.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data66.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... . 442 patterns found. (out of a total of 500 sites) . 56 sites without polymorphism (11.20%). . [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)... . ( 0 sec) [ -20649.5845] [GTR parameters ] . ( 0 sec) [ -20256.6345] [Alpha ][ 0.500960] . ( 0 sec) [ -20220.3498] [ 4963] [depth= 9] . ( 0 sec) [ -19776.7579] [ 4889] [depth= 5] . ( 0 sec) [ -19539.8390] [ 4860] [depth= 1] . ( 1 sec) [ -19539.0484] [ 4855] [depth= 2] . ( 1 sec) [ -19353.7140] [ 4785] [depth= 5] . ( 1 sec) [ -19286.4541] [ 4771] [depth= 6] . ( 1 sec) [ -19187.0373] [ 4748] [depth= 1] . ( 1 sec) [ -19108.1028] [ 4736] [depth= 5] . ( 1 sec) [ -18703.4928] [ 4572] [depth= 5] . ( 1 sec) [ -18533.5442] [ 4564] [depth= 1] . ( 1 sec) [ -18507.8549] [ 4553] [depth= 1] . ( 1 sec) [ -18452.9800] [ 4554] [depth= 1] . ( 1 sec) [ -18257.8309] [ 4551] [depth= 2] . ( 1 sec) [ -18236.5125] [ 4536] [depth= 2] . ( 1 sec) [ -18044.6819] [ 4523] [depth= 2] . ( 1 sec) [ -17967.8972] [ 4520] [depth= 2] . ( 1 sec) [ -17366.6645] [ 4512] [depth= 5] . ( 1 sec) [ -16949.0889] [ 4355] [depth= 5] . ( 1 sec) [ -16850.7631] [ 4350] [depth= 3] . ( 1 sec) [ -16820.5062] [ 4347] [depth= 1] . ( 1 sec) [ -16818.8379] [ 4332] [depth= 12] . ( 1 sec) [ -16637.8472] [ 4280] [depth= 6] . ( 1 sec) [ -16318.9738] [ 4173] [depth= 5] . ( 1 sec) [ -16266.1755] [ 4111] [depth= 1] . ( 1 sec) [ -15948.9227] [ 4034] [depth= 5] . ( 2 sec) [ -15905.4626] [ 4038] [depth= 5] . ( 2 sec) [ -15684.8549] [ 4032] [depth= 2] . ( 2 sec) [ -15575.2879] [ 3920] [depth= 9] . ( 2 sec) [ -15552.2389] [ 3922] [depth= 2] . ( 2 sec) [ -15494.0852] [ 3892] [depth= 3] . ( 2 sec) [ -15483.1291] [ 3891] [depth= 1] . ( 2 sec) [ -15470.7408] [ 3887] [depth= 1] . ( 2 sec) [ -15470.1750] [ 3891] [depth= 1] . ( 2 sec) [ -15445.0369] [ 3891] [depth= 1] . ( 2 sec) [ -15341.7113] [ 3818] [depth= 2] . ( 2 sec) [ -15225.5945] [ 3764] [depth= 8] . ( 2 sec) [ -15127.5233] [ 3755] [depth= 1] . ( 2 sec) [ -14600.1148] [ 3625] [depth= 12] . ( 2 sec) [ -14232.0114] [ 3547] [depth= 3] . ( 2 sec) [ -13990.6125] [ 3468] [depth= 6] . ( 2 sec) [ -13837.8426] [ 3440] [depth= 1] . ( 2 sec) [ -13741.5472] [ 3387] [depth= 1] . ( 2 sec) [ -13639.9556] [ 3338] [depth= 8] . ( 2 sec) [ -13521.7404] [ 3332] [depth= 2] . ( 2 sec) [ -13506.7765] [ 3333] [depth= 9] . ( 2 sec) [ -13353.3374] [ 3292] [depth= 8] . ( 3 sec) [ -13147.0303] [ 3265] [depth= 2] . ( 3 sec) [ -13083.3660] [ 3257] [depth= 1] . ( 3 sec) [ -12782.9972] [ 3145] [depth= 4] . ( 3 sec) [ -12777.1889] [ 3136] [depth= 1] . ( 3 sec) [ -12777.0997] [ 3132] [depth= 6] . ( 3 sec) [ -12761.7712] [ 3135] [depth= 1] . ( 3 sec) [ -12739.9488] [ 3099] [depth= 1] . ( 3 sec) [ -12737.1988] [ 3097] [depth= 2] . ( 3 sec) [ -12736.3684] [ 3089] [depth= 1] . ( 3 sec) [ -12649.8086] [ 3017] [depth= 9] . ( 3 sec) [ -12492.1310] [ 2978] [depth= 13] . ( 3 sec) [ -12465.2982] [ 2973] [depth= 2] . ( 3 sec) [ -12451.0816] [ 2984] [depth= 1] . ( 3 sec) [ -12438.4096] [ 2973] [depth= 1] . ( 3 sec) [ -12432.2232] [ 2994] [depth= 1] . ( 3 sec) [ -12053.5905] [ 2870] [depth= 9] . ( 3 sec) [ -11925.3717] [ 2830] [depth= 1] . ( 4 sec) [ -11921.1917] [ 2834] [depth= 1] . ( 4 sec) [ -11904.5329] [ 2838] [depth= 8] . ( 4 sec) [ -11902.7489] [ 2841] [depth= 2] . ( 4 sec) [ -11859.1349] [ 2804] [depth= 1] . ( 4 sec) [ -11771.1035] [ 2746] [depth= 7] . ( 4 sec) [ -11693.8338] [ 2733] [depth= 2] . ( 4 sec) [ -11652.6821] [ 2696] [depth= 7] . ( 4 sec) [ -11502.4647] [ 2677] [depth= 5] . ( 4 sec) [ -11360.4853] [ 2669] [depth= 10] . ( 4 sec) [ -11351.7063] [ 2688] [depth= 1] . ( 4 sec) [ -11332.5519] [ 2669] [depth= 1] . ( 4 sec) [ -11260.6421] [ 2620] [depth= 6] . ( 4 sec) [ -11257.9890] [ 2620] [depth= 1] . ( 4 sec) [ -11235.6364] [ 2623] [depth= 1] . ( 4 sec) [ -11189.0590] [ 2617] [depth= 1] . ( 5 sec) [ -11134.4366] [ 2614] [depth= 2] . ( 5 sec) [ -10931.6635] [Branch lengths ] . ( 6 sec) [ -10929.5182] [GTR parameters ] . ( 6 sec) [ -10899.0783] [Alpha ][ 0.846281] . ( 6 sec) [ -10894.4007] [ 2590] [depth= 1] . ( 6 sec) [ -10885.8160] [ 2597] [depth= 3] . ( 6 sec) [ -10885.3147] [ 2596] [depth= 1] . ( 6 sec) [ -10848.4248] [ 2564] [depth= 1] . ( 6 sec) [ -10843.0310] [ 2569] [depth= 1] . ( 6 sec) [ -10842.2868] [ 2568] [depth= 1] . ( 6 sec) [ -10838.2791] [ 2554] [depth= 2] . ( 7 sec) [ -10833.6218] [ 2557] [depth= 1] . ( 7 sec) [ -10817.8909] [ 2549] [depth= 2] . ( 7 sec) [ -10812.0173] [ 2558] [depth= 1] . ( 7 sec) [ -10798.3151] [ 2562] [depth= 1] . ( 7 sec) [ -10682.6888] [ 2483] [depth= 3] . ( 7 sec) [ -10643.6540] [ 2449] [depth= 4] . ( 7 sec) [ -10640.7727] [ 2446] [depth= 1] . ( 7 sec) [ -10637.0324] [ 2443] [depth= 1] . ( 7 sec) [ -10555.9740] [ 2407] [depth= 2] . ( 7 sec) [ -10551.8291] [ 2409] [depth= 1] . ( 7 sec) [ -10550.1910] [ 2409] [depth= 1] . ( 7 sec) [ -10517.0775] [ 2391] [depth= 1] . ( 7 sec) [ -10515.7906] [ 2382] [depth= 1] . ( 8 sec) [ -10513.2291] [ 2384] [depth= 1] . ( 8 sec) [ -10509.7128] [ 2381] [depth= 1] . ( 8 sec) [ -10509.5120] [ 2381] [depth= 1] . ( 9 sec) [ -10497.4764] [ 2363] [depth= 1] . ( 9 sec) [ -10463.0301] [Branch lengths ] . ( 10 sec) [ -10462.5863] [GTR parameters ] . ( 10 sec) [ -10459.8948] [Alpha ][ 0.997710] . ( 10 sec) [ -10459.7519] [ 2368] [depth= 2] . ( 12 sec) [ -10459.1484] [ 2361] [depth= 1] . ( 13 sec) [ -10453.2331] [Branch lengths ] . ( 13 sec) [ -10453.2288] [GTR parameters ] . ( 13 sec) [ -10453.1331] [Alpha ][ 1.028810] . ( 16 sec) [ -10452.7175] [Branch lengths ] . ( 37 sec) [ -10452.1355] [ 2350] [depth= 2] . ( 38 sec) [ -10451.1924] [Branch lengths ] . ( 38 sec) [ -10451.1813] [GTR parameters ] . ( 38 sec) [ -10451.1804] [Alpha ][ 1.031957] . ( 60 sec) [ -10451.1300] [Branch lengths ] . ( 60 sec) [ -10451.1300] [Topology ] . ( 61 sec) [ -10451.1275] [Topology ] . ( 61 sec) [ -10451.1268] [Topology ] . ( 62 sec) [ -10451.1267] [GTR parameters ] . ( 62 sec) [ -10451.1267] [Alpha ][ 1.032989] . ( 62 sec) [ -10451.1267] [Topology ] . ( 62 sec) [ -10451.1264] [Topology ] . ( 63 sec) [ -10451.1264] [GTR parameters ] . ( 63 sec) [ -10451.1264] [Alpha ][ 1.032989] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10451.126420. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21420.3270] [GTR parameters ] . ( 1 sec) [ -20989.7208] [Alpha ][ 0.500960] . ( 1 sec) [ -20596.6772] [ 5223] [depth= 8] . ( 1 sec) [ -20173.2946] [ 5186] [depth= 5] . ( 1 sec) [ -19961.8706] [ 5147] [depth= 4] . ( 1 sec) [ -19870.7528] [ 5130] [depth= 7] . ( 1 sec) [ -19700.4552] [ 5070] [depth= 6] . ( 1 sec) [ -19512.5616] [ 5058] [depth= 8] . ( 1 sec) [ -19417.0074] [ 5021] [depth= 1] . ( 2 sec) [ -19296.2333] [ 4972] [depth= 9] . ( 2 sec) [ -19074.4789] [ 4883] [depth= 1] . ( 2 sec) [ -18986.6539] [ 4835] [depth= 9] . ( 2 sec) [ -18894.9790] [ 4754] [depth= 3] . ( 2 sec) [ -18576.1477] [ 4742] [depth= 1] . ( 2 sec) [ -18142.2300] [ 4644] [depth= 9] . ( 2 sec) [ -18046.0277] [ 4603] [depth= 1] . ( 2 sec) [ -17647.6123] [ 4623] [depth= 14] . ( 2 sec) [ -17582.6581] [ 4554] [depth= 8] . ( 2 sec) [ -17483.7672] [ 4525] [depth= 2] . ( 2 sec) [ -17037.0903] [ 4446] [depth= 1] . ( 2 sec) [ -16745.8928] [ 4446] [depth= 1] . ( 2 sec) [ -16631.3574] [ 4318] [depth= 1] . ( 2 sec) [ -16409.8376] [ 4314] [depth= 1] . ( 2 sec) [ -16150.0984] [ 4262] [depth= 7] . ( 2 sec) [ -15962.4117] [ 4132] [depth= 8] . ( 2 sec) [ -15911.3090] [ 4124] [depth= 1] . ( 2 sec) [ -15797.0285] [ 4086] [depth= 8] . ( 2 sec) [ -15751.1797] [ 4083] [depth= 1] . ( 2 sec) [ -15493.0401] [ 4082] [depth= 5] . ( 2 sec) [ -15405.4402] [ 3960] [depth= 10] . ( 2 sec) [ -15268.5236] [ 3954] [depth= 1] . ( 2 sec) [ -15256.5738] [ 3971] [depth= 1] . ( 3 sec) [ -15185.0736] [ 4003] [depth= 1] . ( 3 sec) [ -15143.2019] [ 3968] [depth= 3] . ( 3 sec) [ -15074.7682] [ 3971] [depth= 2] . ( 3 sec) [ -14963.6277] [ 3928] [depth= 4] . ( 3 sec) [ -14749.0072] [ 3764] [depth= 9] . ( 3 sec) [ -14677.1981] [ 3747] [depth= 2] . ( 3 sec) [ -14671.7604] [ 3744] [depth= 2] . ( 3 sec) [ -14501.1512] [ 3707] [depth= 3] . ( 3 sec) [ -14315.5799] [ 3633] [depth= 8] . ( 3 sec) [ -14248.4804] [ 3600] [depth= 4] . ( 3 sec) [ -14224.0571] [ 3591] [depth= 1] . ( 3 sec) [ -14209.7347] [ 3589] [depth= 1] . ( 3 sec) [ -14154.9310] [ 3581] [depth= 2] . ( 3 sec) [ -14146.7240] [ 3578] [depth= 2] . ( 3 sec) [ -14126.0508] [ 3562] [depth= 2] . ( 3 sec) [ -14122.2292] [ 3569] [depth= 2] . ( 3 sec) [ -14095.0748] [ 3547] [depth= 1] . ( 3 sec) [ -14039.9601] [ 3534] [depth= 5] . ( 3 sec) [ -13670.0044] [ 3429] [depth= 8] . ( 3 sec) [ -13601.9632] [ 3410] [depth= 1] . ( 4 sec) [ -13492.6985] [ 3365] [depth= 3] . ( 4 sec) [ -13421.5506] [ 3302] [depth= 3] . ( 4 sec) [ -13396.4838] [ 3293] [depth= 2] . ( 4 sec) [ -13196.9767] [ 3222] [depth= 1] . ( 4 sec) [ -12865.5115] [ 3111] [depth= 3] . ( 4 sec) [ -12549.4450] [ 3069] [depth= 6] . ( 4 sec) [ -12489.8514] [ 3054] [depth= 1] . ( 4 sec) [ -12481.4954] [ 3055] [depth= 1] . ( 4 sec) [ -12399.8467] [ 3053] [depth= 1] . ( 4 sec) [ -12351.9718] [ 3025] [depth= 3] . ( 4 sec) [ -12238.5739] [ 2970] [depth= 5] . ( 4 sec) [ -12148.6898] [ 2971] [depth= 3] . ( 4 sec) [ -12104.0431] [ 2948] [depth= 1] . ( 4 sec) [ -11989.9947] [ 2901] [depth= 5] . ( 4 sec) [ -11894.4925] [ 2889] [depth= 1] . ( 5 sec) [ -11765.5095] [ 2824] [depth= 4] . ( 5 sec) [ -11682.0813] [ 2807] [depth= 1] . ( 5 sec) [ -11553.4751] [ 2812] [depth= 1] . ( 5 sec) [ -11527.0037] [ 2787] [depth= 2] . ( 5 sec) [ -11449.6954] [ 2767] [depth= 2] . ( 5 sec) [ -11442.7193] [ 2761] [depth= 1] . ( 5 sec) [ -11162.0297] [ 2647] [depth= 2] . ( 5 sec) [ -11159.7452] [ 2647] [depth= 1] . ( 5 sec) [ -11151.4383] [ 2643] [depth= 1] . ( 5 sec) [ -11142.6830] [ 2609] [depth= 2] . ( 5 sec) [ -11129.0872] [ 2609] [depth= 2] . ( 5 sec) [ -11116.4011] [ 2602] [depth= 2] . ( 5 sec) [ -11052.9604] [ 2590] [depth= 1] . ( 5 sec) [ -11014.7904] [ 2591] [depth= 1] . ( 5 sec) [ -11013.9665] [ 2596] [depth= 1] . ( 6 sec) [ -10859.9687] [Branch lengths ] . ( 6 sec) [ -10857.4211] [GTR parameters ] . ( 7 sec) [ -10827.5915] [Alpha ][ 0.843725] . ( 7 sec) [ -10789.5014] [ 2551] [depth= 7] . ( 7 sec) [ -10788.2614] [ 2535] [depth= 1] . ( 7 sec) [ -10762.9098] [ 2488] [depth= 1] . ( 7 sec) [ -10760.6554] [ 2501] [depth= 2] . ( 7 sec) [ -10728.8511] [ 2504] [depth= 6] . ( 7 sec) [ -10630.8308] [ 2442] [depth= 4] . ( 7 sec) [ -10623.5490] [ 2434] [depth= 1] . ( 7 sec) [ -10623.5031] [ 2438] [depth= 1] . ( 7 sec) [ -10611.4696] [ 2427] [depth= 2] . ( 7 sec) [ -10529.0474] [ 2391] [depth= 2] . ( 8 sec) [ -10527.2742] [ 2387] [depth= 1] . ( 8 sec) [ -10518.3802] [ 2382] [depth= 1] . ( 8 sec) [ -10515.0960] [ 2376] [depth= 1] . ( 8 sec) [ -10503.2051] [ 2365] [depth= 1] . ( 8 sec) [ -10499.4791] [ 2367] [depth= 1] . ( 8 sec) [ -10498.6043] [ 2363] [depth= 1] . ( 8 sec) [ -10497.7918] [ 2361] [depth= 1] . ( 8 sec) [ -10497.4799] [ 2363] [depth= 1] . ( 9 sec) [ -10496.0481] [ 2361] [depth= 1] . ( 10 sec) [ -10463.0439] [Branch lengths ] . ( 10 sec) [ -10462.5954] [GTR parameters ] . ( 10 sec) [ -10459.7257] [Alpha ][ 1.001644] . ( 12 sec) [ -10459.5038] [ 2364] [depth= 1] . ( 12 sec) [ -10459.3943] [ 2361] [depth= 1] . ( 13 sec) [ -10455.7935] [Branch lengths ] . ( 13 sec) [ -10455.7903] [GTR parameters ] . ( 13 sec) [ -10455.7364] [Alpha ][ 1.024895] . ( 16 sec) [ -10454.2273] [Branch lengths ] . ( 32 sec) [ -10453.7270] [ 2350] [depth= 2] . ( 38 sec) [ -10451.2802] [Branch lengths ] . ( 38 sec) [ -10451.2664] [GTR parameters ] . ( 38 sec) [ -10451.2617] [Alpha ][ 1.032115] . ( 61 sec) [ -10451.1380] [Branch lengths ] . ( 61 sec) [ -10451.1380] [Topology ] . ( 62 sec) [ -10451.1308] [Topology ] . ( 62 sec) [ -10451.1285] [Topology ] . ( 63 sec) [ -10451.1274] [Topology ] . ( 64 sec) [ -10451.1269] [Topology ] . ( 64 sec) [ -10451.1267] [GTR parameters ] . ( 64 sec) [ -10451.1267] [Alpha ][ 1.032115] . ( 64 sec) [ -10451.1267] [Topology ] . ( 65 sec) [ -10451.1264] [Topology ] . ( 65 sec) [ -10451.1264] [GTR parameters ] . ( 65 sec) [ -10451.1264] [Alpha ][ 1.032115] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10451.126422. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22162.8208] [GTR parameters ] . ( 1 sec) [ -21728.1891] [Alpha ][ 0.500960] . ( 1 sec) [ -21419.5023] [ 5286] [depth= 6] . ( 1 sec) [ -21251.3523] [ 5241] [depth= 8] . ( 1 sec) [ -20717.5035] [ 5230] [depth= 4] . ( 1 sec) [ -20715.4474] [ 5212] [depth= 4] . ( 1 sec) [ -20633.0362] [ 5077] [depth= 6] . ( 1 sec) [ -20556.4494] [ 5073] [depth= 2] . ( 1 sec) [ -20177.8834] [ 5000] [depth= 12] . ( 1 sec) [ -19605.5171] [ 4952] [depth= 14] . ( 1 sec) [ -19388.8780] [ 4792] [depth= 16] . ( 2 sec) [ -18974.4938] [ 4740] [depth= 1] . ( 2 sec) [ -18538.7182] [ 4660] [depth= 9] . ( 2 sec) [ -18435.3321] [ 4626] [depth= 1] . ( 2 sec) [ -18314.1392] [ 4580] [depth= 16] . ( 2 sec) [ -18192.9038] [ 4572] [depth= 1] . ( 2 sec) [ -17648.6781] [ 4555] [depth= 1] . ( 2 sec) [ -17638.7164] [ 4518] [depth= 4] . ( 2 sec) [ -17515.4905] [ 4508] [depth= 2] . ( 2 sec) [ -17147.9070] [ 4437] [depth= 1] . ( 2 sec) [ -17081.6598] [ 4415] [depth= 6] . ( 2 sec) [ -17043.3518] [ 4401] [depth= 9] . ( 2 sec) [ -16939.7454] [ 4405] [depth= 1] . ( 2 sec) [ -16819.0817] [ 4319] [depth= 9] . ( 2 sec) [ -16818.0518] [ 4324] [depth= 1] . ( 2 sec) [ -16807.7262] [ 4319] [depth= 1] . ( 2 sec) [ -16526.5339] [ 4258] [depth= 8] . ( 2 sec) [ -16445.4105] [ 4231] [depth= 1] . ( 2 sec) [ -16295.6689] [ 4111] [depth= 5] . ( 2 sec) [ -15986.7866] [ 4062] [depth= 1] . ( 2 sec) [ -15838.3386] [ 4004] [depth= 10] . ( 2 sec) [ -15618.4074] [ 4013] [depth= 1] . ( 2 sec) [ -15558.8289] [ 3876] [depth= 9] . ( 2 sec) [ -15398.1110] [ 3869] [depth= 5] . ( 3 sec) [ -15287.4279] [ 3859] [depth= 1] . ( 3 sec) [ -15245.1364] [ 3852] [depth= 4] . ( 3 sec) [ -15182.5291] [ 3861] [depth= 10] . ( 3 sec) [ -14961.2264] [ 3836] [depth= 9] . ( 3 sec) [ -14809.0861] [ 3728] [depth= 2] . ( 3 sec) [ -14614.8242] [ 3722] [depth= 3] . ( 3 sec) [ -14584.8746] [ 3702] [depth= 1] . ( 3 sec) [ -14440.0112] [ 3643] [depth= 9] . ( 3 sec) [ -14129.8378] [ 3548] [depth= 1] . ( 3 sec) [ -13979.5082] [ 3501] [depth= 7] . ( 3 sec) [ -13958.3216] [ 3509] [depth= 3] . ( 3 sec) [ -13855.0799] [ 3458] [depth= 8] . ( 3 sec) [ -13817.0913] [ 3426] [depth= 1] . ( 3 sec) [ -13418.9451] [ 3279] [depth= 5] . ( 3 sec) [ -13309.4135] [ 3288] [depth= 1] . ( 3 sec) [ -13309.1067] [ 3292] [depth= 1] . ( 3 sec) [ -13213.6199] [ 3281] [depth= 2] . ( 3 sec) [ -13180.2541] [ 3263] [depth= 1] . ( 3 sec) [ -12906.6945] [ 3164] [depth= 4] . ( 3 sec) [ -12870.0509] [ 3152] [depth= 2] . ( 3 sec) [ -12768.0412] [ 3132] [depth= 3] . ( 4 sec) [ -12701.3662] [ 3052] [depth= 5] . ( 4 sec) [ -12697.3336] [ 3053] [depth= 1] . ( 4 sec) [ -12590.1937] [ 3042] [depth= 1] . ( 4 sec) [ -12355.4109] [ 2974] [depth= 1] . ( 4 sec) [ -12328.6082] [ 2975] [depth= 4] . ( 4 sec) [ -12235.6547] [ 2970] [depth= 5] . ( 4 sec) [ -12181.3508] [ 2957] [depth= 7] . ( 4 sec) [ -12065.1665] [ 2932] [depth= 1] . ( 4 sec) [ -12063.8423] [ 2948] [depth= 1] . ( 4 sec) [ -11777.6856] [ 2863] [depth= 2] . ( 4 sec) [ -11774.6422] [ 2871] [depth= 4] . ( 4 sec) [ -11771.5440] [ 2876] [depth= 2] . ( 4 sec) [ -11767.1440] [ 2905] [depth= 1] . ( 4 sec) [ -11736.1904] [ 2900] [depth= 1] . ( 4 sec) [ -11564.7895] [ 2836] [depth= 3] . ( 4 sec) [ -11556.1649] [ 2815] [depth= 1] . ( 4 sec) [ -11516.7140] [ 2844] [depth= 2] . ( 4 sec) [ -11305.8454] [ 2785] [depth= 2] . ( 4 sec) [ -11305.7554] [ 2782] [depth= 1] . ( 5 sec) [ -11298.3668] [ 2775] [depth= 1] . ( 5 sec) [ -11292.1543] [ 2747] [depth= 1] . ( 5 sec) [ -11262.0199] [ 2739] [depth= 1] . ( 5 sec) [ -11118.4223] [ 2695] [depth= 8] . ( 5 sec) [ -11111.2552] [ 2686] [depth= 4] . ( 5 sec) [ -11100.6107] [ 2683] [depth= 2] . ( 5 sec) [ -11090.2706] [ 2671] [depth= 3] . ( 5 sec) [ -11069.9450] [ 2665] [depth= 1] . ( 5 sec) [ -11059.2516] [ 2661] [depth= 2] . ( 5 sec) [ -11022.9103] [ 2638] [depth= 2] . ( 5 sec) [ -11012.2858] [ 2617] [depth= 1] . ( 5 sec) [ -10995.9443] [ 2588] [depth= 1] . ( 5 sec) [ -10977.6143] [ 2598] [depth= 1] . ( 6 sec) [ -10804.3586] [Branch lengths ] . ( 6 sec) [ -10801.7627] [GTR parameters ] . ( 7 sec) [ -10764.7325] [Alpha ][ 0.879047] . ( 7 sec) [ -10727.9359] [ 2550] [depth= 7] . ( 7 sec) [ -10723.7298] [ 2544] [depth= 1] . ( 7 sec) [ -10723.6882] [ 2530] [depth= 1] . ( 7 sec) [ -10646.7330] [ 2461] [depth= 4] . ( 7 sec) [ -10641.1834] [ 2459] [depth= 1] . ( 7 sec) [ -10638.6677] [ 2461] [depth= 1] . ( 8 sec) [ -10637.4542] [ 2460] [depth= 1] . ( 8 sec) [ -10625.2226] [ 2468] [depth= 1] . ( 8 sec) [ -10615.9318] [ 2466] [depth= 1] . ( 8 sec) [ -10614.8527] [ 2461] [depth= 1] . ( 8 sec) [ -10614.0057] [ 2449] [depth= 1] . ( 8 sec) [ -10597.6236] [ 2433] [depth= 1] . ( 8 sec) [ -10592.7412] [ 2419] [depth= 1] . ( 8 sec) [ -10589.8424] [ 2435] [depth= 1] . ( 8 sec) [ -10584.0054] [ 2438] [depth= 1] . ( 8 sec) [ -10566.4480] [ 2416] [depth= 1] . ( 9 sec) [ -10563.4375] [ 2408] [depth= 2] . ( 9 sec) [ -10557.5905] [ 2416] [depth= 1] . ( 9 sec) [ -10553.2877] [ 2408] [depth= 1] . ( 9 sec) [ -10551.0586] [ 2399] [depth= 1] . ( 9 sec) [ -10550.7383] [ 2401] [depth= 1] . ( 9 sec) [ -10550.6784] [ 2399] [depth= 1] . ( 9 sec) [ -10535.5725] [ 2386] [depth= 3] . ( 9 sec) [ -10535.3036] [ 2397] [depth= 1] . ( 9 sec) [ -10499.3658] [ 2365] [depth= 2] . ( 10 sec) [ -10468.4952] [Branch lengths ] . ( 10 sec) [ -10468.0882] [GTR parameters ] . ( 10 sec) [ -10466.2340] [Alpha ][ 1.006493] . ( 10 sec) [ -10466.2081] [ 2367] [depth= 1] . ( 11 sec) [ -10460.5764] [ 2352] [depth= 1] . ( 11 sec) [ -10460.5067] [ 2350] [depth= 1] . ( 12 sec) [ -10460.4703] [ 2350] [depth= 1] . ( 13 sec) [ -10452.1090] [Branch lengths ] . ( 13 sec) [ -10452.0711] [GTR parameters ] . ( 13 sec) [ -10452.0120] [Alpha ][ 1.030877] . ( 16 sec) [ -10451.1620] [Branch lengths ] . ( 38 sec) [ -10451.1288] [Branch lengths ] . ( 38 sec) [ -10451.1288] [Topology ] . ( 39 sec) [ -10451.1275] [Topology ] . ( 40 sec) [ -10451.1271] [Topology ] . ( 40 sec) [ -10451.1267] [GTR parameters ] . ( 40 sec) [ -10451.1264] [Alpha ][ 1.032495] . ( 40 sec) [ -10451.1264] [Topology ] . ( 41 sec) [ -10451.1263] [Topology ] . ( 41 sec) [ -10451.1263] [GTR parameters ] . ( 41 sec) [ -10451.1263] [Alpha ][ 1.032495] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10451.126265. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21168.1774] [GTR parameters ] . ( 1 sec) [ -20734.1937] [Alpha ][ 0.500960] . ( 2 sec) [ -20593.3586] [ 5238] [depth= 9] . ( 2 sec) [ -20547.0048] [ 5257] [depth= 1] . ( 2 sec) [ -20288.0227] [ 5176] [depth= 9] . ( 2 sec) [ -20177.3872] [ 5076] [depth= 8] . ( 2 sec) [ -20075.3497] [ 4997] [depth= 1] . ( 2 sec) [ -19581.8887] [ 4959] [depth= 9] . ( 2 sec) [ -19444.6471] [ 4923] [depth= 3] . ( 2 sec) [ -19072.2155] [ 4914] [depth= 3] . ( 2 sec) [ -18942.1637] [ 4891] [depth= 5] . ( 2 sec) [ -18854.7246] [ 4889] [depth= 7] . ( 2 sec) [ -18611.9096] [ 4873] [depth= 4] . ( 2 sec) [ -18526.6152] [ 4874] [depth= 9] . ( 2 sec) [ -18188.1362] [ 4741] [depth= 10] . ( 2 sec) [ -17873.5530] [ 4618] [depth= 5] . ( 2 sec) [ -17753.5377] [ 4606] [depth= 4] . ( 2 sec) [ -17702.6514] [ 4564] [depth= 1] . ( 2 sec) [ -17694.6625] [ 4562] [depth= 1] . ( 2 sec) [ -17327.2883] [ 4422] [depth= 9] . ( 2 sec) [ -16947.3824] [ 4337] [depth= 9] . ( 2 sec) [ -16909.2569] [ 4265] [depth= 1] . ( 2 sec) [ -16717.3556] [ 4216] [depth= 7] . ( 3 sec) [ -16393.6406] [ 4113] [depth= 1] . ( 3 sec) [ -16054.1553] [ 4041] [depth= 1] . ( 3 sec) [ -15794.0668] [ 3942] [depth= 3] . ( 3 sec) [ -15551.4921] [ 3949] [depth= 1] . ( 3 sec) [ -15321.8116] [ 3916] [depth= 7] . ( 3 sec) [ -14753.3248] [ 3739] [depth= 3] . ( 3 sec) [ -14609.7073] [ 3723] [depth= 4] . ( 3 sec) [ -14584.3833] [ 3719] [depth= 1] . ( 3 sec) [ -14487.2523] [ 3729] [depth= 10] . ( 3 sec) [ -14466.4377] [ 3719] [depth= 3] . ( 3 sec) [ -14352.9653] [ 3676] [depth= 2] . ( 3 sec) [ -13996.4582] [ 3522] [depth= 9] . ( 3 sec) [ -13753.3042] [ 3442] [depth= 12] . ( 3 sec) [ -13651.1865] [ 3324] [depth= 3] . ( 3 sec) [ -13624.9002] [ 3331] [depth= 1] . ( 3 sec) [ -13363.0134] [ 3306] [depth= 8] . ( 3 sec) [ -13353.5013] [ 3311] [depth= 1] . ( 3 sec) [ -13308.2248] [ 3307] [depth= 1] . ( 3 sec) [ -13235.8491] [ 3288] [depth= 3] . ( 3 sec) [ -12901.0632] [ 3248] [depth= 2] . ( 3 sec) [ -12874.0645] [ 3249] [depth= 3] . ( 4 sec) [ -12610.9977] [ 3106] [depth= 7] . ( 4 sec) [ -12546.9414] [ 3082] [depth= 2] . ( 4 sec) [ -12537.8770] [ 3074] [depth= 1] . ( 4 sec) [ -12531.6101] [ 3072] [depth= 1] . ( 4 sec) [ -12486.2157] [ 3045] [depth= 2] . ( 4 sec) [ -12484.1250] [ 3037] [depth= 1] . ( 4 sec) [ -12464.8842] [ 3055] [depth= 1] . ( 4 sec) [ -12461.3983] [ 3051] [depth= 1] . ( 4 sec) [ -12425.7897] [ 3037] [depth= 1] . ( 4 sec) [ -12352.6470] [ 3042] [depth= 4] . ( 4 sec) [ -12341.8727] [ 3043] [depth= 2] . ( 4 sec) [ -12286.5096] [ 3016] [depth= 1] . ( 4 sec) [ -12219.0686] [ 3018] [depth= 10] . ( 4 sec) [ -12207.1209] [ 2990] [depth= 2] . ( 4 sec) [ -12200.2494] [ 2983] [depth= 1] . ( 4 sec) [ -12023.7761] [ 2900] [depth= 3] . ( 4 sec) [ -11953.6503] [ 2864] [depth= 8] . ( 4 sec) [ -11802.2440] [ 2847] [depth= 3] . ( 5 sec) [ -11687.3026] [ 2817] [depth= 1] . ( 5 sec) [ -11681.4142] [ 2815] [depth= 1] . ( 5 sec) [ -11557.8050] [ 2753] [depth= 1] . ( 5 sec) [ -11554.6140] [ 2752] [depth= 4] . ( 5 sec) [ -11489.8086] [ 2759] [depth= 1] . ( 5 sec) [ -11476.1323] [ 2755] [depth= 1] . ( 5 sec) [ -11474.5998] [ 2754] [depth= 1] . ( 5 sec) [ -11461.6229] [ 2751] [depth= 3] . ( 5 sec) [ -11350.5274] [ 2742] [depth= 1] . ( 5 sec) [ -11349.7490] [ 2739] [depth= 1] . ( 5 sec) [ -11327.2416] [ 2706] [depth= 1] . ( 5 sec) [ -11161.7799] [ 2597] [depth= 5] . ( 5 sec) [ -11148.2577] [ 2576] [depth= 4] . ( 5 sec) [ -11094.7229] [ 2560] [depth= 1] . ( 5 sec) [ -11076.1313] [ 2572] [depth= 9] . ( 5 sec) [ -11052.7004] [ 2562] [depth= 1] . ( 5 sec) [ -11029.7298] [ 2563] [depth= 1] . ( 6 sec) [ -11025.3541] [ 2565] [depth= 1] . ( 6 sec) [ -11022.4815] [ 2557] [depth= 1] . ( 6 sec) [ -10814.6503] [Branch lengths ] . ( 7 sec) [ -10811.7780] [GTR parameters ] . ( 7 sec) [ -10778.9564] [Alpha ][ 0.859877] . ( 7 sec) [ -10777.6346] [ 2533] [depth= 4] . ( 7 sec) [ -10713.4017] [ 2503] [depth= 11] . ( 7 sec) [ -10712.9373] [ 2502] [depth= 1] . ( 7 sec) [ -10712.3861] [ 2495] [depth= 1] . ( 7 sec) [ -10697.3893] [ 2446] [depth= 2] . ( 7 sec) [ -10693.2121] [ 2441] [depth= 1] . ( 7 sec) [ -10685.8943] [ 2439] [depth= 2] . ( 8 sec) [ -10661.1271] [ 2424] [depth= 5] . ( 8 sec) [ -10658.1975] [ 2434] [depth= 1] . ( 8 sec) [ -10657.3044] [ 2438] [depth= 2] . ( 8 sec) [ -10649.3515] [ 2442] [depth= 1] . ( 8 sec) [ -10632.2104] [ 2451] [depth= 2] . ( 8 sec) [ -10607.9637] [ 2439] [depth= 6] . ( 8 sec) [ -10604.6488] [ 2432] [depth= 2] . ( 8 sec) [ -10552.3465] [ 2422] [depth= 1] . ( 8 sec) [ -10551.9779] [ 2421] [depth= 1] . ( 8 sec) [ -10520.3455] [ 2384] [depth= 2] . ( 8 sec) [ -10501.9015] [ 2362] [depth= 2] . ( 8 sec) [ -10498.7319] [ 2359] [depth= 1] . ( 9 sec) [ -10490.5544] [ 2355] [depth= 1] . ( 9 sec) [ -10487.0397] [ 2371] [depth= 1] . ( 9 sec) [ -10484.9822] [ 2382] [depth= 1] . ( 9 sec) [ -10480.5004] [ 2378] [depth= 1] . ( 9 sec) [ -10478.6742] [ 2361] [depth= 1] . ( 10 sec) [ -10457.2457] [Branch lengths ] . ( 10 sec) [ -10457.1123] [GTR parameters ] . ( 10 sec) [ -10454.6312] [Alpha ][ 1.006352] . ( 12 sec) [ -10454.3458] [ 2350] [depth= 1] . ( 13 sec) [ -10451.8088] [Branch lengths ] . ( 13 sec) [ -10451.7964] [GTR parameters ] . ( 13 sec) [ -10451.7585] [Alpha ][ 1.026711] . ( 16 sec) [ -10451.2315] [Branch lengths ] . ( 38 sec) [ -10451.1395] [Branch lengths ] . ( 38 sec) [ -10451.1395] [Topology ] . ( 39 sec) [ -10451.1343] [Topology ] . ( 40 sec) [ -10451.1329] [Topology ] . ( 41 sec) [ -10451.1324] [Topology ] . ( 41 sec) [ -10451.1299] [GTR parameters ] . ( 41 sec) [ -10451.1271] [Alpha ][ 1.032270] . ( 41 sec) [ -10451.1271] [Topology ] . ( 42 sec) [ -10451.1265] [Topology ] . ( 42 sec) [ -10451.1265] [GTR parameters ] . ( 42 sec) [ -10451.1265] [Alpha ][ 1.032270] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10451.126491. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22072.9980] [GTR parameters ] . ( 1 sec) [ -21609.9629] [Alpha ][ 0.500960] . ( 1 sec) [ -21603.8822] [ 5294] [depth= 7] . ( 1 sec) [ -21333.8940] [ 5221] [depth= 12] . ( 1 sec) [ -21165.3134] [ 5199] [depth= 5] . ( 1 sec) [ -21077.7485] [ 5182] [depth= 1] . ( 1 sec) [ -20716.6230] [ 5043] [depth= 5] . ( 1 sec) [ -20706.6367] [ 5043] [depth= 6] . ( 1 sec) [ -20542.2463] [ 5016] [depth= 4] . ( 1 sec) [ -20401.4145] [ 5009] [depth= 1] . ( 1 sec) [ -20269.3666] [ 4939] [depth= 6] . ( 1 sec) [ -20032.7279] [ 4878] [depth= 5] . ( 1 sec) [ -19729.7456] [ 4758] [depth= 2] . ( 1 sec) [ -19700.3521] [ 4755] [depth= 2] . ( 1 sec) [ -19618.1157] [ 4748] [depth= 1] . ( 1 sec) [ -19596.4369] [ 4710] [depth= 1] . ( 1 sec) [ -19437.9995] [ 4669] [depth= 1] . ( 1 sec) [ -19434.7210] [ 4664] [depth= 1] . ( 1 sec) [ -19205.7251] [ 4654] [depth= 2] . ( 1 sec) [ -19121.3836] [ 4610] [depth= 3] . ( 1 sec) [ -19018.7646] [ 4600] [depth= 2] . ( 1 sec) [ -18927.4419] [ 4580] [depth= 2] . ( 2 sec) [ -18815.2468] [ 4571] [depth= 4] . ( 2 sec) [ -18493.2525] [ 4496] [depth= 1] . ( 2 sec) [ -18409.6027] [ 4500] [depth= 1] . ( 2 sec) [ -18226.3453] [ 4474] [depth= 1] . ( 2 sec) [ -18059.2930] [ 4480] [depth= 3] . ( 2 sec) [ -17411.2751] [ 4358] [depth= 8] . ( 2 sec) [ -17386.1467] [ 4359] [depth= 1] . ( 2 sec) [ -16927.6166] [ 4191] [depth= 11] . ( 2 sec) [ -16489.6651] [ 4095] [depth= 7] . ( 2 sec) [ -15969.3545] [ 3904] [depth= 6] . ( 2 sec) [ -15798.1673] [ 3839] [depth= 12] . ( 2 sec) [ -15646.2776] [ 3749] [depth= 9] . ( 2 sec) [ -15552.8906] [ 3701] [depth= 1] . ( 2 sec) [ -15247.3790] [ 3672] [depth= 10] . ( 2 sec) [ -15186.3771] [ 3673] [depth= 2] . ( 2 sec) [ -15085.9674] [ 3688] [depth= 6] . ( 2 sec) [ -15082.6573] [ 3695] [depth= 1] . ( 2 sec) [ -14940.4136] [ 3678] [depth= 9] . ( 2 sec) [ -14420.7101] [ 3579] [depth= 3] . ( 2 sec) [ -14387.1661] [ 3575] [depth= 1] . ( 2 sec) [ -14373.8428] [ 3564] [depth= 1] . ( 2 sec) [ -14364.1876] [ 3571] [depth= 1] . ( 3 sec) [ -13478.3538] [ 3396] [depth= 9] . ( 3 sec) [ -13308.2302] [ 3338] [depth= 11] . ( 3 sec) [ -12957.4201] [ 3285] [depth= 7] . ( 3 sec) [ -12955.8513] [ 3301] [depth= 2] . ( 3 sec) [ -12927.4582] [ 3257] [depth= 6] . ( 3 sec) [ -12796.7944] [ 3246] [depth= 6] . ( 3 sec) [ -12772.4315] [ 3243] [depth= 1] . ( 3 sec) [ -12718.2619] [ 3233] [depth= 1] . ( 3 sec) [ -12417.3753] [ 3161] [depth= 7] . ( 3 sec) [ -12357.9048] [ 3107] [depth= 6] . ( 3 sec) [ -12227.5139] [ 3091] [depth= 1] . ( 3 sec) [ -12216.0737] [ 3049] [depth= 7] . ( 3 sec) [ -11846.0413] [ 3042] [depth= 1] . ( 3 sec) [ -11726.5313] [ 2923] [depth= 9] . ( 3 sec) [ -11679.8396] [ 2871] [depth= 6] . ( 3 sec) [ -11654.2752] [ 2852] [depth= 5] . ( 3 sec) [ -11633.6554] [ 2812] [depth= 4] . ( 4 sec) [ -11622.1954] [ 2797] [depth= 2] . ( 4 sec) [ -11585.8043] [ 2794] [depth= 1] . ( 4 sec) [ -11557.6698] [ 2791] [depth= 1] . ( 4 sec) [ -11437.4393] [ 2747] [depth= 2] . ( 4 sec) [ -11373.5336] [ 2727] [depth= 4] . ( 4 sec) [ -11342.5532] [ 2716] [depth= 1] . ( 4 sec) [ -11296.2325] [ 2706] [depth= 2] . ( 4 sec) [ -11293.9889] [ 2706] [depth= 1] . ( 4 sec) [ -11289.8269] [ 2708] [depth= 1] . ( 4 sec) [ -11280.4440] [ 2712] [depth= 1] . ( 4 sec) [ -11240.9102] [ 2704] [depth= 1] . ( 4 sec) [ -11240.4161] [ 2704] [depth= 1] . ( 4 sec) [ -11225.2100] [ 2709] [depth= 1] . ( 4 sec) [ -11193.8757] [ 2712] [depth= 4] . ( 4 sec) [ -11085.6816] [ 2647] [depth= 6] . ( 4 sec) [ -11085.5504] [ 2649] [depth= 1] . ( 4 sec) [ -11084.9789] [ 2646] [depth= 1] . ( 4 sec) [ -11082.8276] [ 2605] [depth= 1] . ( 5 sec) [ -11082.7320] [ 2608] [depth= 2] . ( 5 sec) [ -11074.4996] [ 2580] [depth= 2] . ( 5 sec) [ -11071.8192] [ 2575] [depth= 1] . ( 5 sec) [ -11065.8501] [ 2569] [depth= 1] . ( 5 sec) [ -10924.8704] [Branch lengths ] . ( 5 sec) [ -10923.0023] [GTR parameters ] . ( 6 sec) [ -10890.3286] [Alpha ][ 0.862960] . ( 6 sec) [ -10873.6390] [ 2546] [depth= 2] . ( 6 sec) [ -10726.9122] [ 2470] [depth= 5] . ( 6 sec) [ -10703.5179] [ 2452] [depth= 2] . ( 6 sec) [ -10580.9675] [ 2423] [depth= 2] . ( 6 sec) [ -10565.3293] [ 2430] [depth= 3] . ( 6 sec) [ -10565.0967] [ 2425] [depth= 1] . ( 6 sec) [ -10545.3922] [ 2418] [depth= 3] . ( 6 sec) [ -10522.2669] [ 2413] [depth= 1] . ( 6 sec) [ -10521.9523] [ 2406] [depth= 1] . ( 6 sec) [ -10521.0196] [ 2409] [depth= 1] . ( 7 sec) [ -10519.0603] [ 2402] [depth= 1] . ( 7 sec) [ -10512.3884] [ 2403] [depth= 1] . ( 7 sec) [ -10512.2145] [ 2407] [depth= 1] . ( 7 sec) [ -10506.7513] [ 2405] [depth= 1] . ( 7 sec) [ -10504.6338] [ 2399] [depth= 1] . ( 7 sec) [ -10503.7896] [ 2396] [depth= 1] . ( 8 sec) [ -10502.4362] [ 2393] [depth= 1] . ( 8 sec) [ -10498.8536] [ 2388] [depth= 1] . ( 8 sec) [ -10498.7555] [ 2390] [depth= 1] . ( 9 sec) [ -10471.5513] [Branch lengths ] . ( 9 sec) [ -10471.0373] [GTR parameters ] . ( 9 sec) [ -10469.3136] [Alpha ][ 0.985098] . ( 9 sec) [ -10459.1081] [ 2363] [depth= 2] . ( 11 sec) [ -10459.0713] [ 2347] [depth= 1] . ( 11 sec) [ -10458.5226] [ 2350] [depth= 1] . ( 11 sec) [ -10457.8086] [ 2350] [depth= 1] . ( 12 sec) [ -10452.3083] [Branch lengths ] . ( 12 sec) [ -10452.2541] [GTR parameters ] . ( 12 sec) [ -10452.0871] [Alpha ][ 1.026452] . ( 15 sec) [ -10451.2448] [Branch lengths ] . ( 37 sec) [ -10451.1441] [Branch lengths ] . ( 37 sec) [ -10451.1441] [Topology ] . ( 38 sec) [ -10451.1356] [Topology ] . ( 39 sec) [ -10451.1329] [Topology ] . ( 40 sec) [ -10451.1317] [Topology ] . ( 41 sec) [ -10451.1310] [Topology ] . ( 41 sec) [ -10451.1303] [GTR parameters ] . ( 41 sec) [ -10451.1272] [Alpha ][ 1.032222] . ( 41 sec) [ -10451.1272] [Topology ] . ( 42 sec) [ -10451.1266] [Topology ] . ( 42 sec) [ -10451.1266] [GTR parameters ] . ( 42 sec) [ -10451.1266] [Alpha ][ 1.032222] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10451.126636. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-10526.728407 . ( 1 sec) [ -10524.4761] [GTR parameters ] . ( 1 sec) [ -10524.4715] [Alpha ][ 0.992621] . ( 1 sec) [ -10524.4715] [Topology ] . ( 2 sec) [ -10465.5610] [Topology ] . ( 2 sec) [ -10455.2547] [Topology ] . ( 3 sec) [ -10452.8768] [Topology ] . ( 4 sec) [ -10452.0332] [Topology ] . ( 5 sec) [ -10451.6737] [Topology ] . ( 6 sec) [ -10451.5056] [Topology ] . ( 7 sec) [ -10451.4234] [Topology ] . ( 7 sec) [ -10451.3821] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10451.382088 . ( 14 sec) [ -10451.3223] [GTR parameters ] . ( 14 sec) [ -10451.1965] [Alpha ][ 1.029002] . ( 14 sec) [ -10451.1965] [Topology ] . ( 15 sec) [ -10451.1604] [Topology ] . ( 16 sec) [ -10451.1442] [Topology ] . ( 17 sec) [ -10451.1360] [Topology ] . ( 18 sec) [ -10451.1319] [Topology ] . ( 19 sec) [ -10451.1297] [Topology ] . ( 19 sec) [ -10451.1286] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10451.128613 . ( 26 sec) [ -10451.1286] [GTR parameters ] . ( 26 sec) [ -10451.1276] [Alpha ][ 1.032220] . ( 26 sec) [ -10451.1276] [Topology ] . ( 27 sec) [ -10451.1269] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10451.126877 . ( 34 sec) [ -10451.1269] [GTR parameters ] . ( 34 sec) [ -10451.1269] [Alpha ][ 1.032220] . ( 34 sec) [ -10451.1269] [Topology ] . ( 35 sec) [ -10451.1265] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 48 sec) [ -10524.4761] [GTR parameters ] . ( 48 sec) [ -10524.4715] [Alpha ][ 0.992621] . ( 49 sec) [ -10524.0190] [ 2365] [depth= 1] . ( 49 sec) [ -10522.0793] [ 2364] [depth= 1] . ( 49 sec) [ -10521.8108] [ 2365] [depth= 1] . ( 49 sec) [ -10520.1996] [ 2376] [depth= 2] . ( 49 sec) [ -10518.3449] [ 2374] [depth= 1] . ( 50 sec) [ -10517.2983] [ 2377] [depth= 1] . ( 50 sec) [ -10513.7615] [ 2393] [depth= 1] . ( 50 sec) [ -10508.2770] [ 2377] [depth= 1] . ( 50 sec) [ -10508.1422] [ 2383] [depth= 3] . ( 51 sec) [ -10501.5856] [ 2371] [depth= 3] . ( 51 sec) [ -10460.1834] [Branch lengths ] . ( 52 sec) [ -10460.1404] [GTR parameters ] . ( 52 sec) [ -10460.1321] [Alpha ][ 1.002010] . ( 52 sec) [ -10459.0427] [ 2366] [depth= 1] . ( 52 sec) [ -10458.7659] [ 2350] [depth= 1] . ( 53 sec) [ -10458.7055] [ 2352] [depth= 1] . ( 53 sec) [ -10458.4142] [ 2350] [depth= 1] . ( 53 sec) [ -10457.9983] [ 2350] [depth= 1] . ( 55 sec) [ -10451.8408] [Branch lengths ] . ( 55 sec) [ -10451.8213] [GTR parameters ] . ( 55 sec) [ -10451.7622] [Alpha ][ 1.026487] . ( 58 sec) [ -10451.1997] [Branch lengths ] . ( 80 sec) [ -10451.1386] [Branch lengths ] . ( 80 sec) [ -10451.1386] [Topology ] . ( 81 sec) [ -10451.1333] [Topology ] . ( 82 sec) [ -10451.1317] [Topology ] . ( 82 sec) [ -10451.1309] [Topology ] . ( 83 sec) [ -10451.1304] [GTR parameters ] . ( 83 sec) [ -10451.1274] [Alpha ][ 1.032200] . ( 83 sec) [ -10451.1274] [Topology ] . ( 83 sec) [ -10451.1267] [Topology ] . ( 84 sec) [ -10451.1267] [GTR parameters ] . ( 84 sec) [ -10451.1267] [Alpha ][ 1.032200] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10451.126529 . Log likelihood obtained after SPR moves : -10451.126729 . Log likelihood of the current tree: -10451.126529. . Printing the most likely tree in file 'data66.phy_phyml_tree.txt'... . Best log likelihood : -10451.126265 . Time used 0h1m30s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo