sec) [ -17318.6069] [ 3234] [depth= 1] . ( 22 sec) [ -17252.1378] [ 3232] [depth= 1] . ( 22 sec) [ -17225.3683] [ 3224] [depth= 5] . ( 22 sec) [ -17104.1385] [ 3218] [depth= 1] . ( 23 sec) [ -17095.5851] [ 3207] [depth= 5] . ( 23 sec) [ -17093.6232] [ 3206] [depth= 1] . ( 23 sec) [ -17074.6311] [ 3204] [depth= 5] . ( 23 sec) [ -16991.4499] [ 3190] [depth= 12] . ( 23 sec) [ -16981.1897] [ 3189] [depth= 3] . ( 24 sec) [ -16899.4878] [ 3174] [depth= 17] . ( 24 sec) [ -16860.7914] [ 3153] [depth= 10] . ( 24 sec) [ -16852.5519] [ 3154] [depth= 11] . ( 24 sec) [ -16848.6277] [ 3138] [depth= 2] . ( 25 sec) [ -16754.3827] [ 3132] [depth= 9] . ( 25 sec) [ -16683.6496] [ 3112] [depth= 9] . ( 25 sec) [ -16668.6506] [ 3112] [depth= 1] . ( 25 sec) [ -16665.2014] [ 3111] [depth= 2] . ( 25 sec) [ -16631.3935] [ 3108] [depth= 4] . ( 26 sec) [ -16624.6078] [ 3107] [depth= 1] . ( 26 sec) [ -16541.8837] [ 3096] [depth= 8] . ( 26 sec) [ -16496.5519] [ 3097] [depth= 1] . ( 26 sec) [ -16347.1163] [ 3106] [depth= 16] . ( 26 sec) [ -16185.6353] [ 3040] [depth= 17] . ( 26 sec) [ -16161.5665] [ 3029] [depth= 2] . ( 27 sec) [ -16029.5232] [ 3009] [depth= 10] . ( 27 sec) [ -16028.3390] [ 3001] [depth= 6] . ( 27 sec) [ -16017.7771] [ 3001] [depth= 3] . ( 27 sec) [ -15831.8797] [ 3004] [depth= 1] . ( 27 sec) [ -15744.8931] [ 2998] [depth= 17] . ( 28 sec) [ -15603.5216] [ 2988] [depth= 6] . ( 28 sec) [ -15555.4225] [ 2991] [depth= 16] . ( 28 sec) [ -15497.3453] [ 2991] [depth= 19] . ( 29 sec) [ -15494.2169] [ 2987] [depth= 4] . ( 29 sec) [ -15490.9823] [ 2990] [depth= 1] . ( 29 sec) [ -15435.6202] [ 2988] [depth= 7] . ( 29 sec) [ -15433.6984] [ 2990] [depth= 1] . ( 30 sec) [ -15420.2304] [ 2986] [depth= 4] . ( 30 sec) [ -15418.6590] [ 2984] [depth= 1] . ( 30 sec) [ -15389.3375] [ 2986] [depth= 6] . ( 31 sec) [ -15385.4454] [ 2988] [depth= 1] . ( 31 sec) [ -15377.3812] [ 2987] [depth= 3] . ( 31 sec) [ -15251.0260] [ 2949] [depth= 1] . ( 31 sec) [ -15241.2739] [ 2950] [depth= 2] . ( 31 sec) [ -15240.8241] [ 2949] [depth= 2] . ( 32 sec) [ -15235.5201] [ 2949] [depth= 1] . ( 33 sec) [ -15216.7580] [ 2946] [depth= 1] . ( 33 sec) [ -15212.0878] [ 2943] [depth= 2] . ( 33 sec) [ -15206.8528] [ 2941] [depth= 19] . ( 33 sec) [ -15192.1809] [ 2927] [depth= 2] . ( 34 sec) [ -15162.7968] [ 2927] [depth= 1] . ( 34 sec) [ -15039.9493] [ 2908] [depth= 4] . ( 34 sec) [ -15035.8014] [ 2908] [depth= 1] . ( 34 sec) [ -14988.5214] [ 2882] [depth= 10] . ( 35 sec) [ -14969.1723] [ 2880] [depth= 2] . ( 35 sec) [ -14967.5168] [ 2879] [depth= 1] . ( 35 sec) [ -14967.4451] [ 2882] [depth= 2] . ( 36 sec) [ -14933.4800] [ 2876] [depth= 1] . ( 36 sec) [ -14866.5639] [ 2881] [depth= 3] . ( 36 sec) [ -14866.0082] [ 2879] [depth= 1] . ( 36 sec) [ -14854.5972] [ 2877] [depth= 2] . ( 36 sec) [ -14853.7926] [ 2877] [depth= 1] . ( 36 sec) [ -14763.8017] [ 2851] [depth= 11] . ( 37 sec) [ -14760.8379] [ 2851] [depth= 1] . ( 37 sec) [ -14757.1346] [ 2851] [depth= 1] . ( 37 sec) [ -14623.8568] [ 2846] [depth= 6] . ( 37 sec) [ -14505.1990] [ 2808] [depth= 19] . ( 38 sec) [ -14485.5337] [ 2803] [depth= 3] . ( 38 sec) [ -14471.8328] [ 2799] [depth= 8] . ( 38 sec) [ -14469.6764] [ 2802] [depth= 1] . ( 38 sec) [ -14354.8299] [ 2795] [depth= 7] . ( 38 sec) [ -14352.9869] [ 2798] [depth= 2] . ( 39 sec) [ -14307.7750] [ 2783] [depth= 2] . ( 39 sec) [ -14280.9464] [ 2774] [depth= 5] . ( 39 sec) [ -14269.5231] [ 2775] [depth= 2] . ( 39 sec) [ -14231.4871] [ 2764] [depth= 4] . ( 39 sec) [ -14158.2558] [ 2752] [depth= 1] . ( 40 sec) [ -14144.0967] [ 2748] [depth= 1] . ( 40 sec) [ -14138.5726] [ 2747] [depth= 2] . ( 40 sec) [ -14132.1035] [ 2744] [depth= 2] . ( 40 sec) [ -14132.0650] [ 2742] [depth= 1] . ( 40 sec) [ -14125.5279] [ 2731] [depth= 10] . ( 40 sec) [ -14105.8064] [ 2730] [depth= 2] . ( 40 sec) [ -14057.2605] [ 2723] [depth= 1] . ( 41 sec) [ -14051.0326] [ 2725] [depth= 7] . ( 42 sec) [ -13964.9851] [ 2698] [depth= 6] . ( 42 sec) [ -13964.2193] [ 2700] [depth= 1] . ( 42 sec) [ -13954.3868] [ 2696] [depth= 2] . ( 42 sec) [ -13952.1609] [ 2696] [depth= 1] . ( 42 sec) [ -13947.6838] [ 2697] [depth= 7] . ( 43 sec) [ -13925.1875] [ 2699] [depth= 1] . ( 43 sec) [ -13920.7315] [ 2699] [depth= 2] . ( 44 sec) [ -13913.7354] [ 2699] [depth= 1] . ( 44 sec) [ -13906.6045] [ 2678] [depth= 1] . ( 44 sec) [ -13770.4083] [ 2644] [depth= 13] . ( 44 sec) [ -13730.1653] [ 2638] [depth= 2] . ( 45 sec) [ -13726.9413] [ 2642] [depth= 1] . ( 45 sec) [ -13724.4362] [ 2641] [depth= 1] . ( 45 sec) [ -13707.5208] [ 2637] [depth= 1] . ( 45 sec) [ -13662.9940] [ 2634] [depth= 13] . ( 45 sec) [ -13639.7255] [ 2626] [depth= 1] . ( 46 sec) [ -13639.0282] [ 2627] [depth= 1] . ( 46 sec) [ -13638.4651] [ 2627] [depth= 1] . ( 46 sec) [ -13635.0402] [ 2626] [depth= 1] . ( 47 sec) [ -13631.1513] [ 2625] [depth= 1] . ( 47 sec) [ -13630.7950] [ 2625] [depth= 1] . ( 48 sec) [ -13620.8770] [ 2622] [depth= 2] . ( 48 sec) [ -13615.6313] [ 2623] [depth= 2] . ( 48 sec) [ -13615.1231] [ 2628] [depth= 3] . ( 49 sec) [ -13393.6191] [Branch lengths ] . ( 58 sec) [ -13128.7214] [GTR parameters ] . ( 58 sec) [ -13107.6648] [Alpha ][ 0.364217] . ( 58 sec) [ -12991.5465] [ 2585] [depth= 13] . ( 58 sec) [ -12990.6952] [ 2587] [depth= 1] . ( 59 sec) [ -12987.9900] [ 2584] [depth= 1] . ( 59 sec) [ -12943.4769] [ 2559] [depth= 3] . ( 59 sec) [ -12935.7167] [ 2556] [depth= 1] . ( 60 sec) [ -12913.2176] [ 2547] [depth= 6] . ( 60 sec) [ -12861.8615] [ 2536] [depth= 8] . ( 60 sec) [ -12825.0567] [ 2524] [depth= 2] . ( 60 sec) [ -12807.9365] [ 2520] [depth= 1] . ( 61 sec) [ -12806.9126] [ 2518] [depth= 1] . ( 61 sec) [ -12797.2233] [ 2513] [depth= 2] . ( 61 sec) [ -12769.1563] [ 2497] [depth= 8] . ( 61 sec) [ -12762.2017] [ 2502] [depth= 1] . ( 61 sec) [ -12730.6384] [ 2495] [depth= 10] . ( 63 sec) [ -12696.2307] [ 2487] [depth= 5] . ( 63 sec) [ -12682.7252] [ 2465] [depth= 9] . ( 64 sec) [ -12673.1148] [ 2463] [depth= 4] . ( 64 sec) [ -12661.0873] [ 2462] [depth= 2] . ( 64 sec) [ -12658.0166] [ 2455] [depth= 3] . ( 65 sec) [ -12648.5784] [ 2451] [depth= 1] . ( 65 sec) [ -12645.4886] [ 2454] [depth= 1] . ( 65 sec) [ -12552.4852] [ 2430] [depth= 13] . ( 67 sec) [ -12551.8988] [ 2427] [depth= 3] . ( 67 sec) [ -12548.7231] [ 2425] [depth= 1] . ( 70 sec) [ -12538.6219] [ 2422] [depth= 1] . ( 70 sec) [ -12517.8797] [ 2414] [depth= 1] . ( 70 sec) [ -12512.1659] [ 2413] [depth= 1] . ( 71 sec) [ -12512.0147] [ 2408] [depth= 1] . ( 71 sec) [ -12511.1019] [ 2411] [depth= 1] . ( 72 sec) [ -12508.4632] [ 2410] [depth= 2] . ( 72 sec) [ -12495.6018] [ 2400] [depth= 1] . ( 73 sec) [ -12495.3098] [ 2400] [depth= 1] . ( 73 sec) [ -12462.3933] [ 2391] [depth= 2] . ( 74 sec) [ -12452.1913] [ 2381] [depth= 3] . ( 75 sec) [ -12451.2125] [ 2378] [depth= 2] . ( 75 sec) [ -12445.6194] [ 2375] [depth= 4] . ( 77 sec) [ -12440.9203] [ 2372] [depth= 1] . ( 79 sec) [ -12440.5450] [ 2373] [depth= 1] . ( 79 sec) [ -12439.9749] [ 2374] [depth= 1] . ( 80 sec) [ -12439.8417] [ 2376] [depth= 1] . ( 81 sec) [ -12439.8127] [ 2378] [depth= 1] . ( 81 sec) [ -12439.6235] [ 2377] [depth= 1] . ( 81 sec) [ -12439.4939] [ 2376] [depth= 1] . ( 82 sec) [ -12437.7327] [ 2376] [depth= 9] . ( 82 sec) [ -12435.2194] [ 2376] [depth= 1] . ( 83 sec) [ -12434.0165] [ 2377] [depth= 1] . ( 83 sec) [ -12433.7395] [ 2381] [depth= 2] . ( 83 sec) [ -12431.0570] [ 2379] [depth= 1] . ( 84 sec) [ -12425.7980] [ 2377] [depth= 1] . ( 84 sec) [ -12424.3567] [ 2376] [depth= 2] . ( 84 sec) [ -12423.1898] [ 2372] [depth= 3] . ( 84 sec) [ -12381.6957] [ 2370] [depth= 1] . ( 85 sec) [ -12377.9970] [ 2368] [depth= 2] . ( 85 sec) [ -12377.8877] [ 2369] [depth= 1] . ( 85 sec) [ -12374.4021] [ 2368] [depth= 2] . ( 87 sec) [ -12374.3762] [ 2368] [depth= 2] . ( 88 sec) [ -12373.8876] [ 2368] [depth= 1] . ( 89 sec) [ -12371.5968] [ 2368] [depth= 1] . ( 89 sec) [ -12370.3175] [ 2367] [depth= 2] . ( 89 sec) [ -12369.3132] [ 2365] [depth= 1] . ( 90 sec) [ -12369.2989] [ 2365] [depth= 1] . ( 91 sec) [ -12365.5657] [ 2362] [depth= 1] . ( 91 sec) [ -12365.4332] [ 2362] [depth= 1] . ( 94 sec) [ -12362.0181] [ 2360] [depth= 1] . ( 94 sec) [ -12360.4131] [ 2358] [depth= 1] . ( 95 sec) [ -12358.0882] [ 2358] [depth= 8] . ( 96 sec) [ -12357.0339] [ 2358] [depth= 1] . ( 96 sec) [ -12355.1559] [ 2355] [depth= 1] . ( 97 sec) [ -12354.2979] [ 2355] [depth= 1] . ( 98 sec) [ -12353.4158] [ 2354] [depth= 1] . ( 98 sec) [ -12353.2090] [ 2350] [depth= 2] . ( 99 sec) [ -12353.1568] [ 2352] [depth= 1] . ( 100 sec) [ -12351.7741] [ 2351] [depth= 1] . ( 101 sec) [ -12350.5928] [ 2351] [depth= 1] . ( 103 sec) [ -12309.6106] [Branch lengths ] . ( 109 sec) [ -12308.8262] [GTR parameters ] . ( 109 sec) [ -12307.7944] [Alpha ][ 0.391882] . ( 118 sec) [ -12306.7449] [ 2354] [depth= 10] . ( 119 sec) [ -12306.3451] [ 2356] [depth= 1] . ( 120 sec) [ -12306.3308] [ 2353] [depth= 1] . ( 121 sec) [ -12305.0894] [ 2353] [depth= 1] . ( 125 sec) [ -12304.8871] [ 2354] [depth= 1] . ( 128 sec) [ -12304.8073] [ 2355] [depth= 1] . ( 132 sec) [ -12304.1748] [ 2354] [depth= 1] . ( 134 sec) [ -12303.8289] [ 2356] [depth= 2] . ( 149 sec) [ -12301.1224] [ 2347] [depth= 5] . ( 152 sec) [ -12300.6255] [ 2349] [depth= 3] . ( 152 sec) [ -12300.5848] [ 2348] [depth= 1] . ( 152 sec) [ -12298.4654] [ 2347] [depth= 1] . ( 156 sec) [ -12288.0354] [Branch lengths ] . ( 163 sec) [ -12287.8389] [GTR parameters ] . ( 163 sec) [ -12287.8312] [Alpha ][ 0.394424] . ( 195 sec) [ -12287.5688] [ 2346] [depth= 1] . ( 198 sec) [ -12287.0527] [ 2346] [depth= 1] . ( 218 sec) [ -12286.1631] [Branch lengths ] . ( 225 sec) [ -12286.1580] [GTR parameters ] . ( 226 sec) [ -12286.1566] [Alpha ][ 0.395469] . ( 283 sec) [ -12286.1036] [Branch lengths ] . ( 322 sec) [ -12285.8967] [ 2346] [depth= 1] . ( 430 sec) [ -12285.8635] [Branch lengths ] . ( 433 sec) [ -12285.8608] [GTR parameters ] . ( 433 sec) [ -12285.8608] [Alpha ][ 0.395469] . ( 434 sec) [ -12285.8608] [Topology ] . ( 437 sec) [ -12285.8591] [Topology ] . ( 440 sec) [ -12285.8587] [Topology ] . ( 442 sec) [ -12285.8587] [GTR parameters ] . ( 442 sec) [ -12285.8587] [Alpha ][ 0.395469] . ( 442 sec) [ -12285.8587] [Topology ] . ( 445 sec) [ -12285.8585] [Topology ] . ( 447 sec) [ -12285.8584] [GTR parameters ] . ( 447 sec) [ -12285.8584] [Alpha ][ 0.395469] . Checking for NNIs, optimizing five branches... . ( 471 sec) [ -12285.8581] [Topology ] . Checking for NNIs, optimizing five branches... . ( 493 sec) [ -12285.8580] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12285.857968. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -26269.9071] [GTR parameters ] . ( 3 sec) [ -25614.9771] [Alpha ][ 0.500960] . ( 3 sec) [ -25401.2889] [ 4690] [depth= 8] . ( 3 sec) [ -25300.3128] [ 4669] [depth= 11] . ( 3 sec) [ -25134.7738] [ 4664] [depth= 1] . ( 3 sec) [ -24998.2717] [ 4658] [depth= 17] . ( 3 sec) [ -24920.4507] [ 4642] [depth= 2] . ( 4 sec) [ -24742.1668] [ 4634] [depth= 11] . ( 4 sec) [ -24641.3545] [ 4610] [depth= 15] . ( 4 sec) [ -24548.8755] [ 4560] [depth= 1] . ( 4 sec) [ -24518.4589] [ 4544] [depth= 17] . ( 4 sec) [ -24503.9667] [ 4544] [depth= 3] . ( 4 sec) [ -24322.1066] [ 4539] [depth= 6] . ( 5 sec) [ -24296.0535] [ 4533] [depth= 2] . ( 5 sec) [ -24244.7322] [ 4529] [depth= 7] . ( 5 sec) [ -24187.6751] [ 4493] [depth= 6] . ( 5 sec) [ -24154.9628] [ 4476] [depth= 1] . ( 5 sec) [ -23996.0519] [ 4451] [depth= 8] . ( 5 sec) [ -23974.5340] [ 4448] [depth= 7] . ( 6 sec) [ -23962.8167] [ 4449] [depth= 2] . ( 6 sec) [ -23797.6429] [ 4444] [depth= 2] . ( 6 sec) [ -23690.5801] [ 4425] [depth= 15] . ( 6 sec) [ -23553.4762] [ 4420] [depth= 1] . ( 6 sec) [ -23498.2349] [ 4410] [depth= 8] . ( 6 sec) [ -23432.1242] [ 4404] [depth= 6] . ( 7 sec) [ -22990.8313] [ 4373] [depth= 8] . ( 7 sec) [ -22863.2310] [ 4353] [depth= 6] . ( 7 sec) [ -22619.9555] [ 4317] [depth= 12] . ( 7 sec) [ -22575.1757] [ 4310] [depth= 14] . ( 7 sec) [ -22300.3669] [ 4285] [depth= 14] . ( 7 sec) [ -22145.1562] [ 4273] [depth= 4] . ( 7 sec) [ -21965.1105] [ 4246] [depth= 5] . ( 8 sec) [ -21960.3963] [ 4242] [depth= 10] . ( 8 sec) [ -21909.3788] [ 4242] [depth= 1] . ( 8 sec) [ -21719.3808] [ 4235] [depth= 13] . ( 8 sec) [ -21709.5406] [ 4231] [depth= 1] . ( 8 sec) [ -21609.4496] [ 4208] [depth= 18] . ( 9 sec) [ -21602.2692] [ 4209] [depth= 1] . ( 9 sec) [ -21521.8623] [ 4187] [depth= 13] . ( 9 sec) [ -21520.2275] [ 4178] [depth= 5] . ( 9 sec) [ -21508.6965] [ 4170] [depth= 7] . ( 10 sec) [ -21475.4973] [ 4169] [depth= 1] . ( 10 sec) [ -21440.7592] [ 4167] [depth= 3] . ( 10 sec) [ -21423.1336] [ 4141] [depth= 9] . ( 10 sec) [ -21404.0912] [ 4140] [depth= 2] . ( 10 sec) [ -21317.5081] [ 4111] [depth= 1] . ( 10 sec) [ -21207.9704] [ 4100] [depth= 8] . ( 10 sec) [ -20993.4463] [ 4098] [depth= 1] . ( 11 sec) [ -20759.3538] [ 4065] [depth= 2] . ( 11 sec) [ -20662.3532] [ 4028] [depth= 14] . ( 11 sec) [ -20608.3281] [ 4010] [depth= 4] . ( 11 sec) [ -20583.6903] [ 4009] [depth= 1] . ( 11 sec) [ -20517.6842] [ 4011] [depth= 1] . ( 11 sec) [ -20261.6263] [ 3996] [depth= 9] . ( 11 sec) [ -20229.9424] [ 3987] [depth= 8] . ( 12 sec) [ -20228.4887] [ 3987] [depth= 2] . ( 12 sec) [ -20210.4903] [ 3980] [depth= 9] . ( 12 sec) [ -20182.7169] [ 3975] [depth= 1] . ( 12 sec) [ -20143.2863] [ 3968] [depth= 11] . ( 12 sec) [ -20081.5600] [ 3964] [depth= 1] . ( 12 sec) [ -19920.3762] [ 3926] [depth= 14] . ( 13 sec) [ -19639.4787] [ 3876] [depth= 22] . ( 13 sec) [ -19580.5482] [ 3858] [depth= 11] . ( 13 sec) [ -19548.5039] [ 3851] [depth= 1] . ( 13 sec) [ -19495.6383] [ 3842] [depth= 13] . ( 13 sec) [ -19432.3543] [ 3824] [depth= 9] . ( 14 sec) [ -19356.6772] [ 3823] [depth= 2] . ( 14 sec) [ -19312.6251] [ 3798] [depth= 16] . ( 14 sec) [ -19193.0485] [ 3755] [depth= 15] . ( 14 sec) [ -19158.4628] [ 3753] [depth= 1] . ( 14 sec) [ -19077.5741] [ 3732] [depth= 3] . ( 15 sec) [ -18859.5753] [ 3720] [depth= 16] . ( 15 sec) [ -18611.3174] [ 3686] [depth= 15] . ( 15 sec) [ -18425.5793] [ 3631] [depth= 10] . ( 15 sec) [ -18328.5794] [ 3624] [depth= 23] . ( 16 sec) [ -18315.0039] [ 3622] [depth= 12] . ( 16 sec) [ -18293.7449] [ 3617] [depth= 2] . ( 16 sec) [ -18281.6290] [ 3615] [depth= 9] . ( 16 sec) [ -18281.4587] [ 3617] [depth= 1] . ( 16 sec) [ -18194.6453] [ 3596] [depth= 15] . ( 16 sec) [ -18176.6511] [ 3590] [depth= 1] . ( 17 sec) [ -18085.2999] [ 3554] [depth= 24] . ( 17 sec) [ -17913.9827] [ 3556] [depth= 11] . ( 17 sec) [ -17910.7995] [ 3555] [depth= 1] . ( 18 sec) [ -17821.4427] [ 3538] [depth= 12] . ( 18 sec) [ -17783.9421] [ 3535] [depth= 6] . ( 18 sec) [ -17765.1324] [ 3527] [depth= 8] . ( 18 sec) [ -17762.9077] [ 3527] [depth= 4] . ( 18 sec) [ -17706.7919] [ 3522] [depth= 1] . ( 18 sec) [ -17665.9163] [ 3506] [depth= 17] . ( 19 sec) [ -17564.0583] [ 3472] [depth= 8] . ( 19 sec) [ -17521.1537] [ 3464] [depth= 1] . ( 19 sec) [ -17515.6940] [ 3465] [depth= 2] . ( 19 sec) [ -17507.1332] [ 3460] [depth= 1] . ( 19 sec) [ -17474.5636] [ 3452] [depth= 8] . ( 19 sec) [ -17391.1610] [ 3439] [depth= 4] . ( 19 sec) [ -17382.0970] [ 3437] [depth= 1] . ( 19 sec) [ -17317.5525] [ 3430] [depth= 3] . ( 20 sec) [ -17195.6520] [ 3422] [depth= 11] . ( 20 sec) [ -17175.6453] [ 3420] [depth= 3] . ( 20 sec) [ -17160.2556] [ 3419] [depth= 1] . ( 20 sec) [ -17144.1219] [ 3412] [depth= 1] . ( 20 sec) [ -17119.8581] [ 3409] [depth= 1] . ( 20 sec) [ -17037.1636] [ 3399] [depth= 9] . ( 21 sec) [ -16842.8536] [ 3325] [depth= 9] . ( 21 sec) [ -16769.8845] [ 3319] [depth= 1] . ( 21 sec) [ -16748.8899] [ 3343] [depth= 2] . ( 21 sec) [ -16605.3820] [ 3300] [depth= 12] . ( 21 sec) [ -16521.2520] [ 3278] [depth= 11] . ( 21 sec) [ -16422.9191] [ 3271] [depth= 1] . ( 22 sec) [ -16396.5667] [ 3271] [depth= 2] . ( 22 sec) [ -16343.1586] [ 3256] [depth= 2] . ( 22 sec) [ -16339.9369] [ 3255] [depth= 2] . ( 22 sec) [ -16159.8894] [ 3247] [depth= 11] . ( 22 sec) [ -16138.7526] [ 3247] [depth= 1] . ( 22 sec) [ -16115.7084] [ 3246] [depth= 1] . ( 23 sec) [ -16084.5648] [ 3237] [depth= 9] . ( 23 sec) [ -16033.8282] [ 3214] [depth= 1] . ( 23 sec) [ -15967.8396] [ 3191] [depth= 17] . ( 23 sec) [ -15931.1492] [ 3162] [depth= 8] . ( 23 sec) [ -15865.2180] [ 3138] [depth= 1] . ( 24 sec) [ -15816.2662] [ 3120] [depth= 2] . ( 24 sec) [ -15802.7410] [ 3115] [depth= 1] . ( 24 sec) [ -15734.8268] [ 3118] [depth= 1] . ( 24 sec) [ -15651.0387] [ 3098] [depth= 1] . ( 24 sec) [ -15635.8261] [ 3090] [depth= 11] . ( 25 sec) [ -15607.7046] [ 3090] [depth= 1] . ( 25 sec) [ -15605.6064] [ 3090] [depth= 2] . ( 25 sec) [ -15600.3602] [ 3090] [depth= 1] . ( 26 sec) [ -15535.3261] [ 3088] [depth= 2] . ( 26 sec) [ -15527.7325] [ 3088] [depth= 2] . ( 26 sec) [ -15519.5304] [ 3088] [depth= 1] . ( 26 sec) [ -15346.5251] [ 3077] [depth= 15] . ( 26 sec) [ -15345.5621] [ 3077] [depth= 1] . ( 26 sec) [ -15335.5187] [ 3069] [depth= 3] . ( 26 sec) [ -15301.1881] [ 3059] [depth= 7] . ( 27 sec) [ -15290.1224] [ 3055] [depth= 1] . ( 27 sec) [ -15135.2080] [ 3006] [depth= 5] . ( 27 sec) [ -15101.2806] [ 3002] [depth= 3] . ( 27 sec) [ -15050.4546] [ 3000] [depth= 1] . ( 27 sec) [ -15048.6001] [ 2994] [depth= 8] . ( 27 sec) [ -15042.6894] [ 2991] [depth= 1] . ( 27 sec) [ -15042.5684] [ 2992] [depth= 1] . ( 28 sec) [ -14970.3201] [ 2967] [depth= 12] . ( 28 sec) [ -14865.9996] [ 2964] [depth= 1] . ( 28 sec) [ -14851.4028] [ 2964] [depth= 2] . ( 28 sec) [ -14717.1302] [ 2933] [depth= 5] . ( 28 sec) [ -14682.5323] [ 2925] [depth= 1] . ( 29 sec) [ -14678.4861] [ 2923] [depth= 2] . ( 29 sec) [ -14677.0300] [ 2922] [depth= 1] . ( 29 sec) [ -14672.9131] [ 2917] [depth= 7] . ( 29 sec) [ -14672.6870] [ 2921] [depth= 1] . ( 29 sec) [ -14670.2674] [ 2919] [depth= 1] . ( 29 sec) [ -14666.4851] [ 2919] [depth= 1] . ( 30 sec) [ -14533.1676] [ 2872] [depth= 13] . ( 30 sec) [ -14519.9538] [ 2871] [depth= 6] . ( 30 sec) [ -14327.0468] [ 2802] [depth= 7] . ( 30 sec) [ -14326.1851] [ 2793] [depth= 1] . ( 30 sec) [ -14304.9759] [ 2788] [depth= 1] . ( 30 sec) [ -14257.9788] [ 2786] [depth= 3] . ( 31 sec) [ -14257.6469] [ 2784] [depth= 6] . ( 31 sec) [ -14225.7992] [ 2775] [depth= 8] . ( 31 sec) [ -14217.5050] [ 2774] [depth= 1] . ( 31 sec) [ -14158.3569] [ 2768] [depth= 4] . ( 31 sec) [ -14090.0546] [ 2737] [depth= 19] . ( 31 sec) [ -14079.7472] [ 2733] [depth= 1] . ( 32 sec) [ -14007.8164] [ 2715] [depth= 1] . ( 32 sec) [ -13984.2920] [ 2708] [depth= 6] . ( 32 sec) [ -13971.9252] [ 2706] [depth= 12] . ( 32 sec) [ -13857.7552] [ 2680] [depth= 5] . ( 33 sec) [ -13854.6681] [ 2679] [depth= 4] . ( 33 sec) [ -13831.7547] [ 2680] [depth= 3] . ( 33 sec) [ -13769.1214] [ 2655] [depth= 6] . ( 33 sec) [ -13720.5802] [ 2643] [depth= 2] . ( 33 sec) [ -13711.7262] [ 2635] [depth= 12] . ( 34 sec) [ -13710.9536] [ 2631] [depth= 2] . ( 34 sec) [ -13707.3045] [ 2627] [depth= 1] . ( 34 sec) [ -13654.7671] [ 2608] [depth= 1] . ( 34 sec) [ -13648.2391] [ 2612] [depth= 2] . ( 34 sec) [ -13630.0758] [ 2611] [depth= 1] . ( 34 sec) [ -13609.4361] [ 2608] [depth= 1] . ( 35 sec) [ -13602.0688] [ 2605] [depth= 1] . ( 35 sec) [ -13596.4758] [ 2608] [depth= 5] . ( 35 sec) [ -13586.8003] [ 2605] [depth= 3] . ( 35 sec) [ -13583.5810] [ 2603] [depth= 9] . ( 36 sec) [ -13581.7938] [ 2603] [depth= 2] . ( 36 sec) [ -13535.4442] [ 2594] [depth= 9] . ( 36 sec) [ -13533.0018] [ 2585] [depth= 2] . ( 36 sec) [ -13420.9820] [ 2571] [depth= 11] . ( 36 sec) [ -13419.0137] [ 2567] [depth= 1] . ( 36 sec) [ -13364.2192] [ 2564] [depth= 2] . ( 37 sec) [ -13355.0476] [ 2559] [depth= 3] . ( 37 sec) [ -13354.0076] [ 2560] [depth= 1] . ( 38 sec) [ -13352.4339] [ 2560] [depth= 1] . ( 38 sec) [ -13344.4003] [ 2559] [depth= 2] . ( 38 sec) [ -13267.0161] [ 2562] [depth= 2] . ( 38 sec) [ -13266.0780] [ 2564] [depth= 1] . ( 39 sec) [ -13262.3955] [ 2564] [depth= 1] . ( 39 sec) [ -13248.3405] [ 2553] [depth= 1] . ( 39 sec) [ -13241.6096] [ 2554] [depth= 2] . ( 39 sec) [ -13239.1632] [ 2552] [depth= 1] . ( 40 sec) [ -13238.4979] [ 2552] [depth= 1] . ( 40 sec) [ -13231.4614] [ 2552] [depth= 1] . ( 40 sec) [ -13137.0866] [ 2516] [depth= 19] . ( 40 sec) [ -13131.4213] [ 2513] [depth= 1] . ( 41 sec) [ -13128.8602] [ 2513] [depth= 1] . ( 41 sec) [ -13127.0877] [ 2512] [depth= 1] . ( 41 sec) [ -13126.9026] [ 2514] [depth= 1] . ( 41 sec) [ -13120.2325] [ 2510] [depth= 2] . ( 42 sec) [ -13109.6960] [ 2505] [depth= 9] . ( 42 sec) [ -13101.7142] [ 2507] [depth= 1] . ( 42 sec) [ -13079.5116] [ 2498] [depth= 1] . ( 42 sec) [ -13078.9216] [ 2498] [depth= 1] . ( 43 sec) [ -13078.5711] [ 2498] [depth= 1] . ( 43 sec) [ -13077.9542] [ 2498] [depth= 1] . ( 43 sec) [ -13002.2794] [ 2480] [depth= 1] . ( 43 sec) [ -12932.1879] [ 2473] [depth= 5] . ( 44 sec) [ -12926.9658] [ 2477] [depth= 1] . ( 44 sec) [ -12904.5533] [ 2469] [depth= 3] . ( 44 sec) [ -12903.6633] [ 2474] [depth= 1] . ( 44 sec) [ -12902.7810] [ 2475] [depth= 1] . ( 45 sec) [ -12902.2909] [ 2475] [depth= 1] . ( 45 sec) [ -12900.7236] [ 2475] [depth= 1] . ( 46 sec) [ -12679.3228] [Branch lengths ] . ( 53 sec) [ -12671.0674] [GTR parameters ] . ( 54 sec) [ -12658.1584] [Alpha ][ 0.387744] . ( 54 sec) [ -12657.7718] [ 2473] [depth= 1] . ( 55 sec) [ -12657.5947] [ 2475] [depth= 1] . ( 57 sec) [ -12656.3595] [ 2474] [depth= 2] . ( 57 sec) [ -12646.8671] [ 2472] [depth= 2] . ( 57 sec) [ -12629.8102] [ 2468] [depth= 2] . ( 57 sec) [ -12628.3063] [ 2467] [depth= 1] . ( 59 sec) [ -12620.5914] [ 2464] [depth= 3] . ( 59 sec) [ -12611.4404] [ 2461] [depth= 2] . ( 60 sec) [ -12605.6350] [ 2451] [depth= 4] . ( 61 sec) [ -12601.1619] [ 2452] [depth= 1] . ( 61 sec) [ -12601.1147] [ 2452] [depth= 1] . ( 62 sec) [ -12600.8162] [ 2456] [depth= 3] . ( 63 sec) [ -12600.2363] [ 2455] [depth= 1] . ( 64 sec) [ -12600.1276] [ 2454] [depth= 2] . ( 64 sec) [ -12599.7919] [ 2453] [depth= 2] . ( 65 sec) [ -12597.9779] [ 2451] [depth= 1] . ( 66 sec) [ -12596.8381] [ 2449] [depth= 1] . ( 67 sec) [ -12596.2582] [ 2453] [depth= 1] . ( 67 sec) [ -12590.6568] [ 2448] [depth= 1] . ( 67 sec) [ -12590.0356] [ 2448] [depth= 10] . ( 67 sec) [ -12589.9831] [ 2443] [depth= 3] . ( 68 sec) [ -12586.2962] [ 2443] [depth= 1] . ( 68 sec) [ -12585.3947] [ 2445] [depth= 1] . ( 68 sec) [ -12582.1093] [ 2445] [depth= 1] . ( 69 sec) [ -12569.3356] [ 2443] [depth= 1] . ( 69 sec) [ -12568.1019] [ 2443] [depth= 1] . ( 69 sec) [ -12553.3285] [ 2439] [depth= 2] . ( 70 sec) [ -12532.2098] [ 2434] [depth= 2] . ( 72 sec) [ -12531.0104] [ 2434] [depth= 1] . ( 72 sec) [ -12530.4175] [ 2435] [depth= 1] . ( 72 sec) [ -12521.5703] [ 2430] [depth= 1] . ( 72 sec) [ -12518.8768] [ 2434] [depth= 1] . ( 73 sec) [ -12504.3636] [ 2431] [depth= 2] . ( 74 sec) [ -12489.5358] [ 2425] [depth= 1] . ( 74 sec) [ -12487.6219] [ 2425] [depth= 2] . ( 75 sec) [ -12440.2086] [ 2395] [depth= 11] . ( 75 sec) [ -12439.8032] [ 2394] [depth= 1] . ( 76 sec) [ -12439.0872] [ 2394] [depth= 3] . ( 76 sec) [ -12438.9254] [ 2392] [depth= 4] . ( 77 sec) [ -12435.9673] [ 2387] [depth= 1] . ( 78 sec) [ -12423.8449] [ 2390] [depth= 1] . ( 79 sec) [ -12417.6020] [ 2387] [depth= 1] . ( 81 sec) [ -12405.1485] [ 2384] [depth= 5] . ( 82 sec) [ -12404.7262] [ 2386] [depth= 1] . ( 82 sec) [ -12403.6773] [ 2385] [depth= 1] . ( 83 sec) [ -12400.3858] [ 2385] [depth= 1] . ( 87 sec) [ -12400.2432] [ 2385] [depth= 1] . ( 88 sec) [ -12369.0949] [ 2361] [depth= 6] . ( 89 sec) [ -12368.0624] [ 2361] [depth= 1] . ( 89 sec) [ -12364.6116] [ 2362] [depth= 1] . ( 89 sec) [ -12363.8558] [ 2362] [depth= 1] . ( 90 sec) [ -12363.3292] [ 2364] [depth= 1] . ( 94 sec) [ -12359.8270] [ 2362] [depth= 1] . ( 94 sec) [ -12359.6451] [ 2361] [depth= 5] . ( 96 sec) [ -12358.8381] [ 2360] [depth= 2] . ( 96 sec) [ -12358.6828] [ 2358] [depth= 1] . ( 98 sec) [ -12346.0137] [ 2353] [depth= 5] . ( 98 sec) [ -12340.5301] [ 2351] [depth= 1] . ( 99 sec) [ -12331.1482] [ 2349] [depth= 1] . ( 105 sec) [ -12330.3803] [ 2351] [depth= 1] . ( 107 sec) [ -12300.2521] [Branch lengths ] . ( 114 sec) [ -12300.0378] [GTR parameters ] . ( 115 sec) [ -12299.9390] [Alpha ][ 0.396476] . ( 116 sec) [ -12299.4238] [ 2349] [depth= 1] . ( 119 sec) [ -12299.3554] [ 2349] [depth= 1] . ( 126 sec) [ -12298.6835] [ 2348] [depth= 1] . ( 146 sec) [ -12298.5804] [ 2349] [depth= 4] . ( 153 sec) [ -12298.0610] [ 2354] [depth= 2] . ( 159 sec) [ -12298.0213] [ 2356] [depth= 3] . ( 160 sec) [ -12297.8894] [ 2357] [depth= 1] . ( 163 sec) [ -12297.8772] [ 2356] [depth= 2] . ( 170 sec) [ -12293.5767] [Branch lengths ] . ( 174 sec) [ -12293.5417] [GTR parameters ] . ( 174 sec) [ -12293.5412] [Alpha ][ 0.395737] . ( 224 sec) [ -12292.9160] [ 2353] [depth= 5] . ( 230 sec) [ -12292.8179] [ 2357] [depth= 1] . ( 233 sec) [ -12292.2917] [ 2356] [depth= 6] . ( 234 sec) [ -12292.2494] [ 2355] [depth= 1] . ( 239 sec) [ -12292.1093] [ 2352] [depth= 1] . ( 242 sec) [ -12289.2163] [Branch lengths ] . ( 247 sec) [ -12289.1936] [GTR parameters ] . ( 247 sec) [ -12289.1926] [Alpha ][ 0.394722] . ( 274 sec) [ -12289.0741] [ 2353] [depth= 1] . ( 291 sec) [ -12288.3083] [ 2356] [depth= 4] . ( 292 sec) [ -12287.8565] [ 2356] [depth= 1] . ( 298 sec) [ -12287.1105] [ 2355] [depth= 1] . ( 311 sec) [ -12286.3036] [Branch lengths ] . ( 312 sec) [ -12286.2964] [GTR parameters ] . ( 312 sec) [ -12286.2963] [Alpha ][ 0.395117] . ( 390 sec) [ -12286.2775] [Branch lengths ] . ( 424 sec) [ -12286.1516] [ 2354] [depth= 1] . ( 432 sec) [ -12286.0794] [ 2352] [depth= 1] . ( 557 sec) [ -12285.9548] [Branch lengths ] . ( 562 sec) [ -12285.9514] [GTR parameters ] . ( 562 sec) [ -12285.9513] [Alpha ][ 0.394721] . ( 562 sec) [ -12285.9513] [Topology ] . ( 566 sec) [ -12285.8835] [Topology ] . ( 570 sec) [ -12285.3493] [Topology ] . ( 574 sec) [ -12285.2487] [Topology ] . ( 577 sec) [ -12285.2086] [Topology ] . ( 581 sec) [ -12285.1914] [Topology ] . ( 584 sec) [ -12285.1838] [Topology ] . ( 588 sec) [ -12285.1805] [Topology ] . ( 590 sec) [ -12285.1780] [GTR parameters ] . ( 591 sec) [ -12285.1778] [Alpha ][ 0.395116] . ( 591 sec) [ -12285.1778] [Topology ] . ( 594 sec) [ -12285.1762] [Topology ] . ( 598 sec) [ -12285.1755] [Topology ] . ( 599 sec) [ -12285.1754] [GTR parameters ] . ( 599 sec) [ -12285.1754] [Alpha ][ 0.395116] . ( 599 sec) [ -12285.1754] [Topology ] . ( 602 sec) [ -12285.1750] [Topology ] . ( 604 sec) [ -12285.1750] [GTR parameters ] . ( 604 sec) [ -12285.1750] [Alpha ][ 0.395116] . Checking for NNIs, optimizing five branches... . ( 626 sec) [ -12285.1746] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12285.174555. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 5 sec) [ -27059.6948] [GTR parameters ] . ( 6 sec) [ -26394.3874] [Alpha ][ 0.500960] . ( 6 sec) [ -26285.1679] [ 4763] [depth= 11] . ( 7 sec) [ -26091.1291] [ 4744] [depth= 9] . ( 7 sec) [ -25883.7383] [ 4742] [depth= 1] . ( 7 sec) [ -25859.5598] [ 4732] [depth= 9] . ( 8 sec) [ -25818.1544] [ 4723] [depth= 1] . ( 8 sec) [ -25709.8425] [ 4717] [depth= 16] . ( 8 sec) [ -25457.2975] [ 4707] [depth= 1] . ( 8 sec) [ -25353.4249] [ 4690] [depth= 5] . ( 9 sec) [ -25258.6962] [ 4659] [depth= 6] . ( 9 sec) [ -25190.8643] [ 4645] [depth= 7] . ( 10 sec) [ -25166.7302] [ 4637] [depth= 1] . ( 10 sec) [ -25153.2423] [ 4630] [depth= 10] . ( 10 sec) [ -25123.8977] [ 4627] [depth= 8] . ( 10 sec) [ -25101.8436] [ 4625] [depth= 4] . ( 11 sec) [ -25054.8901] [ 4611] [depth= 26] . ( 11 sec) [ -24910.2142] [ 4580] [depth= 29] . ( 11 sec) [ -24878.7602] [ 4582] [depth= 23] . ( 12 sec) [ -24864.7973] [ 4580] [depth= 7] . ( 12 sec) [ -24859.3196] [ 4580] [depth= 1] . ( 12 sec) [ -24775.2966] [ 4543] [depth= 22] . ( 12 sec) [ -24775.0538] [ 4532] [depth= 3] . ( 13 sec) [ -24761.1681] [ 4530] [depth= 3] . ( 13 sec) [ -24750.1912] [ 4523] [depth= 2] . ( 14 sec) [ -24724.9019] [ 4522] [depth= 1] . ( 14 sec) [ -24664.0625] [ 4505] [depth= 15] . ( 14 sec) [ -24505.8229] [ 4494] [depth= 5] . ( 14 sec) [ -24030.9070] [ 4495] [depth= 1] . ( 15 sec) [ -23938.2991] [ 4472] [depth= 16] . ( 15 sec) [ -23627.3850] [ 4477] [depth= 1] . ( 15 sec) [ -23173.3861] [ 4412] [depth= 11] . ( 16 sec) [ -23014.0291] [ 4362] [depth= 14] . ( 16 sec) [ -22953.5580] [ 4347] [depth= 23] . ( 16 sec) [ -22696.4853] [ 4288] [depth= 13] . ( 16 sec) [ -22653.9668] [ 4286] [depth= 4] . ( 17 sec) [ -22536.6318] [ 4278] [depth= 15] . ( 17 sec) [ -22515.5396] [ 4272] [depth= 1] . ( 17 sec) [ -22500.5533] [ 4263] [depth= 7] . ( 18 sec) [ -22498.1478] [ 4258] [depth= 7] . ( 18 sec) [ -22450.2672] [ 4260] [depth= 1] . ( 18 sec) [ -22440.9360] [ 4259] [depth= 4] . ( 18 sec) [ -22419.1557] [ 4258] [depth= 1] . ( 19 sec) [ -22418.0114] [ 4246] [depth= 9] . ( 19 sec) [ -22106.1332] [ 4172] [depth= 25] . ( 19 sec) [ -22071.4609] [ 4167] [depth= 7] . ( 19 sec) [ -22050.7200] [ 4169] [depth= 4] . ( 20 sec) [ -21980.5955] [ 4147] [depth= 7] . ( 20 sec) [ -21939.3486] [ 4141] [depth= 3] . ( 20 sec) [ -21888.7360] [ 4122] [depth= 8] . ( 21 sec) [ -21880.8609] [ 4122] [depth= 2] . ( 21 sec) [ -21879.8727] [ 4127] [depth= 1] . ( 21 sec) [ -21778.2506] [ 4093] [depth= 8] . ( 22 sec) [ -21747.6321] [ 4087] [depth= 2] . ( 22 sec) [ -21738.4374] [ 4081] [depth= 1] . ( 22 sec) [ -21732.1071] [ 4081] [depth= 1] . ( 22 sec) [ -21699.6072] [ 4078] [depth= 1] . ( 23 sec) [ -21690.5980] [ 4075] [depth= 3] . ( 23 sec) [ -21587.2216] [ 4070] [depth= 19] . ( 23 sec) [ -21555.5427] [ 4058] [depth= 9] . ( 24 sec) [ -21319.6880] [ 3999] [depth= 9] . ( 24 sec) [ -21180.3785] [ 4029] [depth= 13] . ( 24 sec) [ -21176.2820] [ 4027] [depth= 1] . ( 25 sec) [ -21142.6992] [ 4016] [depth= 11] . ( 25 sec) [ -21134.8737] [ 4017] [depth= 1] . ( 26 sec) [ -21066.2821] [ 4009] [depth= 11] . ( 26 sec) [ -21024.2703] [ 3993] [depth= 3] . ( 26 sec) [ -21015.3548] [ 3993] [depth= 2] . ( 26 sec) [ -20890.9630] [ 3982] [depth= 9] . ( 27 sec) [ -20559.0139] [ 3931] [depth= 1] . ( 27 sec) [ -20417.7590] [ 3896] [depth= 19] . ( 28 sec) [ -20360.2625] [ 3872] [depth= 1] . ( 28 sec) [ -20201.2271] [ 3861] [depth= 19] . ( 29 sec) [ -19996.4521] [ 3826] [depth= 3] . ( 29 sec) [ -19967.7333] [ 3817] [depth= 17] . ( 29 sec) [ -19907.6044] [ 3816] [depth= 1] . ( 29 sec) [ -19842.5728] [ 3799] [depth= 18] . ( 29 sec) [ -19801.0211] [ 3798] [depth= 1] . ( 30 sec) [ -19729.4601] [ 3785] [depth= 4] . ( 30 sec) [ -19728.8247] [ 3790] [depth= 4] . ( 30 sec) [ -19694.4538] [ 3766] [depth= 6] . ( 30 sec) [ -19453.4723] [ 3752] [depth= 12] . ( 30 sec) [ -19212.1040] [ 3724] [depth= 1] . ( 31 sec) [ -19146.6124] [ 3715] [depth= 9] . ( 31 sec) [ -19103.6655] [ 3693] [depth= 5] . ( 31 sec) [ -19063.3300] [ 3655] [depth= 18] . ( 31 sec) [ -18845.3127] [ 3612] [depth= 16] . ( 31 sec) [ -18804.0245] [ 3611] [depth= 1] . ( 31 sec) [ -18704.2913] [ 3569] [depth= 1] . ( 32 sec) [ -18703.9575] [ 3570] [depth= 1] . ( 32 sec) [ -18605.4469] [ 3550] [depth= 8] . ( 32 sec) [ -18595.7062] [ 3549] [depth= 1] . ( 32 sec) [ -18582.3665] [ 3550] [depth= 2] . ( 32 sec) [ -18498.2756] [ 3535] [depth= 7] . ( 33 sec) [ -18325.9258] [ 3516] [depth= 11] . ( 33 sec) [ -18258.9664] [ 3469] [depth= 14] . ( 33 sec) [ -18169.1602] [ 3435] [depth= 2] . ( 33 sec) [ -18126.9457] [ 3435] [depth= 12] . ( 33 sec) [ -18089.5870] [ 3432] [depth= 7] . ( 33 sec) [ -18081.0560] [ 3430] [depth= 1] . ( 34 sec) [ -17967.5914] [ 3404] [depth= 4] . ( 34 sec) [ -17921.6582] [ 3392] [depth= 1] . ( 34 sec) [ -17919.1893] [ 3395] [depth= 7] . ( 34 sec) [ -17915.2611] [ 3394] [depth= 1] . ( 35 sec) [ -17895.3713] [ 3392] [depth= 3] . ( 35 sec) [ -17874.2502] [ 3384] [depth= 1] . ( 35 sec) [ -17848.7158] [ 3380] [depth= 2] . ( 35 sec) [ -17758.2026] [ 3356] [depth= 2] . ( 35 sec) [ -17736.5393] [ 3354] [depth= 10] . ( 36 sec) [ -17709.9753] [ 3360] [depth= 1] . ( 36 sec) [ -17680.8069] [ 3354] [depth= 1] . ( 36 sec) [ -17666.3366] [ 3347] [depth= 1] . ( 36 sec) [ -17616.3117] [ 3325] [depth= 15] . ( 36 sec) [ -17521.2189] [ 3325] [depth= 1] . ( 36 sec) [ -17516.0867] [ 3325] [depth= 1] . ( 37 sec) [ -17284.0303] [ 3334] [depth= 8] . ( 37 sec) [ -17274.1332] [ 3327] [depth= 16] . ( 37 sec) [ -17263.4592] [ 3316] [depth= 8] . ( 37 sec) [ -17242.2799] [ 3307] [depth= 2] . ( 38 sec) [ -17211.1043] [ 3305] [depth= 1] . ( 38 sec) [ -17114.7115] [ 3281] [depth= 2] . ( 38 sec) [ -16947.5887] [ 3266] [depth= 3] . ( 38 sec) [ -16945.0609] [ 3266] [depth= 1] . ( 38 sec) [ -16901.2777] [ 3252] [depth= 9] . ( 39 sec) [ -16872.1052] [ 3249] [depth= 14] . ( 39 sec) [ -16685.2536] [ 3247] [depth= 1] . ( 39 sec) [ -16653.3934] [ 3238] [depth= 4] . ( 40 sec) [ -16640.2611] [ 3229] [depth= 15] . ( 40 sec) [ -16500.7706] [ 3192] [depth= 8] . ( 40 sec) [ -16273.3794] [ 3192] [depth= 5] . ( 40 sec) [ -16228.4060] [ 3169] [depth= 31] . ( 40 sec) [ -16166.3583] [ 3168] [depth= 17] . ( 41 sec) [ -16164.8458] [ 3160] [depth= 9] . ( 41 sec) [ -16126.9855] [ 3157] [depth= 1] . ( 41 sec) [ -16095.4665] [ 3154] [depth= 8] . ( 41 sec) [ -16053.4681] [ 3149] [depth= 2] . ( 41 sec) [ -16014.9495] [ 3136] [depth= 8] . ( 42 sec) [ -16007.1346] [ 3137] [depth= 1] . ( 42 sec) [ -15942.8891] [ 3109] [depth= 1] . ( 42 sec) [ -15821.8339] [ 3108] [depth= 14] . ( 42 sec) [ -15630.6023] [ 3070] [depth= 3] . ( 42 sec) [ -15544.2422] [ 3057] [depth= 14] . ( 42 sec) [ -15510.7926] [ 3063] [depth= 1] . ( 43 sec) [ -15386.0457] [ 3049] [depth= 3] . ( 43 sec) [ -15335.3171] [ 3039] [depth= 5] . ( 43 sec) [ -15265.4295] [ 3016] [depth= 1] . ( 43 sec) [ -15224.9038] [ 3016] [depth= 8] . ( 43 sec) [ -15189.7106] [ 3007] [depth= 10] . ( 43 sec) [ -15173.4326] [ 3005] [depth= 1] . ( 44 sec) [ -15144.9017] [ 2991] [depth= 2] . ( 44 sec) [ -15137.4652] [ 2994] [depth= 2] . ( 44 sec) [ -15125.3804] [ 2995] [depth= 1] . ( 44 sec) [ -15106.9776] [ 2979] [depth= 2] . ( 45 sec) [ -15095.5113] [ 2979] [depth= 1] . ( 45 sec) [ -14961.4439] [ 2940] [depth= 2] . ( 45 sec) [ -14959.7394] [ 2941] [depth= 4] . ( 45 sec) [ -14933.2401] [ 2923] [depth= 14] . ( 45 sec) [ -14927.0094] [ 2924] [depth= 1] . ( 45 sec) [ -14925.9767] [ 2924] [depth= 4] . ( 46 sec) [ -14837.5553] [ 2893] [depth= 10] . ( 46 sec) [ -14778.0345] [ 2880] [depth= 1] . ( 46 sec) [ -14766.8169] [ 2880] [depth= 1] . ( 46 sec) [ -14747.7540] [ 2880] [depth= 7] . ( 46 sec) [ -14745.9736] [ 2883] [depth= 1] . ( 47 sec) [ -14717.0356] [ 2872] [depth= 6] . ( 47 sec) [ -14652.7815] [ 2854] [depth= 9] . ( 47 sec) [ -14647.7680] [ 2855] [depth= 2] . ( 47 sec) [ -14638.0535] [ 2855] [depth= 1] . ( 48 sec) [ -14597.3487] [ 2831] [depth= 20] . ( 48 sec) [ -14596.9850] [ 2831] [depth= 1] . ( 48 sec) [ -14527.7598] [ 2816] [depth= 11] . ( 48 sec) [ -14470.5050] [ 2798] [depth= 3] . ( 48 sec) [ -14430.4928] [ 2783] [depth= 2] . ( 49 sec) [ -14411.3280] [ 2779] [depth= 2] . ( 49 sec) [ -14359.9058] [ 2762] [depth= 2] . ( 49 sec) [ -14342.9111] [ 2760] [depth= 2] . ( 49 sec) [ -14283.1613] [ 2737] [depth= 13] . ( 49 sec) [ -14278.9186] [ 2738] [depth= 1] . ( 50 sec) [ -14271.7667] [ 2737] [depth= 1] . ( 50 sec) [ -14270.8160] [ 2740] [depth= 1] . ( 51 sec) [ -14267.5511] [ 2740] [depth= 1] . ( 51 sec) [ -14203.6972] [ 2741] [depth= 2] . ( 51 sec) [ -14199.3759] [ 2737] [depth= 5] . ( 52 sec) [ -13838.3489] [ 2670] [depth= 19] . ( 52 sec) [ -13823.6701] [ 2670] [depth= 1] . ( 53 sec) [ -13818.1026] [ 2667] [depth= 2] . ( 53 sec) [ -13817.4037] [ 2667] [depth= 1] . ( 53 sec) [ -13807.7593] [ 2662] [depth= 1] . ( 54 sec) [ -13776.3726] [ 2653] [depth= 2] . ( 54 sec) [ -13774.6221] [ 2651] [depth= 1] . ( 55 sec) [ -13772.1471] [ 2650] [depth= 1] . ( 55 sec) [ -13739.2725] [ 2642] [depth= 2] . ( 56 sec) [ -13738.0043] [ 2644] [depth= 1] . ( 56 sec) [ -13727.4135] [ 2636] [depth= 12] . ( 56 sec) [ -13716.7977] [ 2634] [depth= 1] . ( 57 sec) [ -13486.2298] [ 2629] [depth= 2] . ( 57 sec) [ -13469.1134] [ 2624] [depth= 1] . ( 58 sec) [ -13467.8649] [ 2624] [depth= 3] . ( 58 sec) [ -13436.9809] [ 2622] [depth= 2] . ( 59 sec) [ -13433.6726] [ 2627] [depth= 1] . ( 59 sec) [ -13414.8556] [ 2625] [depth= 2] . ( 60 sec) [ -13384.3076] [ 2614] [depth= 1] . ( 60 sec) [ -13372.2681] [ 2600] [depth= 19] . ( 60 sec) [ -13341.0593] [ 2573] [depth= 16] . ( 61 sec) [ -13307.5065] [ 2569] [depth= 17] . ( 61 sec) [ -13306.2712] [ 2569] [depth= 1] . ( 61 sec) [ -13213.3589] [ 2541] [depth= 15] . ( 62 sec) [ -13199.3023] [ 2537] [depth= 2] . ( 62 sec) [ -13175.7801] [ 2532] [depth= 2] . ( 62 sec) [ -13158.5827] [ 2526] [depth= 17] . ( 64 sec) [ -12891.1396] [Branch lengths ] . ( 73 sec) [ -12877.9231] [GTR parameters ] . ( 73 sec) [ -12862.7792] [Alpha ][ 0.381534] . ( 74 sec) [ -12853.4162] [ 2525] [depth= 4] . ( 75 sec) [ -12838.3992] [ 2519] [depth= 1] . ( 76 sec) [ -12815.5492] [ 2511] [depth= 1] . ( 77 sec) [ -12791.5128] [ 2499] [depth= 1] . ( 77 sec) [ -12789.1965] [ 2495] [depth= 1] . ( 77 sec) [ -12761.6362] [ 2477] [depth= 14] . ( 77 sec) [ -12758.7412] [ 2474] [depth= 1] . ( 79 sec) [ -12758.1460] [ 2477] [depth= 1] . ( 79 sec) [ -12756.7521] [ 2474] [depth= 1] . ( 80 sec) [ -12748.7751] [ 2472] [depth= 1] . ( 80 sec) [ -12744.0921] [ 2466] [depth= 5] . ( 81 sec) [ -12743.1470] [ 2464] [depth= 2] . ( 82 sec) [ -12729.6021] [ 2455] [depth= 3] . ( 82 sec) [ -12727.5380] [ 2453] [depth= 1] . ( 83 sec) [ -12727.3835] [ 2452] [depth= 2] . ( 84 sec) [ -12714.8161] [ 2448] [depth= 2] . ( 85 sec) [ -12713.6309] [ 2447] [depth= 3] . ( 86 sec) [ -12711.8258] [ 2444] [depth= 1] . ( 87 sec) [ -12711.8096] [ 2444] [depth= 1] . ( 89 sec) [ -12711.1929] [ 2444] [depth= 1] . ( 89 sec) [ -12709.3927] [ 2442] [depth= 2] . ( 90 sec) [ -12709.2111] [ 2443] [depth= 1] . ( 91 sec) [ -12708.6525] [ 2443] [depth= 1] . ( 91 sec) [ -12707.3139] [ 2444] [depth= 1] . ( 91 sec) [ -12702.8035] [ 2445] [depth= 1] . ( 92 sec) [ -12700.4832] [ 2445] [depth= 1] . ( 94 sec) [ -12700.2961] [ 2445] [depth= 1] . ( 94 sec) [ -12697.2218] [ 2443] [depth= 5] . ( 94 sec) [ -12690.6467] [ 2438] [depth= 1] . ( 95 sec) [ -12687.0413] [ 2436] [depth= 2] . ( 95 sec) [ -12685.0896] [ 2433] [depth= 5] . ( 96 sec) [ -12591.9912] [ 2447] [depth= 1] . ( 96 sec) [ -12588.1577] [ 2433] [depth= 1] . ( 97 sec) [ -12580.4633] [ 2432] [depth= 2] . ( 97 sec) [ -12580.4318] [ 2431] [depth= 1] . ( 98 sec) [ -12561.7816] [ 2422] [depth= 11] . ( 98 sec) [ -12561.4039] [ 2422] [depth= 1] . ( 99 sec) [ -12558.8742] [ 2422] [depth= 1] . ( 100 sec) [ -12556.9422] [ 2422] [depth= 1] . ( 100 sec) [ -12543.4826] [ 2418] [depth= 3] . ( 100 sec) [ -12539.9707] [ 2416] [depth= 4] . ( 102 sec) [ -12531.2471] [ 2413] [depth= 1] . ( 102 sec) [ -12527.8650] [ 2412] [depth= 1] . ( 104 sec) [ -12525.4195] [ 2413] [depth= 1] . ( 105 sec) [ -12522.2321] [ 2411] [depth= 1] . ( 106 sec) [ -12521.8830] [ 2411] [depth= 1] . ( 106 sec) [ -12520.3779] [ 2409] [depth= 2] . ( 107 sec) [ -12487.0141] [ 2396] [depth= 2] . ( 109 sec) [ -12480.9364] [ 2393] [depth= 2] . ( 111 sec) [ -12480.3557] [ 2397] [depth= 1] . ( 111 sec) [ -12479.4405] [ 2398] [depth= 1] . ( 112 sec) [ -12479.0428] [ 2399] [depth= 2] . ( 114 sec) [ -12478.0615] [ 2399] [depth= 1] . ( 116 sec) [ -12477.4873] [ 2399] [depth= 1] . ( 116 sec) [ -12476.7945] [ 2400] [depth= 7] . ( 117 sec) [ -12474.8257] [ 2398] [depth= 4] . ( 117 sec) [ -12474.1542] [ 2400] [depth= 1] . ( 119 sec) [ -12473.3962] [ 2402] [depth= 1] . ( 120 sec) [ -12473.3267] [ 2402] [depth= 1] . ( 120 sec) [ -12471.6458] [ 2400] [depth= 1] . ( 123 sec) [ -12471.2648] [ 2400] [depth= 1] . ( 123 sec) [ -12470.3589] [ 2398] [depth= 1] . ( 124 sec) [ -12467.7368] [ 2398] [depth= 1] . ( 125 sec) [ -12467.7136] [ 2398] [depth= 1] . ( 125 sec) [ -12466.2818] [ 2399] [depth= 1] . ( 125 sec) [ -12465.9426] [ 2399] [depth= 1] . ( 126 sec) [ -12463.7415] [ 2404] [depth= 1] . ( 127 sec) [ -12462.8356] [ 2401] [depth= 4] . ( 127 sec) [ -12462.3777] [ 2401] [depth= 1] . ( 129 sec) [ -12457.5355] [ 2400] [depth= 1] . ( 129 sec) [ -12436.9014] [ 2390] [depth= 6] . ( 130 sec) [ -12432.9817] [ 2381] [depth= 2] . ( 130 sec) [ -12432.6654] [ 2382] [depth= 1] . ( 131 sec) [ -12432.2427] [ 2382] [depth= 1] . ( 131 sec) [ -12431.3451] [ 2382] [depth= 2] . ( 132 sec) [ -12426.4086] [ 2381] [depth= 3] . ( 133 sec) [ -12426.3884] [ 2381] [depth= 1] . ( 135 sec) [ -12425.7712] [ 2379] [depth= 1] . ( 135 sec) [ -12425.3415] [ 2382] [depth= 1] . ( 140 sec) [ -12423.0158] [ 2380] [depth= 1] . ( 140 sec) [ -12420.6800] [ 2382] [depth= 5] . ( 141 sec) [ -12420.4425] [ 2381] [depth= 4] . ( 141 sec) [ -12419.7035] [ 2378] [depth= 1] . ( 142 sec) [ -12419.0884] [ 2378] [depth= 1] . ( 143 sec) [ -12390.2005] [Branch lengths ] . ( 148 sec) [ -12390.0997] [GTR parameters ] . ( 149 sec) [ -12390.0387] [Alpha ][ 0.388563] . ( 150 sec) [ -12389.7104] [ 2378] [depth= 1] . ( 151 sec) [ -12384.9476] [ 2372] [depth= 3] . ( 151 sec) [ -12383.0815] [ 2372] [depth= 1] . ( 152 sec) [ -12363.4151] [ 2373] [depth= 1] . ( 152 sec) [ -12348.7589] [ 2365] [depth= 6] . ( 153 sec) [ -12348.3743] [ 2364] [depth= 1] . ( 154 sec) [ -12339.8863] [ 2369] [depth= 7] . ( 156 sec) [ -12337.3585] [ 2361] [depth= 6] . ( 157 sec) [ -12336.1329] [ 2360] [depth= 6] . ( 158 sec) [ -12330.7318] [ 2359] [depth= 1] . ( 160 sec) [ -12329.5327] [ 2355] [depth= 2] . ( 160 sec) [ -12328.3644] [ 2353] [depth= 1] . ( 161 sec) [ -12323.5838] [ 2354] [depth= 1] . ( 162 sec) [ -12323.2514] [ 2354] [depth= 11] . ( 171 sec) [ -12319.9111] [ 2354] [depth= 1] . ( 171 sec) [ -12318.3869] [ 2355] [depth= 1] . ( 174 sec) [ -12314.1690] [ 2355] [depth= 1] . ( 174 sec) [ -12314.0724] [ 2354] [depth= 1] . ( 176 sec) [ -12313.7653] [ 2356] [depth= 3] . ( 177 sec) [ -12313.0661] [ 2358] [depth= 1] . ( 178 sec) [ -12312.1146] [ 2358] [depth= 1] . ( 178 sec) [ -12311.9122] [ 2358] [depth= 1] . ( 179 sec) [ -12311.4716] [ 2359] [depth= 1] . ( 179 sec) [ -12309.7318] [ 2359] [depth= 1] . ( 179 sec) [ -12309.7190] [ 2354] [depth= 5] . ( 186 sec) [ -12309.6066] [ 2354] [depth= 1] . ( 186 sec) [ -12308.3630] [ 2354] [depth= 1] . ( 188 sec) [ -12307.8687] [ 2353] [depth= 1] . ( 191 sec) [ -12306.8325] [ 2353] [depth= 1] . ( 192 sec) [ -12306.1062] [ 2353] [depth= 1] . ( 195 sec) [ -12305.3561] [ 2353] [depth= 1] . ( 201 sec) [ -12296.9181] [Branch lengths ] . ( 206 sec) [ -12296.7700] [GTR parameters ] . ( 206 sec) [ -12296.7410] [Alpha ][ 0.393499] . ( 219 sec) [ -12296.4791] [ 2351] [depth= 1] . ( 220 sec) [ -12295.8895] [ 2351] [depth= 1] . ( 232 sec) [ -12292.2427] [ 2350] [depth= 3] . ( 237 sec) [ -12292.1650] [ 2350] [depth= 1] . ( 243 sec) [ -12292.0581] [ 2354] [depth= 8] . ( 251 sec) [ -12291.9694] [ 2354] [depth= 1] . ( 251 sec) [ -12291.7078] [ 2354] [depth= 1] . ( 253 sec) [ -12291.4932] [ 2355] [depth= 2] . ( 262 sec) [ -12291.4780] [ 2354] [depth= 1] . ( 264 sec) [ -12288.9982] [Branch lengths ] . ( 269 sec) [ -12288.9210] [GTR parameters ] . ( 269 sec) [ -12288.9210] [Alpha ][ 0.393892] . ( 275 sec) [ -12288.3063] [ 2355] [depth= 3] . ( 292 sec) [ -12288.2651] [ 2349] [depth= 1] . ( 294 sec) [ -12287.5644] [ 2349] [depth= 2] . ( 311 sec) [ -12287.3234] [ 2349] [depth= 1] . ( 316 sec) [ -12287.2544] [ 2349] [depth= 1] . ( 325 sec) [ -12286.5001] [Branch lengths ] . ( 329 sec) [ -12286.4800] [GTR parameters ] . ( 329 sec) [ -12286.4790] [Alpha ][ 0.394784] . ( 363 sec) [ -12286.3311] [ 2348] [depth= 3] . ( 380 sec) [ -12285.3789] [Branch lengths ] . ( 384 sec) [ -12285.3680] [GTR parameters ] . ( 385 sec) [ -12285.3680] [Alpha ][ 0.394784] . ( 438 sec) [ -12285.3335] [Branch lengths ] . ( 547 sec) [ -12285.2797] [ 2346] [depth= 1] . ( 573 sec) [ -12285.1753] [Branch lengths ] . ( 575 sec) [ -12285.1747] [GTR parameters ] . ( 575 sec) [ -12285.1747] [Alpha ][ 0.394784] . ( 576 sec) [ -12285.1747] [Topology ] . ( 579 sec) [ -12285.1741] [Topology ] . ( 580 sec) [ -12285.1741] [GTR parameters ] . ( 580 sec) [ -12285.1741] [Alpha ][ 0.394784] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12285.174143. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 2 sec) [ -12806.7417] [GTR parameters ] . ( 2 sec) [ -12644.1413] [Alpha ][ 0.500960] . ( 2 sec) [ -12644.1413] [Topology ] . ( 5 sec) [ -12429.9217] [Topology ] . ( 8 sec) [ -12393.9974] [Topology ] . ( 11 sec) [ -12384.0402] [Topology ] . ( 14 sec) [ -12379.8706] [Topology ] . ( 17 sec) [ -12375.5020] [Topology ] . ( 20 sec) [ -12372.0127] [Topology ] . ( 23 sec) [ -12367.8036] [Topology ] . ( 26 sec) [ -12358.6163] [Topology ] . ( 30 sec) [ -12347.6738] [Topology ] . ( 38 sec) [ -12325.5729] [GTR parameters ] . ( 39 sec) [ -12316.6221] [Alpha ][ 0.402047] . ( 39 sec) [ -12316.6221] [Topology ] . ( 42 sec) [ -12311.6903] [Topology ] . ( 45 sec) [ -12310.8725] [Topology ] . ( 48 sec) [ -12310.7349] [Topology ] . ( 51 sec) [ -12310.6936] [Topology ] . ( 54 sec) [ -12310.6783] [Topology ] . ( 57 sec) [ -12310.6717] [Topology ] . ( 60 sec) [ -12310.6688] [Topology ] . Checking for NNIs, optimizing five branches... . ( 81 sec) [ -12310.6353] [Topology ] . ( 86 sec) [ -12310.5799] [GTR parameters ] . ( 86 sec) [ -12310.5503] [Alpha ][ 0.397259] . ( 86 sec) [ -12310.5503] [Topology ] . ( 89 sec) [ -12309.9367] [Topology ] . ( 92 sec) [ -12309.5523] [Topology ] . ( 95 sec) [ -12309.4877] [Topology ] . ( 98 sec) [ -12309.4700] [Topology ] . ( 101 sec) [ -12309.4642] [Topology ] . ( 104 sec) [ -12309.4621] [Topology ] . ( 107 sec) [ -12309.4611] [Topology ] . Checking for NNIs, optimizing five branches... . ( 128 sec) [ -12308.9047] [Topology ] . ( 130 sec) [ -12308.9028] [GTR parameters ] . ( 130 sec) [ -12308.9010] [Alpha ][ 0.395957] . ( 130 sec) [ -12308.9010] [Topology ] . ( 133 sec) [ -12308.8597] [Topology ] . ( 136 sec) [ -12308.8541] [Topology ] . ( 139 sec) [ -12308.8529] [Topology ] . ( 142 sec) [ -12308.8526] [Topology ] . Checking for NNIs, optimizing five branches... . ( 164 sec) [ -12308.8520] [Topology ] . ( 166 sec) [ -12308.8516] [GTR parameters ] . ( 166 sec) [ -12308.8516] [Alpha ][ 0.395957] . ( 166 sec) [ -12308.8516] [Topology ] . ( 169 sec) [ -12308.8485] [Topology ] . ( 172 sec) [ -12308.8392] [Topology ] . ( 175 sec) [ -12308.8360] [Topology ] . ( 178 sec) [ -12308.8347] [Topology ] . ( 181 sec) [ -12308.8342] [Topology ] . Checking for NNIs, optimizing five branches... . ( 202 sec) [ -12308.8340] [Topology ] . ( 203 sec) [ -12308.8340] [GTR parameters ] . ( 203 sec) [ -12308.8340] [Alpha ][ 0.395957] . ( 203 sec) [ -12308.8340] [Topology ] . ( 206 sec) [ -12308.8338] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 252 sec) [ -12806.7417] [GTR parameters ] . ( 253 sec) [ -12644.1413] [Alpha ][ 0.500960] . ( 253 sec) [ -12640.5693] [ 2378] [depth= 1] . ( 253 sec) [ -12635.2836] [ 2377] [depth= 1] . ( 255 sec) [ -12633.3264] [ 2376] [depth= 1] . ( 255 sec) [ -12632.1744] [ 2375] [depth= 1] . ( 256 sec) [ -12631.1947] [ 2375] [depth= 1] . ( 256 sec) [ -12631.0543] [ 2377] [depth= 2] . ( 256 sec) [ -12621.1528] [ 2373] [depth= 1] . ( 257 sec) [ -12616.5645] [ 2371] [depth= 2] . ( 258 sec) [ -12615.3601] [ 2371] [depth= 1] . ( 258 sec) [ -12613.0246] [ 2371] [depth= 1] . ( 258 sec) [ -12613.0102] [ 2371] [depth= 1] . ( 259 sec) [ -12612.9641] [ 2376] [depth= 2] . ( 259 sec) [ -12597.5377] [ 2374] [depth= 2] . ( 260 sec) [ -12594.2473] [ 2374] [depth= 1] . ( 260 sec) [ -12588.6016] [ 2374] [depth= 1] . ( 260 sec) [ -12584.6516] [ 2376] [depth= 1] . ( 261 sec) [ -12584.1393] [ 2376] [depth= 1] . ( 261 sec) [ -12581.1476] [ 2376] [depth= 1] . ( 262 sec) [ -12579.9040] [ 2378] [depth= 1] . ( 262 sec) [ -12576.6041] [ 2374] [depth= 1] . ( 262 sec) [ -12573.8256] [ 2374] [depth= 1] . ( 262 sec) [ -12573.0713] [ 2374] [depth= 1] . ( 263 sec) [ -12569.5781] [ 2374] [depth= 1] . ( 263 sec) [ -12569.3060] [ 2374] [depth= 1] . ( 264 sec) [ -12568.6374] [ 2379] [depth= 1] . ( 264 sec) [ -12561.5306] [ 2374] [depth= 1] . ( 265 sec) [ -12554.0244] [ 2374] [depth= 1] . ( 265 sec) [ -12553.6436] [ 2374] [depth= 1] . ( 267 sec) [ -12550.0187] [ 2373] [depth= 1] . ( 267 sec) [ -12549.6405] [ 2373] [depth= 1] . ( 267 sec) [ -12549.5125] [ 2373] [depth= 1] . ( 269 sec) [ -12543.0054] [ 2377] [depth= 2] . ( 269 sec) [ -12538.7970] [ 2375] [depth= 1] . ( 270 sec) [ -12533.1491] [ 2379] [depth= 4] . ( 270 sec) [ -12522.1439] [ 2377] [depth= 1] . ( 271 sec) [ -12521.9624] [ 2377] [depth= 1] . ( 271 sec) [ -12519.4216] [ 2377] [depth= 4] . ( 272 sec) [ -12518.5251] [ 2378] [depth= 1] . ( 272 sec) [ -12514.8310] [ 2377] [depth= 2] . ( 273 sec) [ -12514.6170] [ 2379] [depth= 3] . ( 273 sec) [ -12512.8933] [ 2381] [depth= 1] . ( 274 sec) [ -12511.8103] [ 2380] [depth= 2] . ( 275 sec) [ -12506.6788] [ 2380] [depth= 1] . ( 276 sec) [ -12495.4536] [ 2375] [depth= 1] . ( 276 sec) [ -12493.4723] [ 2376] [depth= 1] . ( 277 sec) [ -12491.2285] [ 2373] [depth= 1] . ( 279 sec) [ -12489.6622] [ 2372] [depth= 1] . ( 279 sec) [ -12488.3437] [ 2372] [depth= 1] . ( 279 sec) [ -12487.5915] [ 2372] [depth= 2] . ( 280 sec) [ -12482.1687] [ 2368] [depth= 2] . ( 280 sec) [ -12478.3744] [ 2368] [depth= 1] . ( 281 sec) [ -12477.9765] [ 2369] [depth= 1] . ( 282 sec) [ -12472.8172] [ 2369] [depth= 1] . ( 282 sec) [ -12471.7730] [ 2365] [depth= 6] . ( 282 sec) [ -12469.9536] [ 2369] [depth= 1] . ( 282 sec) [ -12467.8135] [ 2368] [depth= 4] . ( 282 sec) [ -12458.2790] [ 2367] [depth= 6] . ( 283 sec) [ -12458.1156] [ 2369] [depth= 1] . ( 284 sec) [ -12457.9181] [ 2369] [depth= 1] . ( 284 sec) [ -12457.0392] [ 2368] [depth= 1] . ( 284 sec) [ -12448.8020] [ 2366] [depth= 4] . ( 285 sec) [ -12445.6451] [ 2359] [depth= 6] . ( 286 sec) [ -12442.9493] [ 2358] [depth= 1] . ( 286 sec) [ -12442.8119] [ 2359] [depth= 1] . ( 286 sec) [ -12438.9573] [ 2358] [depth= 1] . ( 286 sec) [ -12437.4520] [ 2357] [depth= 1] . ( 287 sec) [ -12436.2481] [ 2356] [depth= 1] . ( 288 sec) [ -12435.9965] [ 2357] [depth= 1] . ( 288 sec) [ -12431.0452] [ 2360] [depth= 5] . ( 289 sec) [ -12430.6763] [ 2361] [depth= 1] . ( 289 sec) [ -12429.9133] [ 2363] [depth= 1] . ( 290 sec) [ -12429.5187] [ 2362] [depth= 1] . ( 291 sec) [ -12428.2098] [ 2367] [depth= 1] . ( 293 sec) [ -12426.7986] [ 2367] [depth= 1] . ( 293 sec) [ -12426.3159] [ 2363] [depth= 3] . ( 294 sec) [ -12424.6844] [ 2363] [depth= 1] . ( 295 sec) [ -12423.8755] [ 2364] [depth= 4] . ( 295 sec) [ -12419.8666] [ 2365] [depth= 5] . ( 295 sec) [ -12414.1931] [ 2363] [depth= 4] . ( 296 sec) [ -12413.8846] [ 2358] [depth= 1] . ( 296 sec) [ -12413.0258] [ 2359] [depth= 1] . ( 296 sec) [ -12412.3386] [ 2358] [depth= 1] . ( 297 sec) [ -12411.9320] [ 2354] [depth= 1] . ( 297 sec) [ -12411.2544] [ 2356] [depth= 1] . ( 298 sec) [ -12410.2268] [ 2357] [depth= 3] . ( 299 sec) [ -12349.3503] [Branch lengths ] . ( 306 sec) [ -12332.5440] [GTR parameters ] . ( 306 sec) [ -12320.3894] [Alpha ][ 0.384885] . ( 309 sec) [ -12319.8239] [ 2356] [depth= 1] . ( 311 sec) [ -12319.8106] [ 2356] [depth= 1] . ( 314 sec) [ -12319.7713] [ 2356] [depth= 1] . ( 317 sec) [ -12319.7603] [ 2356] [depth= 1] . ( 320 sec) [ -12314.6753] [ 2354] [depth= 2] . ( 320 sec) [ -12307.1725] [ 2349] [depth= 3] . ( 330 sec) [ -12305.4347] [ 2347] [depth= 1] . ( 331 sec) [ -12305.2827] [ 2345] [depth= 1] . ( 334 sec) [ -12304.7428] [ 2349] [depth= 4] . ( 334 sec) [ -12301.8262] [ 2348] [depth= 5] . ( 335 sec) [ -12301.3594] [ 2349] [depth= 1] . ( 339 sec) [ -12301.0713] [ 2352] [depth= 1] . ( 340 sec) [ -12300.6510] [ 2351] [depth= 1] . ( 343 sec) [ -12299.7754] [ 2350] [depth= 1] . ( 343 sec) [ -12299.6027] [ 2348] [depth= 1] . ( 350 sec) [ -12299.3527] [ 2348] [depth= 1] . ( 355 sec) [ -12299.0501] [ 2350] [depth= 2] . ( 355 sec) [ -12297.3192] [ 2348] [depth= 2] . ( 357 sec) [ -12297.0273] [ 2348] [depth= 1] . ( 357 sec) [ -12296.0859] [ 2347] [depth= 1] . ( 358 sec) [ -12296.0601] [ 2345] [depth= 1] . ( 359 sec) [ -12289.9001] [Branch lengths ] . ( 363 sec) [ -12289.6398] [GTR parameters ] . ( 363 sec) [ -12289.6101] [Alpha ][ 0.389881] . ( 365 sec) [ -12289.2025] [ 2346] [depth= 1] . ( 385 sec) [ -12289.1551] [ 2347] [depth= 1] . ( 409 sec) [ -12288.9393] [ 2348] [depth= 7] . ( 413 sec) [ -12288.8465] [ 2348] [depth= 1] . ( 414 sec) [ -12288.5863] [ 2350] [depth= 1] . ( 415 sec) [ -12286.9888] [Branch lengths ] . ( 419 sec) [ -12286.9774] [GTR parameters ] . ( 419 sec) [ -12286.9697] [Alpha ][ 0.392411] . ( 479 sec) [ -12286.7521] [Branch lengths ] . ( 591 sec) [ -12286.2441] [ 2346] [depth= 1] . ( 593 sec) [ -12286.0356] [ 2346] [depth= 1] . ( 628 sec) [ -12285.8079] [Branch lengths ] . ( 632 sec) [ -12285.7957] [GTR parameters ] . ( 633 sec) [ -12285.7889] [Alpha ][ 0.394808] . ( 633 sec) [ -12285.7889] [Topology ] . ( 636 sec) [ -12285.7576] [Topology ] . ( 639 sec) [ -12285.7488] [Topology ] . ( 642 sec) [ -12285.7452] [Topology ] . ( 645 sec) [ -12285.7436] [Topology ] . ( 648 sec) [ -12285.7429] [Topology ] . ( 648 sec) [ -12285.7429] [GTR parameters ] . ( 649 sec) [ -12285.7429] [Alpha ][ 0.394808] . ( 649 sec) [ -12285.7429] [Topology ] . ( 652 sec) [ -12285.7426] [Topology ] . ( 653 sec) [ -12285.7425] [GTR parameters ] . ( 653 sec) [ -12285.7425] [Alpha ][ 0.394808] . Checking for NNIs, optimizing five branches... . ( 674 sec) [ -12285.6121] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -12308.833763 . Log likelihood obtained after SPR moves : -12285.612068 . Log likelihood of the current tree: -12285.612068. . Printing the most likely tree in file 'nucleic_M2975_93x982_2006.phy_phyml_tree.txt'... . Best log likelihood : -12285.174143 . Time used 0h11m36s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 3225.33user 0.00system 56:21.91elapsed 95%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps