.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2862_54x1011_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... . 587 patterns found. (out of a total of 1011 sites) . 443 sites without polymorphism (43.82%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 16Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -43238.2932] [GTR parameters ] . ( 1 sec) [ -41999.3805] [Alpha ][ 0.500960] . ( 1 sec) [ -40168.1264] [ 8043] [depth= 9] . ( 1 sec) [ -38868.3253] [ 7933] [depth= 8] . ( 1 sec) [ -38712.6376] [ 7868] [depth= 9] . ( 1 sec) [ -38683.2002] [ 7788] [depth= 1] . ( 1 sec) [ -38017.0475] [ 7712] [depth= 12] . ( 2 sec) [ -37867.3666] [ 7702] [depth= 1] . ( 2 sec) [ -37607.8062] [ 7591] [depth= 6] . ( 2 sec) [ -37357.7928] [ 7486] [depth= 2] . ( 2 sec) [ -37057.2981] [ 7362] [depth= 10] . ( 2 sec) [ -37025.1385] [ 7349] [depth= 3] . ( 2 sec) [ -36862.9957] [ 7321] [depth= 6] . ( 2 sec) [ -36694.6031] [ 7277] [depth= 2] . ( 2 sec) [ -36371.6897] [ 7248] [depth= 8] . ( 2 sec) [ -36295.4755] [ 7233] [depth= 4] . ( 2 sec) [ -36073.7239] [ 7204] [depth= 2] . ( 2 sec) [ -35148.0567] [ 7127] [depth= 17] . ( 2 sec) [ -33906.3111] [ 7110] [depth= 1] . ( 2 sec) [ -33839.4194] [ 7048] [depth= 1] . ( 2 sec) [ -33475.5951] [ 7011] [depth= 2] . ( 3 sec) [ -33211.5948] [ 6941] [depth= 1] . ( 3 sec) [ -32574.9743] [ 6818] [depth= 2] . ( 3 sec) [ -32468.3081] [ 6742] [depth= 7] . ( 3 sec) [ -31990.2373] [ 6722] [depth= 4] . ( 3 sec) [ -31703.2417] [ 6645] [depth= 10] . ( 3 sec) [ -31048.8613] [ 6640] [depth= 1] . ( 3 sec) [ -30727.0141] [ 6640] [depth= 3] . ( 3 sec) [ -30692.9752] [ 6660] [depth= 14] . ( 3 sec) [ -30114.9534] [ 6530] [depth= 15] . ( 3 sec) [ -29861.8572] [ 6514] [depth= 10] . ( 3 sec) [ -29372.4098] [ 6440] [depth= 5] . ( 3 sec) [ -29107.3384] [ 6429] [depth= 8] . ( 3 sec) [ -28797.2652] [ 6430] [depth= 1] . ( 4 sec) [ -28467.5217] [ 6323] [depth= 4] . ( 4 sec) [ -28137.1188] [ 6319] [depth= 4] . ( 4 sec) [ -27492.5844] [ 6272] [depth= 14] . ( 4 sec) [ -27378.8691] [ 6270] [depth= 3] . ( 4 sec) [ -27369.1094] [ 6222] [depth= 3] . ( 4 sec) [ -27254.8203] [ 6208] [depth= 1] . ( 4 sec) [ -27198.2579] [ 6189] [depth= 1] . ( 4 sec) [ -26954.3144] [ 6141] [depth= 2] . ( 4 sec) [ -26938.4754] [ 6120] [depth= 2] . ( 4 sec) [ -26933.4953] [ 6121] [depth= 1] . ( 4 sec) [ -26599.7742] [ 6076] [depth= 2] . ( 5 sec) [ -26518.3976] [ 6043] [depth= 6] . ( 5 sec) [ -26068.2603] [ 5839] [depth= 6] . ( 5 sec) [ -26065.6462] [ 5841] [depth= 1] . ( 5 sec) [ -26020.2014] [ 5840] [depth= 2] . ( 5 sec) [ -25726.0066] [ 5799] [depth= 7] . ( 5 sec) [ -25616.2283] [ 5788] [depth= 1] . ( 5 sec) [ -25383.2942] [ 5656] [depth= 9] . ( 5 sec) [ -25355.4797] [ 5622] [depth= 1] . ( 5 sec) [ -25198.4989] [ 5568] [depth= 1] . ( 5 sec) [ -24501.3980] [ 5520] [depth= 6] . ( 5 sec) [ -24322.4546] [ 5437] [depth= 7] . ( 5 sec) [ -24100.3875] [ 5426] [depth= 1] . ( 6 sec) [ -23986.7685] [ 5391] [depth= 4] . ( 6 sec) [ -23772.9906] [ 5338] [depth= 5] . ( 6 sec) [ -23672.3306] [ 5333] [depth= 1] . ( 6 sec) [ -23290.0984] [ 5231] [depth= 4] . ( 6 sec) [ -22872.3633] [ 5228] [depth= 1] . ( 6 sec) [ -22223.6394] [ 5179] [depth= 6] . ( 6 sec) [ -22205.4391] [ 5189] [depth= 1] . ( 6 sec) [ -21985.5507] [ 5104] [depth= 5] . ( 6 sec) [ -21834.2066] [ 5087] [depth= 1] . ( 6 sec) [ -21625.6271] [ 5094] [depth= 6] . ( 6 sec) [ -21458.1386] [ 5049] [depth= 1] . ( 6 sec) [ -21447.4503] [ 5047] [depth= 2] . ( 6 sec) [ -21211.9932] [ 4977] [depth= 4] . ( 7 sec) [ -20969.5629] [ 4951] [depth= 1] . ( 7 sec) [ -20277.2844] [ 4840] [depth= 5] . ( 7 sec) [ -20218.9098] [ 4817] [depth= 3] . ( 7 sec) [ -20125.2892] [ 4720] [depth= 7] . ( 7 sec) [ -20115.1995] [ 4720] [depth= 2] . ( 7 sec) [ -20111.6342] [ 4687] [depth= 1] . ( 7 sec) [ -19766.3964] [ 4685] [depth= 1] . ( 7 sec) [ -19757.5496] [ 4673] [depth= 1] . ( 7 sec) [ -19687.5736] [ 4671] [depth= 2] . ( 7 sec) [ -19609.7364] [ 4670] [depth= 1] . ( 7 sec) [ -19372.0553] [ 4585] [depth= 6] . ( 7 sec) [ -19249.5728] [ 4536] [depth= 4] . ( 8 sec) [ -19239.8362] [ 4519] [depth= 2] . ( 8 sec) [ -18903.3447] [ 4498] [depth= 2] . ( 8 sec) [ -18845.7184] [ 4485] [depth= 3] . ( 8 sec) [ -18730.9087] [ 4450] [depth= 1] . ( 8 sec) [ -18710.3309] [ 4450] [depth= 1] . ( 8 sec) [ -18710.0722] [ 4476] [depth= 1] . ( 8 sec) [ -18694.3122] [ 4450] [depth= 1] . ( 8 sec) [ -18668.1887] [ 4424] [depth= 4] . ( 8 sec) [ -18642.4191] [ 4424] [depth= 1] . ( 8 sec) [ -18639.8347] [ 4424] [depth= 2] . ( 8 sec) [ -18624.6962] [ 4422] [depth= 1] . ( 8 sec) [ -18573.1716] [ 4396] [depth= 4] . ( 9 sec) [ -18510.7940] [ 4332] [depth= 6] . ( 9 sec) [ -18508.8015] [ 4332] [depth= 1] . ( 9 sec) [ -18452.1843] [ 4331] [depth= 1] . ( 9 sec) [ -18446.6475] [ 4317] [depth= 1] . ( 9 sec) [ -18421.9618] [ 4296] [depth= 1] . ( 9 sec) [ -18419.8147] [ 4296] [depth= 1] . ( 9 sec) [ -18414.7161] [ 4296] [depth= 2] . ( 9 sec) [ -18229.1790] [ 4254] [depth= 6] . ( 9 sec) [ -18203.2980] [ 4226] [depth= 2] . ( 9 sec) [ -18202.7528] [ 4219] [depth= 1] . ( 10 sec) [ -17867.1337] [ 4167] [depth= 1] . ( 10 sec) [ -17671.0699] [ 4096] [depth= 6] . ( 10 sec) [ -17602.9700] [ 4096] [depth= 2] . ( 10 sec) [ -17562.5222] [ 4158] [depth= 1] . ( 10 sec) [ -17399.6847] [ 4052] [depth= 10] . ( 10 sec) [ -17385.6427] [ 4056] [depth= 1] . ( 10 sec) [ -17371.2849] [ 4053] [depth= 2] . ( 10 sec) [ -17362.4762] [ 4038] [depth= 1] . ( 10 sec) [ -17346.4753] [ 4031] [depth= 2] . ( 10 sec) [ -17283.9421] [ 3997] [depth= 1] . ( 10 sec) [ -17264.5929] [ 3989] [depth= 1] . ( 11 sec) [ -17257.3307] [ 3989] [depth= 4] . ( 11 sec) [ -17226.6447] [ 3985] [depth= 4] . ( 11 sec) [ -16970.7146] [Branch lengths ] . ( 15 sec) [ -16460.0091] [GTR parameters ] . ( 15 sec) [ -16388.4373] [Alpha ][ 0.308933] . ( 15 sec) [ -16364.6932] [ 3967] [depth= 3] . ( 15 sec) [ -16363.0988] [ 3966] [depth= 1] . ( 15 sec) [ -16359.7593] [ 3971] [depth= 1] . ( 16 sec) [ -16357.0699] [ 3961] [depth= 1] . ( 16 sec) [ -16356.9735] [ 3960] [depth= 1] . ( 16 sec) [ -16352.0494] [ 3954] [depth= 1] . ( 16 sec) [ -16349.6408] [ 3956] [depth= 1] . ( 16 sec) [ -16347.4789] [ 3960] [depth= 1] . ( 16 sec) [ -16345.6237] [ 3958] [depth= 1] . ( 16 sec) [ -16344.8206] [ 3958] [depth= 1] . ( 16 sec) [ -16341.4776] [ 3958] [depth= 1] . ( 17 sec) [ -16339.8018] [ 3957] [depth= 2] . ( 17 sec) [ -16334.8477] [ 3956] [depth= 2] . ( 17 sec) [ -16333.5128] [ 3950] [depth= 1] . ( 18 sec) [ -16333.4842] [ 3951] [depth= 1] . ( 18 sec) [ -16332.0120] [ 3952] [depth= 2] . ( 19 sec) [ -16330.4390] [ 3952] [depth= 1] . ( 19 sec) [ -16329.0900] [ 3952] [depth= 1] . ( 19 sec) [ -16322.2181] [ 3948] [depth= 1] . ( 19 sec) [ -16312.1245] [ 3947] [depth= 2] . ( 20 sec) [ -16311.6934] [ 3946] [depth= 1] . ( 21 sec) [ -16308.7697] [ 3941] [depth= 1] . ( 23 sec) [ -16308.7521] [ 3941] [depth= 1] . ( 23 sec) [ -16285.0813] [Branch lengths ] . ( 27 sec) [ -16270.4838] [GTR parameters ] . ( 27 sec) [ -16269.8246] [Alpha ][ 0.295961] . ( 28 sec) [ -16269.7192] [ 3943] [depth= 1] . ( 31 sec) [ -16269.6944] [ 3943] [depth= 1] . ( 36 sec) [ -16261.2090] [Branch lengths ] . ( 39 sec) [ -16259.4989] [GTR parameters ] . ( 39 sec) [ -16259.4757] [Alpha ][ 0.293789] . ( 47 sec) [ -16256.0998] [Branch lengths ] . ( 90 sec) [ -16255.3840] [Branch lengths ] . ( 90 sec) [ -16255.3840] [Topology ] . ( 92 sec) [ -16255.2963] [Topology ] . ( 93 sec) [ -16255.2675] [Topology ] . ( 95 sec) [ -16255.2541] [Topology ] . ( 96 sec) [ -16255.2474] [Topology ] . ( 97 sec) [ -16255.2439] [Topology ] . ( 99 sec) [ -16255.2420] [Topology ] . ( 101 sec) [ -16253.9770] [GTR parameters ] . ( 101 sec) [ -16253.9576] [Alpha ][ 0.291861] . ( 101 sec) [ -16253.9576] [Topology ] . ( 103 sec) [ -16253.6674] [Topology ] . ( 104 sec) [ -16253.5671] [Topology ] . ( 105 sec) [ -16253.5178] [Topology ] . ( 107 sec) [ -16253.4920] [Topology ] . ( 108 sec) [ -16253.4784] [Topology ] . ( 109 sec) [ -16253.4710] [Topology ] . ( 113 sec) [ -16253.3009] [GTR parameters ] . ( 113 sec) [ -16253.2861] [Alpha ][ 0.290203] . ( 113 sec) [ -16253.2861] [Topology ] . ( 115 sec) [ -16253.2266] [Topology ] . ( 116 sec) [ -16253.2037] [Topology ] . ( 117 sec) [ -16253.1921] [Topology ] . ( 119 sec) [ -16253.1858] [Topology ] . ( 120 sec) [ -16253.1825] [Topology ] . ( 121 sec) [ -16253.1806] [Topology ] . ( 124 sec) [ -16253.1385] [GTR parameters ] . ( 124 sec) [ -16253.1344] [Alpha ][ 0.289141] . ( 124 sec) [ -16253.1344] [Topology ] . ( 125 sec) [ -16253.1194] [Topology ] . ( 126 sec) [ -16253.1138] [Topology ] . ( 128 sec) [ -16253.1110] [Topology ] . ( 129 sec) [ -16253.1094] [Topology ] . ( 131 sec) [ -16253.1086] [Topology ] . ( 134 sec) [ -16253.0978] [GTR parameters ] . ( 134 sec) [ -16253.0974] [Alpha ][ 0.288741] . ( 134 sec) [ -16253.0974] [Topology ] . ( 135 sec) [ -16253.0931] [Topology ] . ( 137 sec) [ -16253.0914] [Topology ] . ( 138 sec) [ -16253.0905] [Topology ] . ( 139 sec) [ -16253.0884] [GTR parameters ] . ( 139 sec) [ -16253.0884] [Alpha ][ 0.288741] . ( 139 sec) [ -16253.0884] [Topology ] . ( 140 sec) [ -16253.0867] [Topology ] . ( 142 sec) [ -16253.0859] [Topology ] . ( 143 sec) [ -16253.0855] [GTR parameters ] . ( 143 sec) [ -16253.0855] [Alpha ][ 0.288452] . ( 143 sec) [ -16253.0855] [Topology ] . ( 145 sec) [ -16253.0847] [Topology ] . ( 145 sec) [ -16253.0845] [GTR parameters ] . ( 145 sec) [ -16253.0845] [Alpha ][ 0.288452] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -16253.084494. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -40874.2156] [GTR parameters ] . ( 1 sec) [ -39693.1633] [Alpha ][ 0.500960] . ( 1 sec) [ -39336.2115] [ 7864] [depth= 16] . ( 1 sec) [ -38037.3038] [ 7830] [depth= 9] . ( 1 sec) [ -37379.8753] [ 7768] [depth= 1] . ( 1 sec) [ -36904.5396] [ 7727] [depth= 10] . ( 2 sec) [ -36692.9331] [ 7727] [depth= 1] . ( 2 sec) [ -36319.6179] [ 7721] [depth= 9] . ( 2 sec) [ -35139.8335] [ 7585] [depth= 8] . ( 2 sec) [ -35014.2876] [ 7540] [depth= 1] . ( 2 sec) [ -34444.0135] [ 7421] [depth= 7] . ( 2 sec) [ -34182.0265] [ 7410] [depth= 8] . ( 2 sec) [ -34138.2844] [ 7390] [depth= 1] . ( 2 sec) [ -33988.3223] [ 7340] [depth= 6] . ( 2 sec) [ -32468.9120] [ 7235] [depth= 6] . ( 2 sec) [ -32311.2323] [ 7167] [depth= 1] . ( 2 sec) [ -31949.0720] [ 7095] [depth= 4] . ( 2 sec) [ -31650.9155] [ 7057] [depth= 5] . ( 2 sec) [ -30915.8235] [ 7025] [depth= 1] . ( 2 sec) [ -30692.4919] [ 6946] [depth= 11] . ( 3 sec) [ -30330.9432] [ 6941] [depth= 6] . ( 3 sec) [ -30237.1540] [ 6888] [depth= 1] . ( 3 sec) [ -30022.9819] [ 6837] [depth= 7] . ( 3 sec) [ -29942.0564] [ 6774] [depth= 1] . ( 3 sec) [ -29825.3367] [ 6775] [depth= 1] . ( 3 sec) [ -29694.5426] [ 6680] [depth= 11] . ( 3 sec) [ -29543.8803] [ 6641] [depth= 2] . ( 3 sec) [ -29412.9945] [ 6630] [depth= 3] . ( 3 sec) [ -29094.6446] [ 6556] [depth= 12] . ( 3 sec) [ -28912.2359] [ 6545] [depth= 2] . ( 3 sec) [ -28718.0733] [ 6455] [depth= 3] . ( 3 sec) [ -28543.5614] [ 6417] [depth= 1] . ( 4 sec) [ -28100.6809] [ 6241] [depth= 10] . ( 4 sec) [ -28068.1931] [ 6273] [depth= 1] . ( 4 sec) [ -28019.9501] [ 6231] [depth= 1] . ( 4 sec) [ -27773.8401] [ 6172] [depth= 5] . ( 4 sec) [ -27667.3106] [ 6181] [depth= 1] . ( 4 sec) [ -27537.2870] [ 6117] [depth= 10] . ( 4 sec) [ -27242.2133] [ 6026] [depth= 2] . ( 4 sec) [ -27103.4486] [ 5979] [depth= 1] . ( 4 sec) [ -27098.6169] [ 5990] [depth= 1] . ( 4 sec) [ -26867.2177] [ 5947] [depth= 9] . ( 4 sec) [ -26134.6068] [ 5862] [depth= 10] . ( 4 sec) [ -25718.7834] [ 5799] [depth= 7] . ( 5 sec) [ -25556.5113] [ 5771] [depth= 7] . ( 5 sec) [ -25238.8619] [ 5745] [depth= 1] . ( 5 sec) [ -24972.4058] [ 5687] [depth= 2] . ( 5 sec) [ -24850.6755] [ 5682] [depth= 11] . ( 5 sec) [ -24500.8705] [ 5594] [depth= 6] . ( 5 sec) [ -24348.5954] [ 5567] [depth= 2] . ( 5 sec) [ -24088.3428] [ 5515] [depth= 7] . ( 5 sec) [ -24076.8560] [ 5505] [depth= 2] . ( 5 sec) [ -23835.6842] [ 5398] [depth= 10] . ( 5 sec) [ -23368.8883] [ 5331] [depth= 2] . ( 5 sec) [ -23244.8658] [ 5293] [depth= 9] . ( 5 sec) [ -23205.9703] [ 5282] [depth= 2] . ( 5 sec) [ -22757.3615] [ 5318] [depth= 1] . ( 5 sec) [ -22696.3046] [ 5297] [depth= 11] . ( 6 sec) [ -22671.5121] [ 5287] [depth= 11] . ( 6 sec) [ -22620.9401] [ 5261] [depth= 1] . ( 6 sec) [ -22575.9466] [ 5247] [depth= 1] . ( 6 sec) [ -22533.9901] [ 5250] [depth= 5] . ( 6 sec) [ -22508.6709] [ 5230] [depth= 1] . ( 6 sec) [ -22274.9345] [ 5095] [depth= 9] . ( 6 sec) [ -21137.3653] [ 5068] [depth= 2] . ( 6 sec) [ -21103.2537] [ 5094] [depth= 1] . ( 6 sec) [ -20981.1217] [ 5059] [depth= 1] . ( 6 sec) [ -20391.3938] [ 4956] [depth= 4] . ( 6 sec) [ -20378.7134] [ 4953] [depth= 2] . ( 7 sec) [ -20375.1238] [ 4951] [depth= 8] . ( 7 sec) [ -20356.3418] [ 4950] [depth= 1] . ( 7 sec) [ -20354.1501] [ 4951] [depth= 1] . ( 7 sec) [ -20228.6817] [ 4928] [depth= 6] . ( 7 sec) [ -19876.3949] [ 4813] [depth= 6] . ( 7 sec) [ -19870.3336] [ 4814] [depth= 1] . ( 7 sec) [ -19813.0000] [ 4768] [depth= 2] . ( 7 sec) [ -19708.7566] [ 4733] [depth= 2] . ( 7 sec) [ -19698.9601] [ 4731] [depth= 2] . ( 7 sec) [ -19683.1047] [ 4743] [depth= 1] . ( 7 sec) [ -19619.4057] [ 4743] [depth= 1] . ( 7 sec) [ -19475.8162] [ 4780] [depth= 1] . ( 8 sec) [ -19305.6294] [ 4711] [depth= 2] . ( 8 sec) [ -19187.0255] [ 4634] [depth= 2] . ( 8 sec) [ -19102.3850] [ 4591] [depth= 4] . ( 8 sec) [ -18990.2303] [ 4581] [depth= 1] . ( 8 sec) [ -18921.5794] [ 4575] [depth= 3] . ( 8 sec) [ -18921.1577] [ 4567] [depth= 3] . ( 8 sec) [ -18867.9723] [ 4533] [depth= 3] . ( 8 sec) [ -18628.3932] [ 4473] [depth= 4] . ( 8 sec) [ -18425.9553] [ 4403] [depth= 5] . ( 8 sec) [ -18423.5427] [ 4413] [depth= 6] . ( 8 sec) [ -18322.9173] [ 4382] [depth= 3] . ( 8 sec) [ -18248.9704] [ 4302] [depth= 8] . ( 8 sec) [ -18225.1102] [ 4291] [depth= 3] . ( 9 sec) [ -18204.6227] [ 4294] [depth= 3] . ( 9 sec) [ -18199.6470] [ 4293] [depth= 1] . ( 9 sec) [ -18047.0521] [ 4241] [depth= 3] . ( 9 sec) [ -17942.6485] [ 4271] [depth= 1] . ( 9 sec) [ -17940.2480] [ 4269] [depth= 3] . ( 9 sec) [ -17912.4697] [ 4239] [depth= 1] . ( 9 sec) [ -17884.8369] [ 4237] [depth= 1] . ( 9 sec) [ -17854.7259] [ 4234] [depth= 1] . ( 10 sec) [ -17851.5737] [ 4234] [depth= 3] . ( 10 sec) [ -17835.8796] [ 4235] [depth= 1] . ( 10 sec) [ -17832.7472] [ 4235] [depth= 1] . ( 10 sec) [ -17826.7316] [ 4237] [depth= 2] . ( 10 sec) [ -17701.5418] [ 4209] [depth= 2] . ( 10 sec) [ -17686.9426] [ 4193] [depth= 4] . ( 10 sec) [ -17669.3214] [ 4173] [depth= 4] . ( 11 sec) [ -17655.2859] [ 4098] [depth= 2] . ( 11 sec) [ -17653.3752] [ 4134] [depth= 2] . ( 11 sec) [ -17561.0585] [ 4134] [depth= 1] . ( 11 sec) [ -17552.5808] [ 4125] [depth= 1] . ( 12 sec) [ -17224.1806] [Branch lengths ] . ( 15 sec) [ -16665.0290] [GTR parameters ] . ( 15 sec) [ -16587.2255] [Alpha ][ 0.301966] . ( 15 sec) [ -16587.0921] [ 4125] [depth= 1] . ( 16 sec) [ -16586.9650] [ 4125] [depth= 1] . ( 16 sec) [ -16586.8967] [ 4127] [depth= 1] . ( 16 sec) [ -16584.1526] [ 4132] [depth= 1] . ( 16 sec) [ -16580.1490] [ 4127] [depth= 2] . ( 16 sec) [ -16577.8692] [ 4129] [depth= 1] . ( 17 sec) [ -16577.2628] [ 4128] [depth= 1] . ( 17 sec) [ -16548.9566] [ 4104] [depth= 1] . ( 17 sec) [ -16546.9735] [ 4100] [depth= 2] . ( 17 sec) [ -16542.3730] [ 4089] [depth= 1] . ( 17 sec) [ -16532.9944] [ 4088] [depth= 2] . ( 17 sec) [ -16532.8816] [ 4086] [depth= 1] . ( 17 sec) [ -16503.7925] [ 4048] [depth= 1] . ( 17 sec) [ -16493.6261] [ 4032] [depth= 2] . ( 17 sec) [ -16492.9122] [ 4037] [depth= 1] . ( 18 sec) [ -16483.2539] [ 4027] [depth= 1] . ( 18 sec) [ -16483.0517] [ 4024] [depth= 1] . ( 18 sec) [ -16482.4276] [ 4029] [depth= 3] . ( 18 sec) [ -16481.6289] [ 4030] [depth= 3] . ( 19 sec) [ -16480.8546] [ 4030] [depth= 1] . ( 19 sec) [ -16465.0489] [ 4009] [depth= 5] . ( 19 sec) [ -16431.3527] [ 3995] [depth= 2] . ( 19 sec) [ -16424.8087] [ 3994] [depth= 1] . ( 20 sec) [ -16424.7905] [ 3994] [depth= 1] . ( 20 sec) [ -16424.7705] [ 3997] [depth= 2] . ( 20 sec) [ -16417.3325] [ 3992] [depth= 3] . ( 20 sec) [ -16416.6099] [ 3993] [depth= 1] . ( 20 sec) [ -16416.5331] [ 3993] [depth= 1] . ( 20 sec) [ -16416.4221] [ 3995] [depth= 1] . ( 20 sec) [ -16398.3056] [ 3953] [depth= 1] . ( 20 sec) [ -16398.0997] [ 3956] [depth= 1] . ( 21 sec) [ -16397.4701] [ 3951] [depth= 1] . ( 21 sec) [ -16396.8629] [ 3951] [depth= 1] . ( 21 sec) [ -16394.1658] [ 3953] [depth= 1] . ( 21 sec) [ -16391.2553] [ 3951] [depth= 1] . ( 21 sec) [ -16390.1656] [ 3949] [depth= 1] . ( 21 sec) [ -16390.0559] [ 3953] [depth= 1] . ( 22 sec) [ -16381.9975] [ 3950] [depth= 2] . ( 22 sec) [ -16379.8716] [ 3951] [depth= 2] . ( 22 sec) [ -16374.1112] [ 3948] [depth= 2] . ( 22 sec) [ -16373.9909] [ 3949] [depth= 1] . ( 23 sec) [ -16372.4849] [ 3962] [depth= 3] . ( 23 sec) [ -16371.3094] [ 3961] [depth= 1] . ( 23 sec) [ -16369.7959] [ 3961] [depth= 1] . ( 24 sec) [ -16366.6828] [ 3962] [depth= 1] . ( 24 sec) [ -16359.3781] [ 3962] [depth= 1] . ( 24 sec) [ -16311.9926] [Branch lengths ] . ( 28 sec) [ -16294.5337] [GTR parameters ] . ( 28 sec) [ -16294.4398] [Alpha ][ 0.297189] . ( 28 sec) [ -16293.6071] [ 3962] [depth= 1] . ( 29 sec) [ -16293.5382] [ 3962] [depth= 1] . ( 29 sec) [ -16284.2332] [ 3948] [depth= 3] . ( 29 sec) [ -16283.9508] [ 3949] [depth= 1] . ( 30 sec) [ -16283.1084] [ 3949] [depth= 1] . ( 31 sec) [ -16281.3640] [ 3946] [depth= 1] . ( 32 sec) [ -16281.3477] [ 3946] [depth= 1] . ( 34 sec) [ -16281.2048] [ 3945] [depth= 1] . ( 37 sec) [ -16269.0498] [Branch lengths ] . ( 41 sec) [ -16267.6426] [GTR parameters ] . ( 41 sec) [ -16267.5649] [Alpha ][ 0.293004] . ( 50 sec) [ -16262.7913] [Branch lengths ] . ( 93 sec) [ -16258.0054] [Branch lengths ] . ( 93 sec) [ -16258.0054] [Topology ] . ( 94 sec) [ -16255.7317] [Topology ] . ( 96 sec) [ -16255.5365] [Topology ] . ( 97 sec) [ -16255.4959] [Topology ] . ( 98 sec) [ -16255.4821] [Topology ] . ( 100 sec) [ -16255.4763] [Topology ] . ( 101 sec) [ -16255.4736] [Topology ] . ( 102 sec) [ -16255.4722] [Topology ] . ( 105 sec) [ -16254.0017] [GTR parameters ] . ( 105 sec) [ -16253.9928] [Alpha ][ 0.291466] . ( 105 sec) [ -16253.9928] [Topology ] . ( 107 sec) [ -16253.6825] [Topology ] . ( 108 sec) [ -16253.5751] [Topology ] . ( 109 sec) [ -16253.5225] [Topology ] . ( 111 sec) [ -16253.4951] [Topology ] . ( 112 sec) [ -16253.4807] [Topology ] . ( 113 sec) [ -16253.4729] [Topology ] . ( 114 sec) [ -16253.2991] [GTR parameters ] . ( 114 sec) [ -16253.2896] [Alpha ][ 0.289888] . ( 115 sec) [ -16253.2896] [Topology ] . ( 116 sec) [ -16253.2315] [Topology ] . ( 117 sec) [ -16253.2089] [Topology ] . ( 119 sec) [ -16253.1974] [Topology ] . ( 120 sec) [ -16253.1913] [Topology ] . ( 121 sec) [ -16253.1880] [Topology ] . ( 123 sec) [ -16253.1861] [Topology ] . ( 125 sec) [ -16253.1388] [GTR parameters ] . ( 125 sec) [ -16253.1367] [Alpha ][ 0.289098] . ( 125 sec) [ -16253.1367] [Topology ] . ( 127 sec) [ -16253.1202] [Topology ] . ( 128 sec) [ -16253.1138] [Topology ] . ( 130 sec) [ -16253.1106] [Topology ] . ( 131 sec) [ -16253.1088] [Topology ] . ( 132 sec) [ -16253.1079] [Topology ] . ( 134 sec) [ -16253.0979] [GTR parameters ] . ( 134 sec) [ -16253.0975] [Alpha ][ 0.288700] . ( 134 sec) [ -16253.0975] [Topology ] . ( 136 sec) [ -16253.0932] [Topology ] . ( 137 sec) [ -16253.0914] [Topology ] . ( 138 sec) [ -16253.0905] [Topology ] . ( 139 sec) [ -16253.0885] [GTR parameters ] . ( 139 sec) [ -16253.0885] [Alpha ][ 0.288700] . ( 139 sec) [ -16253.0885] [Topology ] . ( 141 sec) [ -16253.0869] [Topology ] . ( 142 sec) [ -16253.0861] [Topology ] . ( 143 sec) [ -16253.0857] [GTR parameters ] . ( 143 sec) [ -16253.0857] [Alpha ][ 0.288700] . ( 143 sec) [ -16253.0857] [Topology ] . ( 145 sec) [ -16253.0850] [Topology ] . ( 146 sec) [ -16253.0849] [GTR parameters ] . ( 146 sec) [ -16253.0848] [Alpha ][ 0.288412] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -16253.084807. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -41432.5643] [GTR parameters ] . ( 1 sec) [ -40244.3964] [Alpha ][ 0.500960] . ( 1 sec) [ -39615.6263] [ 8006] [depth= 8] . ( 1 sec) [ -39423.2507] [ 7931] [depth= 10] . ( 1 sec) [ -39257.9208] [ 7906] [depth= 1] . ( 1 sec) [ -39042.4679] [ 7879] [depth= 4] . ( 2 sec) [ -38781.6287] [ 7683] [depth= 3] . ( 2 sec) [ -37652.4017] [ 7661] [depth= 8] . ( 2 sec) [ -37339.3103] [ 7619] [depth= 4] . ( 2 sec) [ -37280.4534] [ 7598] [depth= 3] . ( 2 sec) [ -37175.7459] [ 7565] [depth= 8] . ( 2 sec) [ -36919.5605] [ 7552] [depth= 3] . ( 2 sec) [ -36627.6342] [ 7454] [depth= 4] . ( 2 sec) [ -36374.7778] [ 7453] [depth= 4] . ( 2 sec) [ -35768.1081] [ 7351] [depth= 18] . ( 2 sec) [ -35749.6141] [ 7376] [depth= 1] . ( 2 sec) [ -35438.8693] [ 7288] [depth= 20] . ( 2 sec) [ -34899.3976] [ 7191] [depth= 1] . ( 2 sec) [ -34683.6367] [ 7114] [depth= 7] . ( 2 sec) [ -34668.0254] [ 7094] [depth= 1] . ( 3 sec) [ -34393.8155] [ 7007] [depth= 1] . ( 3 sec) [ -34081.4962] [ 6949] [depth= 6] . ( 3 sec) [ -33443.5110] [ 6804] [depth= 7] . ( 3 sec) [ -33432.6301] [ 6841] [depth= 1] . ( 3 sec) [ -33369.6340] [ 6842] [depth= 1] . ( 3 sec) [ -32984.4679] [ 6754] [depth= 2] . ( 3 sec) [ -32653.7925] [ 6638] [depth= 16] . ( 3 sec) [ -32449.1456] [ 6595] [depth= 11] . ( 3 sec) [ -32442.0072] [ 6593] [depth= 1] . ( 3 sec) [ -32433.7347] [ 6595] [depth= 1] . ( 3 sec) [ -32306.9368] [ 6499] [depth= 16] . ( 3 sec) [ -31846.6085] [ 6482] [depth= 13] . ( 3 sec) [ -31422.1953] [ 6468] [depth= 1] . ( 4 sec) [ -31406.6045] [ 6460] [depth= 1] . ( 4 sec) [ -31063.8563] [ 6422] [depth= 14] . ( 4 sec) [ -30725.6610] [ 6364] [depth= 1] . ( 4 sec) [ -30109.9020] [ 6303] [depth= 4] . ( 4 sec) [ -29561.0638] [ 6271] [depth= 2] . ( 4 sec) [ -29280.1515] [ 6264] [depth= 9] . ( 4 sec) [ -29184.6127] [ 6245] [depth= 2] . ( 4 sec) [ -29006.1734] [ 6251] [depth= 3] . ( 4 sec) [ -29006.0395] [ 6251] [depth= 1] . ( 4 sec) [ -28906.1719] [ 6204] [depth= 11] . ( 4 sec) [ -28872.4266] [ 6192] [depth= 1] . ( 4 sec) [ -28811.6314] [ 6201] [depth= 2] . ( 4 sec) [ -28744.2455] [ 6166] [depth= 13] . ( 5 sec) [ -28305.7341] [ 6134] [depth= 7] . ( 5 sec) [ -27940.4384] [ 6036] [depth= 12] . ( 5 sec) [ -27772.5439] [ 6006] [depth= 2] . ( 5 sec) [ -27298.8533] [ 5894] [depth= 15] . ( 5 sec) [ -26796.1335] [ 5841] [depth= 15] . ( 5 sec) [ -26567.1417] [ 5901] [depth= 1] . ( 5 sec) [ -25688.1246] [ 5866] [depth= 1] . ( 5 sec) [ -25017.4294] [ 5625] [depth= 16] . ( 5 sec) [ -24011.0464] [ 5544] [depth= 2] . ( 5 sec) [ -23816.2236] [ 5607] [depth= 1] . ( 5 sec) [ -23613.9568] [ 5639] [depth= 1] . ( 5 sec) [ -23511.6364] [ 5645] [depth= 1] . ( 6 sec) [ -22966.7554] [ 5544] [depth= 23] . ( 6 sec) [ -22472.6100] [ 5345] [depth= 11] . ( 6 sec) [ -22345.2256] [ 5330] [depth= 16] . ( 6 sec) [ -22011.9137] [ 5228] [depth= 5] . ( 6 sec) [ -21801.3006] [ 5219] [depth= 3] . ( 6 sec) [ -21764.7833] [ 5140] [depth= 16] . ( 6 sec) [ -21594.7814] [ 5109] [depth= 1] . ( 6 sec) [ -21452.9413] [ 5045] [depth= 2] . ( 6 sec) [ -21227.9429] [ 4964] [depth= 4] . ( 6 sec) [ -21216.9320] [ 4981] [depth= 5] . ( 6 sec) [ -21215.2312] [ 4981] [depth= 1] . ( 7 sec) [ -21158.1993] [ 4966] [depth= 2] . ( 7 sec) [ -21047.2928] [ 4947] [depth= 1] . ( 7 sec) [ -21007.5561] [ 4907] [depth= 1] . ( 7 sec) [ -20913.1254] [ 4864] [depth= 3] . ( 7 sec) [ -20912.3462] [ 4857] [depth= 3] . ( 7 sec) [ -20878.4191] [ 4847] [depth= 17] . ( 7 sec) [ -20816.1259] [ 4817] [depth= 3] . ( 7 sec) [ -20798.4811] [ 4755] [depth= 8] . ( 7 sec) [ -20651.6854] [ 4721] [depth= 13] . ( 7 sec) [ -20443.0962] [ 4678] [depth= 1] . ( 7 sec) [ -20407.4004] [ 4660] [depth= 1] . ( 7 sec) [ -20366.7418] [ 4705] [depth= 1] . ( 8 sec) [ -20196.5721] [ 4639] [depth= 12] . ( 8 sec) [ -20169.5217] [ 4636] [depth= 1] . ( 8 sec) [ -20080.5682] [ 4608] [depth= 1] . ( 8 sec) [ -20066.8183] [ 4572] [depth= 1] . ( 8 sec) [ -19780.8787] [ 4520] [depth= 13] . ( 8 sec) [ -19772.5393] [ 4517] [depth= 2] . ( 8 sec) [ -19564.7683] [ 4493] [depth= 3] . ( 8 sec) [ -19546.1396] [ 4484] [depth= 10] . ( 8 sec) [ -19445.9153] [ 4425] [depth= 4] . ( 8 sec) [ -19374.4217] [ 4438] [depth= 4] . ( 8 sec) [ -19322.9794] [ 4427] [depth= 4] . ( 8 sec) [ -19104.9524] [ 4414] [depth= 1] . ( 8 sec) [ -18998.9081] [ 4366] [depth= 5] . ( 9 sec) [ -18910.8047] [ 4345] [depth= 3] . ( 9 sec) [ -18883.5435] [ 4334] [depth= 1] . ( 9 sec) [ -18805.3138] [ 4329] [depth= 1] . ( 9 sec) [ -18340.9438] [ 4225] [depth= 2] . ( 9 sec) [ -18329.2212] [ 4242] [depth= 1] . ( 9 sec) [ -18318.5151] [ 4246] [depth= 7] . ( 9 sec) [ -18276.2296] [ 4245] [depth= 1] . ( 9 sec) [ -18272.3745] [ 4235] [depth= 3] . ( 9 sec) [ -18271.0713] [ 4231] [depth= 1] . ( 9 sec) [ -18262.0332] [ 4231] [depth= 1] . ( 9 sec) [ -18258.7081] [ 4253] [depth= 3] . ( 10 sec) [ -18112.2895] [ 4212] [depth= 5] . ( 10 sec) [ -18082.4969] [ 4210] [depth= 1] . ( 10 sec) [ -18069.8373] [ 4211] [depth= 1] . ( 10 sec) [ -18048.8642] [ 4209] [depth= 1] . ( 10 sec) [ -18044.3271] [ 4261] [depth= 1] . ( 10 sec) [ -18018.4454] [ 4259] [depth= 2] . ( 10 sec) [ -17989.0349] [ 4262] [depth= 1] . ( 10 sec) [ -17899.6215] [ 4194] [depth= 3] . ( 10 sec) [ -17884.4132] [ 4191] [depth= 1] . ( 10 sec) [ -17864.1655] [ 4201] [depth= 1] . ( 10 sec) [ -17859.6397] [ 4191] [depth= 1] . ( 10 sec) [ -17818.1959] [ 4202] [depth= 4] . ( 11 sec) [ -17783.8277] [ 4218] [depth= 1] . ( 11 sec) [ -17757.6133] [ 4229] [depth= 1] . ( 11 sec) [ -17753.0875] [ 4229] [depth= 3] . ( 11 sec) [ -17752.4819] [ 4232] [depth= 1] . ( 12 sec) [ -17312.8741] [Branch lengths ] . ( 15 sec) [ -16822.5797] [GTR parameters ] . ( 15 sec) [ -16747.9070] [Alpha ][ 0.311857] . ( 15 sec) [ -16701.4892] [ 4164] [depth= 4] . ( 15 sec) [ -16617.7044] [ 4086] [depth= 5] . ( 15 sec) [ -16616.1697] [ 4087] [depth= 1] . ( 15 sec) [ -16616.1320] [ 4087] [depth= 1] . ( 16 sec) [ -16615.7939] [ 4083] [depth= 1] . ( 16 sec) [ -16556.8720] [ 4052] [depth= 3] . ( 16 sec) [ -16556.5455] [ 4051] [depth= 1] . ( 16 sec) [ -16556.4972] [ 4052] [depth= 1] . ( 16 sec) [ -16556.2738] [ 4051] [depth= 1] . ( 17 sec) [ -16498.9317] [ 3996] [depth= 6] . ( 17 sec) [ -16484.9355] [ 3994] [depth= 1] . ( 17 sec) [ -16484.3629] [ 3991] [depth= 2] . ( 17 sec) [ -16484.0179] [ 3996] [depth= 1] . ( 18 sec) [ -16471.0513] [ 3990] [depth= 1] . ( 18 sec) [ -16469.0433] [ 3987] [depth= 1] . ( 18 sec) [ -16469.0231] [ 3987] [depth= 1] . ( 18 sec) [ -16453.3604] [ 3979] [depth= 1] . ( 19 sec) [ -16443.9841] [ 3964] [depth= 2] . ( 19 sec) [ -16437.3840] [ 3965] [depth= 2] . ( 19 sec) [ -16436.6820] [ 3966] [depth= 1] . ( 19 sec) [ -16436.6457] [ 3965] [depth= 2] . ( 19 sec) [ -16435.8665] [ 3964] [depth= 1] . ( 19 sec) [ -16435.7361] [ 3968] [depth= 1] . ( 19 sec) [ -16435.7237] [ 3968] [depth= 1] . ( 20 sec) [ -16433.6500] [ 3969] [depth= 1] . ( 20 sec) [ -16432.9977] [ 3966] [depth= 1] . ( 20 sec) [ -16405.9928] [ 3963] [depth= 2] . ( 21 sec) [ -16405.9565] [ 3963] [depth= 1] . ( 21 sec) [ -16405.6104] [ 3964] [depth= 1] . ( 21 sec) [ -16359.1909] [ 3950] [depth= 3] . ( 21 sec) [ -16359.0200] [ 3951] [depth= 1] . ( 21 sec) [ -16351.8557] [ 3949] [depth= 2] . ( 21 sec) [ -16351.4271] [ 3954] [depth= 2] . ( 21 sec) [ -16350.9900] [ 3955] [depth= 1] . ( 22 sec) [ -16349.8072] [ 3947] [depth= 2] . ( 22 sec) [ -16348.8609] [ 3948] [depth= 1] . ( 22 sec) [ -16348.8098] [ 3943] [depth= 1] . ( 22 sec) [ -16348.7171] [ 3941] [depth= 2] . ( 23 sec) [ -16348.5696] [ 3942] [depth= 1] . ( 24 sec) [ -16294.1519] [Branch lengths ] . ( 27 sec) [ -16274.2684] [GTR parameters ] . ( 27 sec) [ -16273.1626] [Alpha ][ 0.294899] . ( 29 sec) [ -16272.7120] [ 3944] [depth= 1] . ( 34 sec) [ -16272.5664] [ 3943] [depth= 1] . ( 36 sec) [ -16264.1765] [Branch lengths ] . ( 39 sec) [ -16262.3309] [GTR parameters ] . ( 39 sec) [ -16262.2934] [Alpha ][ 0.292083] . ( 47 sec) [ -16258.4060] [Branch lengths ] . ( 90 sec) [ -16257.5312] [Branch lengths ] . ( 90 sec) [ -16257.5312] [Topology ] . ( 91 sec) [ -16256.5615] [Topology ] . ( 93 sec) [ -16256.0563] [Topology ] . ( 94 sec) [ -16255.9127] [Topology ] . ( 96 sec) [ -16255.8540] [Topology ] . ( 97 sec) [ -16255.8277] [Topology ] . ( 98 sec) [ -16255.8147] [Topology ] . ( 100 sec) [ -16255.8078] [Topology ] . ( 103 sec) [ -16254.1498] [GTR parameters ] . ( 103 sec) [ -16254.1487] [Alpha ][ 0.291503] . ( 103 sec) [ -16254.1487] [Topology ] . ( 104 sec) [ -16253.7812] [Topology ] . ( 106 sec) [ -16253.6473] [Topology ] . ( 107 sec) [ -16253.5811] [Topology ] . ( 108 sec) [ -16253.5465] [Topology ] . ( 110 sec) [ -16253.5281] [Topology ] . ( 111 sec) [ -16253.5182] [Topology ] . ( 114 sec) [ -16253.3253] [GTR parameters ] . ( 114 sec) [ -16253.3154] [Alpha ][ 0.289896] . ( 114 sec) [ -16253.3154] [Topology ] . ( 116 sec) [ -16253.2439] [Topology ] . ( 117 sec) [ -16253.2160] [Topology ] . ( 118 sec) [ -16253.2017] [Topology ] . ( 120 sec) [ -16253.1941] [Topology ] . ( 121 sec) [ -16253.1900] [Topology ] . ( 122 sec) [ -16253.1877] [Topology ] . ( 124 sec) [ -16253.1411] [GTR parameters ] . ( 124 sec) [ -16253.1390] [Alpha ][ 0.289101] . ( 124 sec) [ -16253.1390] [Topology ] . ( 126 sec) [ -16253.1222] [Topology ] . ( 127 sec) [ -16253.1156] [Topology ] . ( 128 sec) [ -16253.1121] [Topology ] . ( 130 sec) [ -16253.1103] [Topology ] . ( 131 sec) [ -16253.1093] [Topology ] . ( 132 sec) [ -16253.1087] [Topology ] . ( 135 sec) [ -16253.0969] [GTR parameters ] . ( 135 sec) [ -16253.0965] [Alpha ][ 0.288722] . ( 135 sec) [ -16253.0965] [Topology ] . ( 136 sec) [ -16253.0920] [Topology ] . ( 138 sec) [ -16253.0902] [Topology ] . ( 139 sec) [ -16253.0893] [Topology ] . ( 139 sec) [ -16253.0891] [GTR parameters ] . ( 140 sec) [ -16253.0891] [Alpha ][ 0.288722] . ( 140 sec) [ -16253.0891] [Topology ] . ( 141 sec) [ -16253.0885] [Topology ] . ( 141 sec) [ -16253.0867] [GTR parameters ] . ( 141 sec) [ -16253.0867] [Alpha ][ 0.288722] . ( 141 sec) [ -16253.0867] [Topology ] . ( 143 sec) [ -16253.0855] [Topology ] . ( 144 sec) [ -16253.0850] [Topology ] . ( 146 sec) [ -16253.0847] [GTR parameters ] . ( 146 sec) [ -16253.0846] [Alpha ][ 0.288433] . ( 146 sec) [ -16253.0846] [Topology ] . ( 147 sec) [ -16253.0841] [Topology ] . ( 148 sec) [ -16253.0840] [GTR parameters ] . ( 148 sec) [ -16253.0840] [Alpha ][ 0.288433] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -16253.084018. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -41975.6931] [GTR parameters ] . ( 1 sec) [ -40767.8051] [Alpha ][ 0.500960] . ( 1 sec) [ -40474.3568] [ 7881] [depth= 13] . ( 1 sec) [ -40184.9344] [ 7818] [depth= 14] . ( 1 sec) [ -39382.7550] [ 7715] [depth= 2] . ( 1 sec) [ -38793.4830] [ 7633] [depth= 10] . ( 2 sec) [ -38379.0751] [ 7548] [depth= 5] . ( 2 sec) [ -38194.3927] [ 7539] [depth= 6] . ( 2 sec) [ -37742.8386] [ 7516] [depth= 2] . ( 2 sec) [ -37677.4503] [ 7510] [depth= 8] . ( 2 sec) [ -37589.0779] [ 7468] [depth= 4] . ( 2 sec) [ -37288.5643] [ 7426] [depth= 9] . ( 2 sec) [ -37034.8550] [ 7396] [depth= 5] . ( 2 sec) [ -36942.4735] [ 7366] [depth= 5] . ( 2 sec) [ -36306.4776] [ 7321] [depth= 2] . ( 2 sec) [ -36170.8986] [ 7309] [depth= 3] . ( 2 sec) [ -35111.4312] [ 7161] [depth= 8] . ( 2 sec) [ -34407.0762] [ 7161] [depth= 8] . ( 2 sec) [ -34395.3726] [ 7078] [depth= 8] . ( 2 sec) [ -34216.6174] [ 7122] [depth= 1] . ( 2 sec) [ -33576.3821] [ 7001] [depth= 11] . ( 3 sec) [ -33172.1968] [ 7023] [depth= 1] . ( 3 sec) [ -32489.1251] [ 6923] [depth= 2] . ( 3 sec) [ -32278.0664] [ 6982] [depth= 14] . ( 3 sec) [ -32256.7799] [ 6873] [depth= 1] . ( 3 sec) [ -32190.7811] [ 6813] [depth= 7] . ( 3 sec) [ -31548.2724] [ 6718] [depth= 8] . ( 3 sec) [ -31352.4863] [ 6720] [depth= 18] . ( 3 sec) [ -31331.9996] [ 6678] [depth= 1] . ( 3 sec) [ -31287.2469] [ 6592] [depth= 1] . ( 3 sec) [ -30752.3827] [ 6584] [depth= 13] . ( 3 sec) [ -30070.8173] [ 6560] [depth= 1] . ( 3 sec) [ -29586.3321] [ 6541] [depth= 15] . ( 3 sec) [ -29279.4036] [ 6456] [depth= 4] . ( 4 sec) [ -29183.3922] [ 6424] [depth= 3] . ( 4 sec) [ -28586.9793] [ 6296] [depth= 6] . ( 4 sec) [ -28213.9362] [ 6247] [depth= 1] . ( 4 sec) [ -27630.7721] [ 6027] [depth= 14] . ( 4 sec) [ -27107.9571] [ 5890] [depth= 17] . ( 4 sec) [ -26953.4717] [ 5876] [depth= 1] . ( 4 sec) [ -26947.8356] [ 5875] [depth= 1] . ( 4 sec) [ -26790.5877] [ 5832] [depth= 19] . ( 4 sec) [ -26301.7230] [ 5787] [depth= 20] . ( 4 sec) [ -25468.5496] [ 5641] [depth= 17] . ( 4 sec) [ -25344.0427] [ 5537] [depth= 1] . ( 5 sec) [ -25079.4010] [ 5448] [depth= 13] . ( 5 sec) [ -25029.8620] [ 5452] [depth= 11] . ( 5 sec) [ -24928.1322] [ 5428] [depth= 15] . ( 5 sec) [ -24211.8210] [ 5201] [depth= 16] . ( 5 sec) [ -24210.3940] [ 5202] [depth= 1] . ( 5 sec) [ -23846.0283] [ 5173] [depth= 10] . ( 5 sec) [ -21507.2592] [ 5116] [depth= 15] . ( 5 sec) [ -21369.6633] [ 5099] [depth= 8] . ( 5 sec) [ -21296.4899] [ 5096] [depth= 1] . ( 5 sec) [ -20794.2789] [ 4985] [depth= 4] . ( 5 sec) [ -20772.3277] [ 4978] [depth= 1] . ( 5 sec) [ -20634.7311] [ 4954] [depth= 2] . ( 6 sec) [ -20417.3121] [ 4860] [depth= 3] . ( 6 sec) [ -20275.5584] [ 4835] [depth= 4] . ( 6 sec) [ -20181.9360] [ 4808] [depth= 8] . ( 6 sec) [ -20180.7670] [ 4808] [depth= 2] . ( 6 sec) [ -20150.9104] [ 4797] [depth= 1] . ( 6 sec) [ -20143.8433] [ 4782] [depth= 7] . ( 6 sec) [ -20120.3914] [ 4759] [depth= 1] . ( 6 sec) [ -20112.5817] [ 4760] [depth= 1] . ( 6 sec) [ -20086.3927] [ 4750] [depth= 1] . ( 6 sec) [ -20035.3774] [ 4709] [depth= 3] . ( 6 sec) [ -19950.9576] [ 4684] [depth= 6] . ( 7 sec) [ -19882.6612] [ 4656] [depth= 1] . ( 7 sec) [ -19818.1593] [ 4654] [depth= 1] . ( 7 sec) [ -19482.6017] [ 4625] [depth= 9] . ( 7 sec) [ -19442.5383] [ 4651] [depth= 1] . ( 7 sec) [ -19409.2590] [ 4609] [depth= 8] . ( 7 sec) [ -19372.0290] [ 4567] [depth= 2] . ( 7 sec) [ -19157.0517] [ 4530] [depth= 4] . ( 7 sec) [ -19155.4564] [ 4527] [depth= 10] . ( 7 sec) [ -18963.4023] [ 4521] [depth= 1] . ( 7 sec) [ -18943.4609] [ 4502] [depth= 10] . ( 7 sec) [ -18925.0199] [ 4478] [depth= 8] . ( 7 sec) [ -18892.0996] [ 4502] [depth= 5] . ( 8 sec) [ -18795.8026] [ 4441] [depth= 14] . ( 8 sec) [ -18680.7758] [ 4400] [depth= 5] . ( 8 sec) [ -18537.4413] [ 4401] [depth= 4] . ( 8 sec) [ -18492.3870] [ 4329] [depth= 5] . ( 8 sec) [ -18270.9369] [ 4342] [depth= 1] . ( 8 sec) [ -18240.6798] [ 4318] [depth= 2] . ( 8 sec) [ -18233.4876] [ 4317] [depth= 1] . ( 8 sec) [ -18232.7831] [ 4319] [depth= 1] . ( 8 sec) [ -18201.4099] [ 4324] [depth= 1] . ( 8 sec) [ -18178.4586] [ 4330] [depth= 1] . ( 9 sec) [ -17996.4961] [ 4306] [depth= 1] . ( 9 sec) [ -17979.9599] [ 4296] [depth= 1] . ( 9 sec) [ -17960.0113] [ 4291] [depth= 7] . ( 9 sec) [ -17959.7993] [ 4293] [depth= 2] . ( 9 sec) [ -17954.4023] [ 4293] [depth= 1] . ( 9 sec) [ -17940.5486] [ 4287] [depth= 3] . ( 9 sec) [ -17935.8860] [ 4287] [depth= 2] . ( 9 sec) [ -17920.6631] [ 4249] [depth= 2] . ( 9 sec) [ -17710.0030] [ 4212] [depth= 2] . ( 9 sec) [ -17708.2656] [ 4212] [depth= 1] . ( 10 sec) [ -17686.1579] [ 4212] [depth= 1] . ( 10 sec) [ -17680.4609] [ 4188] [depth= 3] . ( 10 sec) [ -17504.2845] [ 4190] [depth= 2] . ( 10 sec) [ -17395.5350] [ 4138] [depth= 3] . ( 10 sec) [ -17394.5032] [ 4136] [depth= 2] . ( 10 sec) [ -17366.2299] [ 4124] [depth= 1] . ( 10 sec) [ -17307.9610] [ 4114] [depth= 1] . ( 11 sec) [ -17038.2550] [Branch lengths ] . ( 13 sec) [ -16757.9498] [GTR parameters ] . ( 14 sec) [ -16682.8695] [Alpha ][ 0.308743] . ( 14 sec) [ -16645.1062] [ 4066] [depth= 8] . ( 14 sec) [ -16599.7784] [ 4044] [depth= 2] . ( 14 sec) [ -16522.2919] [ 4011] [depth= 3] . ( 14 sec) [ -16521.5391] [ 4010] [depth= 1] . ( 14 sec) [ -16515.5883] [ 4008] [depth= 1] . ( 15 sec) [ -16505.0884] [ 4007] [depth= 1] . ( 15 sec) [ -16502.0636] [ 4008] [depth= 1] . ( 15 sec) [ -16423.0692] [ 3991] [depth= 6] . ( 15 sec) [ -16419.4012] [ 3989] [depth= 3] . ( 15 sec) [ -16414.0994] [ 3988] [depth= 2] . ( 15 sec) [ -16410.8546] [ 3990] [depth= 1] . ( 16 sec) [ -16407.7104] [ 3989] [depth= 2] . ( 16 sec) [ -16403.9265] [ 3978] [depth= 1] . ( 16 sec) [ -16402.7698] [ 3978] [depth= 1] . ( 16 sec) [ -16381.6611] [ 3966] [depth= 1] . ( 16 sec) [ -16364.6259] [ 3953] [depth= 3] . ( 17 sec) [ -16362.3788] [ 3947] [depth= 1] . ( 17 sec) [ -16357.0680] [ 3942] [depth= 1] . ( 18 sec) [ -16356.7309] [ 3943] [depth= 1] . ( 18 sec) [ -16354.5061] [ 3940] [depth= 1] . ( 18 sec) [ -16354.4815] [ 3945] [depth= 1] . ( 18 sec) [ -16350.2998] [ 3949] [depth= 1] . ( 19 sec) [ -16342.9917] [ 3949] [depth= 1] . ( 19 sec) [ -16342.9511] [ 3953] [depth= 1] . ( 19 sec) [ -16341.4170] [ 3952] [depth= 1] . ( 19 sec) [ -16341.2039] [ 3952] [depth= 1] . ( 20 sec) [ -16341.0029] [ 3951] [depth= 1] . ( 21 sec) [ -16340.9314] [ 3952] [depth= 1] . ( 21 sec) [ -16340.8712] [ 3952] [depth= 1] . ( 21 sec) [ -16339.4816] [ 3949] [depth= 1] . ( 21 sec) [ -16339.3594] [ 3950] [depth= 1] . ( 22 sec) [ -16294.0567] [Branch lengths ] . ( 25 sec) [ -16276.3484] [GTR parameters ] . ( 25 sec) [ -16275.6898] [Alpha ][ 0.295683] . ( 28 sec) [ -16275.2651] [ 3946] [depth= 1] . ( 29 sec) [ -16275.1404] [ 3945] [depth= 1] . ( 34 sec) [ -16263.2866] [Branch lengths ] . ( 37 sec) [ -16261.8547] [GTR parameters ] . ( 37 sec) [ -16261.8489] [Alpha ][ 0.294414] . ( 46 sec) [ -16257.8363] [Branch lengths ] . ( 89 sec) [ -16256.9820] [Branch lengths ] . ( 89 sec) [ -16256.9820] [Topology ] . ( 90 sec) [ -16255.7513] [Topology ] . ( 91 sec) [ -16255.6039] [Topology ] . ( 93 sec) [ -16255.5666] [Topology ] . ( 94 sec) [ -16255.5515] [Topology ] . ( 96 sec) [ -16255.5438] [Topology ] . ( 97 sec) [ -16255.5391] [Topology ] . ( 98 sec) [ -16255.5362] [Topology ] . ( 100 sec) [ -16254.0774] [GTR parameters ] . ( 101 sec) [ -16254.0497] [Alpha ][ 0.292048] . ( 101 sec) [ -16254.0497] [Topology ] . ( 102 sec) [ -16253.7260] [Topology ] . ( 103 sec) [ -16253.6167] [Topology ] . ( 105 sec) [ -16253.5631] [Topology ] . ( 106 sec) [ -16253.5350] [Topology ] . ( 107 sec) [ -16253.5200] [Topology ] . ( 109 sec) [ -16253.5119] [Topology ] . ( 111 sec) [ -16253.3232] [GTR parameters ] . ( 111 sec) [ -16253.3070] [Alpha ][ 0.290301] . ( 111 sec) [ -16253.3070] [Topology ] . ( 113 sec) [ -16253.2412] [Topology ] . ( 114 sec) [ -16253.2159] [Topology ] . ( 115 sec) [ -16253.2031] [Topology ] . ( 117 sec) [ -16253.1962] [Topology ] . ( 118 sec) [ -16253.1924] [Topology ] . ( 120 sec) [ -16253.1904] [Topology ] . ( 121 sec) [ -16253.1438] [GTR parameters ] . ( 121 sec) [ -16253.1393] [Alpha ][ 0.289191] . ( 121 sec) [ -16253.1393] [Topology ] . ( 123 sec) [ -16253.1227] [Topology ] . ( 124 sec) [ -16253.1165] [Topology ] . ( 125 sec) [ -16253.1133] [Topology ] . ( 127 sec) [ -16253.1115] [Topology ] . ( 128 sec) [ -16253.1106] [Topology ] . ( 128 sec) [ -16253.0995] [GTR parameters ] . ( 128 sec) [ -16253.0990] [Alpha ][ 0.288752] . ( 128 sec) [ -16253.0990] [Topology ] . ( 130 sec) [ -16253.0944] [Topology ] . ( 131 sec) [ -16253.0925] [Topology ] . ( 133 sec) [ -16253.0915] [Topology ] . ( 134 sec) [ -16253.0889] [GTR parameters ] . ( 134 sec) [ -16253.0889] [Alpha ][ 0.288752] . ( 134 sec) [ -16253.0889] [Topology ] . ( 135 sec) [ -16253.0870] [Topology ] . ( 137 sec) [ -16253.0860] [Topology ] . ( 138 sec) [ -16253.0857] [GTR parameters ] . ( 138 sec) [ -16253.0856] [Alpha ][ 0.288464] . ( 138 sec) [ -16253.0856] [Topology ] . ( 139 sec) [ -16253.0847] [Topology ] . ( 139 sec) [ -16253.0846] [GTR parameters ] . ( 140 sec) [ -16253.0846] [Alpha ][ 0.288464] . ( 140 sec) [ -16253.0846] [Topology ] . ( 141 sec) [ -16253.0840] [Topology ] . ( 141 sec) [ -16253.0839] [GTR parameters ] . ( 141 sec) [ -16253.0839] [Alpha ][ 0.288464] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -16253.083940. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -42560.8160] [GTR parameters ] . ( 1 sec) [ -41356.1663] [Alpha ][ 0.500960] . ( 2 sec) [ -41085.6752] [ 7941] [depth= 7] . ( 2 sec) [ -41059.4179] [ 7924] [depth= 2] . ( 2 sec) [ -40282.4777] [ 7839] [depth= 2] . ( 2 sec) [ -40041.6940] [ 7820] [depth= 10] . ( 2 sec) [ -39322.5843] [ 7690] [depth= 3] . ( 2 sec) [ -38917.9845] [ 7663] [depth= 1] . ( 2 sec) [ -38769.6989] [ 7613] [depth= 2] . ( 2 sec) [ -38332.2427] [ 7578] [depth= 6] . ( 2 sec) [ -38138.7420] [ 7505] [depth= 2] . ( 2 sec) [ -37560.6664] [ 7481] [depth= 9] . ( 2 sec) [ -37454.4073] [ 7459] [depth= 10] . ( 2 sec) [ -36838.9402] [ 7414] [depth= 2] . ( 2 sec) [ -36179.5592] [ 7266] [depth= 11] . ( 3 sec) [ -36098.8737] [ 7239] [depth= 1] . ( 3 sec) [ -34306.6210] [ 7109] [depth= 11] . ( 3 sec) [ -33667.9239] [ 7123] [depth= 6] . ( 3 sec) [ -32961.4225] [ 6954] [depth= 10] . ( 3 sec) [ -32866.7176] [ 6971] [depth= 1] . ( 3 sec) [ -32356.4546] [ 6800] [depth= 16] . ( 3 sec) [ -32074.9518] [ 6807] [depth= 20] . ( 3 sec) [ -31749.3853] [ 6726] [depth= 6] . ( 3 sec) [ -31450.7498] [ 6729] [depth= 2] . ( 3 sec) [ -31105.9905] [ 6712] [depth= 5] . ( 3 sec) [ -30920.8786] [ 6665] [depth= 11] . ( 3 sec) [ -30684.1395] [ 6613] [depth= 6] . ( 3 sec) [ -30672.6481] [ 6612] [depth= 7] . ( 4 sec) [ -30491.7920] [ 6603] [depth= 2] . ( 4 sec) [ -30211.3608] [ 6567] [depth= 2] . ( 4 sec) [ -30146.0906] [ 6553] [depth= 1] . ( 4 sec) [ -29533.6447] [ 6503] [depth= 15] . ( 4 sec) [ -29478.1872] [ 6482] [depth= 4] . ( 4 sec) [ -29118.4091] [ 6421] [depth= 15] . ( 4 sec) [ -28630.8356] [ 6388] [depth= 1] . ( 4 sec) [ -28491.6280] [ 6329] [depth= 3] . ( 4 sec) [ -27707.6733] [ 6329] [depth= 16] . ( 4 sec) [ -26315.8640] [ 6289] [depth= 13] . ( 4 sec) [ -26260.1618] [ 6227] [depth= 15] . ( 4 sec) [ -25928.7728] [ 6217] [depth= 3] . ( 5 sec) [ -25717.1066] [ 6155] [depth= 2] . ( 5 sec) [ -25662.3042] [ 6128] [depth= 1] . ( 5 sec) [ -25533.9918] [ 6090] [depth= 4] . ( 5 sec) [ -24956.7780] [ 6075] [depth= 4] . ( 5 sec) [ -24710.6460] [ 5974] [depth= 9] . ( 5 sec) [ -24523.6986] [ 6010] [depth= 2] . ( 5 sec) [ -24048.5408] [ 5821] [depth= 9] . ( 5 sec) [ -23874.4922] [ 5744] [depth= 11] . ( 5 sec) [ -23860.7394] [ 5754] [depth= 1] . ( 5 sec) [ -23632.9088] [ 5672] [depth= 7] . ( 5 sec) [ -23516.1325] [ 5646] [depth= 1] . ( 5 sec) [ -23471.5521] [ 5627] [depth= 5] . ( 6 sec) [ -23463.3668] [ 5565] [depth= 2] . ( 6 sec) [ -23187.9932] [ 5517] [depth= 10] . ( 6 sec) [ -23161.3106] [ 5539] [depth= 1] . ( 6 sec) [ -23160.0025] [ 5509] [depth= 1] . ( 6 sec) [ -23114.2971] [ 5488] [depth= 9] . ( 6 sec) [ -21832.9959] [ 5358] [depth= 6] . ( 6 sec) [ -21686.0656] [ 5356] [depth= 1] . ( 6 sec) [ -21674.1204] [ 5341] [depth= 2] . ( 6 sec) [ -21616.6165] [ 5300] [depth= 1] . ( 6 sec) [ -21614.1414] [ 5304] [depth= 1] . ( 6 sec) [ -21478.4664] [ 5299] [depth= 1] . ( 7 sec) [ -21379.4095] [ 5293] [depth= 4] . ( 7 sec) [ -21352.4197] [ 5275] [depth= 2] . ( 7 sec) [ -21026.6483] [ 5169] [depth= 2] . ( 7 sec) [ -20937.6608] [ 5110] [depth= 2] . ( 7 sec) [ -20259.2687] [ 5071] [depth= 1] . ( 7 sec) [ -20174.3020] [ 5046] [depth= 3] . ( 7 sec) [ -20152.3663] [ 5045] [depth= 7] . ( 7 sec) [ -20035.7725] [ 4979] [depth= 1] . ( 7 sec) [ -19980.0928] [ 4925] [depth= 9] . ( 7 sec) [ -19727.6030] [ 4894] [depth= 1] . ( 7 sec) [ -19681.6856] [ 4887] [depth= 13] . ( 7 sec) [ -19584.9323] [ 4813] [depth= 11] . ( 7 sec) [ -19504.9440] [ 4825] [depth= 1] . ( 8 sec) [ -19499.4985] [ 4815] [depth= 1] . ( 8 sec) [ -19483.1214] [ 4815] [depth= 1] . ( 8 sec) [ -19030.0626] [ 4672] [depth= 10] . ( 8 sec) [ -19029.2223] [ 4672] [depth= 1] . ( 8 sec) [ -18992.7155] [ 4669] [depth= 5] . ( 8 sec) [ -18953.1371] [ 4667] [depth= 2] . ( 8 sec) [ -18920.8818] [ 4655] [depth= 1] . ( 8 sec) [ -18874.7529] [ 4656] [depth= 9] . ( 8 sec) [ -18860.8059] [ 4612] [depth= 1] . ( 8 sec) [ -18850.0391] [ 4613] [depth= 1] . ( 9 sec) [ -18750.9150] [ 4591] [depth= 1] . ( 9 sec) [ -18584.4954] [ 4500] [depth= 10] . ( 9 sec) [ -18577.7564] [ 4506] [depth= 1] . ( 9 sec) [ -18542.7587] [ 4501] [depth= 1] . ( 9 sec) [ -18421.3190] [ 4477] [depth= 2] . ( 9 sec) [ -18418.7675] [ 4479] [depth= 1] . ( 9 sec) [ -18291.7708] [ 4395] [depth= 4] . ( 9 sec) [ -18069.9280] [ 4327] [depth= 2] . ( 9 sec) [ -18065.1778] [ 4316] [depth= 2] . ( 9 sec) [ -18055.7714] [ 4333] [depth= 4] . ( 9 sec) [ -17863.3645] [ 4275] [depth= 2] . ( 10 sec) [ -17856.4998] [ 4274] [depth= 1] . ( 10 sec) [ -17799.4883] [ 4200] [depth= 9] . ( 10 sec) [ -17770.6234] [ 4188] [depth= 1] . ( 10 sec) [ -17749.6627] [ 4183] [depth= 1] . ( 10 sec) [ -17715.5635] [ 4219] [depth= 1] . ( 10 sec) [ -17702.0932] [ 4211] [depth= 1] . ( 10 sec) [ -17621.1008] [ 4207] [depth= 3] . ( 10 sec) [ -17620.2686] [ 4171] [depth= 1] . ( 10 sec) [ -17557.7705] [ 4126] [depth= 9] . ( 11 sec) [ -17527.7761] [ 4114] [depth= 1] . ( 11 sec) [ -17483.1516] [ 4090] [depth= 5] . ( 11 sec) [ -17448.6852] [ 4069] [depth= 1] . ( 11 sec) [ -17402.6114] [ 4068] [depth= 1] . ( 11 sec) [ -17402.0504] [ 4069] [depth= 1] . ( 11 sec) [ -17395.9483] [ 4069] [depth= 1] . ( 11 sec) [ -17368.3589] [ 4049] [depth= 2] . ( 11 sec) [ -17367.8834] [ 4050] [depth= 1] . ( 11 sec) [ -17364.9654] [ 4044] [depth= 1] . ( 11 sec) [ -17364.8231] [ 4044] [depth= 1] . ( 11 sec) [ -17364.7140] [ 4044] [depth= 1] . ( 12 sec) [ -16987.5439] [Branch lengths ] . ( 15 sec) [ -16669.6787] [GTR parameters ] . ( 15 sec) [ -16593.5986] [Alpha ][ 0.307887] . ( 15 sec) [ -16588.9941] [ 4032] [depth= 1] . ( 15 sec) [ -16588.8979] [ 4031] [depth= 1] . ( 15 sec) [ -16588.6018] [ 4029] [depth= 2] . ( 16 sec) [ -16587.2785] [ 4026] [depth= 1] . ( 16 sec) [ -16584.2891] [ 4014] [depth= 1] . ( 16 sec) [ -16583.2935] [ 4014] [depth= 2] . ( 16 sec) [ -16572.4792] [ 4006] [depth= 2] . ( 16 sec) [ -16549.5342] [ 3997] [depth= 2] . ( 16 sec) [ -16549.4478] [ 3997] [depth= 1] . ( 16 sec) [ -16506.6540] [ 3954] [depth= 1] . ( 16 sec) [ -16505.9839] [ 3957] [depth= 1] . ( 17 sec) [ -16505.9293] [ 3958] [depth= 1] . ( 17 sec) [ -16442.2469] [ 3960] [depth= 4] . ( 17 sec) [ -16439.8790] [ 3961] [depth= 1] . ( 18 sec) [ -16439.0510] [ 3961] [depth= 1] . ( 18 sec) [ -16431.6479] [ 3967] [depth= 4] . ( 18 sec) [ -16405.4961] [ 3960] [depth= 2] . ( 18 sec) [ -16393.3114] [ 3955] [depth= 2] . ( 19 sec) [ -16390.6201] [ 3954] [depth= 1] . ( 19 sec) [ -16390.2064] [ 3954] [depth= 1] . ( 19 sec) [ -16388.1593] [ 3958] [depth= 1] . ( 20 sec) [ -16388.1124] [ 3958] [depth= 1] . ( 20 sec) [ -16386.4479] [ 3963] [depth= 1] . ( 21 sec) [ -16386.4339] [ 3962] [depth= 1] . ( 22 sec) [ -16386.4203] [ 3962] [depth= 2] . ( 22 sec) [ -16382.2504] [ 3964] [depth= 2] . ( 22 sec) [ -16380.8003] [ 3968] [depth= 1] . ( 23 sec) [ -16340.4984] [Branch lengths ] . ( 26 sec) [ -16321.5580] [GTR parameters ] . ( 27 sec) [ -16320.2977] [Alpha ][ 0.289832] . ( 27 sec) [ -16292.0253] [ 3955] [depth= 4] . ( 28 sec) [ -16291.5496] [ 3955] [depth= 1] . ( 29 sec) [ -16290.7038] [ 3949] [depth= 1] . ( 31 sec) [ -16290.1732] [ 3948] [depth= 1] . ( 34 sec) [ -16288.9492] [ 3948] [depth= 2] . ( 34 sec) [ -16286.3666] [ 3945] [depth= 2] . ( 35 sec) [ -16276.2180] [Branch lengths ] . ( 38 sec) [ -16273.3700] [GTR parameters ] . ( 38 sec) [ -16273.3648] [Alpha ][ 0.290884] . ( 39 sec) [ -16273.2055] [ 3940] [depth= 1] . ( 41 sec) [ -16273.1480] [ 3942] [depth= 1] . ( 46 sec) [ -16264.1507] [Branch lengths ] . ( 49 sec) [ -16263.6052] [GTR parameters ] . ( 50 sec) [ -16263.6050] [Alpha ][ 0.291175] . ( 58 sec) [ -16255.5988] [Branch lengths ] . ( 101 sec) [ -16254.0353] [Branch lengths ] . ( 101 sec) [ -16254.0353] [Topology ] . ( 102 sec) [ -16253.9272] [Topology ] . ( 104 sec) [ -16253.8931] [Topology ] . ( 105 sec) [ -16253.8782] [Topology ] . ( 106 sec) [ -16253.8712] [Topology ] . ( 108 sec) [ -16253.8678] [Topology ] . ( 109 sec) [ -16253.8662] [Topology ] . ( 112 sec) [ -16253.4059] [GTR parameters ] . ( 112 sec) [ -16253.4030] [Alpha ][ 0.290273] . ( 112 sec) [ -16253.4030] [Topology ] . ( 113 sec) [ -16253.2942] [Topology ] . ( 115 sec) [ -16253.2566] [Topology ] . ( 116 sec) [ -16253.2379] [Topology ] . ( 117 sec) [ -16253.2282] [Topology ] . ( 119 sec) [ -16253.2229] [Topology ] . ( 120 sec) [ -16253.2201] [Topology ] . ( 122 sec) [ -16253.1596] [GTR parameters ] . ( 122 sec) [ -16253.1559] [Alpha ][ 0.289252] . ( 122 sec) [ -16253.1559] [Topology ] . ( 124 sec) [ -16253.1338] [Topology ] . ( 125 sec) [ -16253.1253] [Topology ] . ( 126 sec) [ -16253.1210] [Topology ] . ( 128 sec) [ -16253.1186] [Topology ] . ( 129 sec) [ -16253.1174] [Topology ] . ( 130 sec) [ -16253.1167] [Topology ] . ( 132 sec) [ -16253.1013] [GTR parameters ] . ( 133 sec) [ -16253.1007] [Alpha ][ 0.288793] . ( 133 sec) [ -16253.1007] [Topology ] . ( 134 sec) [ -16253.0953] [Topology ] . ( 135 sec) [ -16253.0931] [Topology ] . ( 137 sec) [ -16253.0920] [Topology ] . ( 138 sec) [ -16253.0914] [Topology ] . ( 138 sec) [ -16253.0885] [GTR parameters ] . ( 138 sec) [ -16253.0885] [Alpha ][ 0.288793] . ( 139 sec) [ -16253.0885] [Topology ] . ( 140 sec) [ -16253.0869] [Topology ] . ( 141 sec) [ -16253.0861] [Topology ] . ( 143 sec) [ -16253.0856] [GTR parameters ] . ( 143 sec) [ -16253.0854] [Alpha ][ 0.288500] . ( 144 sec) [ -16253.0854] [Topology ] . ( 145 sec) [ -16253.0846] [Topology ] . ( 145 sec) [ -16253.0844] [GTR parameters ] . ( 145 sec) [ -16253.0844] [Alpha ][ 0.288500] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -16253.084425. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -17550.8937] [GTR parameters ] . ( 1 sec) [ -17215.2965] [Alpha ][ 0.500960] . ( 1 sec) [ -17215.2965] [Topology ] . ( 3 sec) [ -16916.1845] [Topology ] . ( 4 sec) [ -16885.7882] [Topology ] . ( 5 sec) [ -16874.7992] [Topology ] . ( 7 sec) [ -16870.7493] [Topology ] . ( 8 sec) [ -16869.9252] [Topology ] . ( 9 sec) [ -16869.5950] [Topology ] . ( 11 sec) [ -16869.3884] [Topology ] . ( 12 sec) [ -16868.8474] [Topology ] . ( 13 sec) [ -16868.7091] [Topology ] . Checking for NNIs, optimizing five branches... . ( 27 sec) [ -16867.1125] [Topology ] . ( 30 sec) [ -16387.4659] [GTR parameters ] . ( 30 sec) [ -16321.3264] [Alpha ][ 0.313611] . ( 30 sec) [ -16321.3264] [Topology ] . ( 31 sec) [ -16296.0653] [Topology ] . ( 33 sec) [ -16291.6763] [Topology ] . ( 34 sec) [ -16289.9335] [Topology ] . ( 35 sec) [ -16289.0499] [Topology ] . ( 37 sec) [ -16288.5757] [Topology ] . ( 38 sec) [ -16288.3125] [Topology ] . ( 39 sec) [ -16288.1637] [Topology ] . Checking for NNIs, optimizing five branches... . ( 55 sec) [ -16267.6195] [GTR parameters ] . ( 55 sec) [ -16266.6873] [Alpha ][ 0.298004] . ( 55 sec) [ -16266.6873] [Topology ] . ( 57 sec) [ -16262.3457] [Topology ] . ( 58 sec) [ -16260.7450] [Topology ] . ( 59 sec) [ -16259.9619] [Topology ] . ( 61 sec) [ -16259.5615] [Topology ] . ( 62 sec) [ -16259.3516] [Topology ] . ( 63 sec) [ -16259.2400] [Topology ] . Checking for NNIs, optimizing five branches... . ( 79 sec) [ -16256.2006] [GTR parameters ] . ( 79 sec) [ -16256.1187] [Alpha ][ 0.293725] . ( 79 sec) [ -16256.1187] [Topology ] . ( 80 sec) [ -16255.1543] [Topology ] . ( 82 sec) [ -16254.7746] [Topology ] . ( 83 sec) [ -16254.5860] [Topology ] . ( 84 sec) [ -16254.4883] [Topology ] . ( 86 sec) [ -16254.4368] [Topology ] . ( 87 sec) [ -16254.4090] [Topology ] . Checking for NNIs, optimizing five branches... . ( 101 sec) [ -16253.8029] [GTR parameters ] . ( 101 sec) [ -16253.7748] [Alpha ][ 0.291349] . ( 101 sec) [ -16253.7748] [Topology ] . ( 102 sec) [ -16253.5624] [Topology ] . ( 104 sec) [ -16253.4790] [Topology ] . ( 105 sec) [ -16253.4367] [Topology ] . ( 106 sec) [ -16253.4143] [Topology ] . ( 108 sec) [ -16253.4022] [Topology ] . ( 109 sec) [ -16253.3957] [Topology ] . Checking for NNIs, optimizing five branches... . ( 125 sec) [ -16253.2584] [GTR parameters ] . ( 125 sec) [ -16253.2484] [Alpha ][ 0.289732] . ( 125 sec) [ -16253.2484] [Topology ] . ( 126 sec) [ -16253.1980] [Topology ] . ( 128 sec) [ -16253.1787] [Topology ] . ( 129 sec) [ -16253.1688] [Topology ] . ( 130 sec) [ -16253.1635] [Topology ] . ( 132 sec) [ -16253.1607] [Topology ] . ( 133 sec) [ -16253.1591] [Topology ] . Checking for NNIs, optimizing five branches... . ( 147 sec) [ -16253.1248] [GTR parameters ] . ( 147 sec) [ -16253.1232] [Alpha ][ 0.289024] . ( 147 sec) [ -16253.1232] [Topology ] . ( 148 sec) [ -16253.1111] [Topology ] . ( 150 sec) [ -16253.1063] [Topology ] . ( 151 sec) [ -16253.1038] [Topology ] . ( 152 sec) [ -16253.1025] [Topology ] . ( 154 sec) [ -16253.1018] [Topology ] . Checking for NNIs, optimizing five branches... . ( 166 sec) [ -16253.0943] [GTR parameters ] . ( 167 sec) [ -16253.0940] [Alpha ][ 0.288675] . ( 167 sec) [ -16253.0940] [Topology ] . ( 168 sec) [ -16253.0908] [Topology ] . ( 169 sec) [ -16253.0895] [Topology ] . ( 171 sec) [ -16253.0888] [Topology ] . Checking for NNIs, optimizing five branches... . ( 184 sec) [ -16253.0869] [GTR parameters ] . ( 184 sec) [ -16253.0869] [Alpha ][ 0.288675] . ( 184 sec) [ -16253.0869] [Topology ] . ( 186 sec) [ -16253.0856] [Topology ] . ( 187 sec) [ -16253.0850] [Topology ] . Checking for NNIs, optimizing five branches... . ( 200 sec) [ -16253.0850] [GTR parameters ] . ( 200 sec) [ -16253.0850] [Alpha ][ 0.288675] . ( 200 sec) [ -16253.0850] [Topology ] . ( 201 sec) [ -16253.0846] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 226 sec) [ -17550.8937] [GTR parameters ] . ( 226 sec) [ -17215.2965] [Alpha ][ 0.500960] . ( 227 sec) [ -17215.2819] [ 3954] [depth= 1] . ( 227 sec) [ -17212.5717] [ 3953] [depth= 1] . ( 227 sec) [ -17211.0309] [ 3956] [depth= 1] . ( 227 sec) [ -17210.9694] [ 3957] [depth= 1] . ( 227 sec) [ -17209.0242] [ 3961] [depth= 2] . ( 227 sec) [ -17208.2432] [ 3961] [depth= 2] . ( 228 sec) [ -17196.5597] [ 3953] [depth= 1] . ( 228 sec) [ -17188.0683] [ 3957] [depth= 1] . ( 228 sec) [ -17187.7368] [ 3956] [depth= 3] . ( 229 sec) [ -17183.4824] [ 3957] [depth= 3] . ( 229 sec) [ -17182.6056] [ 3957] [depth= 1] . ( 229 sec) [ -17182.2647] [ 3957] [depth= 1] . ( 229 sec) [ -17182.0751] [ 3957] [depth= 1] . ( 229 sec) [ -17179.9553] [ 3956] [depth= 2] . ( 230 sec) [ -17171.8169] [ 3955] [depth= 2] . ( 230 sec) [ -17170.6583] [ 3954] [depth= 1] . ( 230 sec) [ -17170.3929] [ 3954] [depth= 1] . ( 230 sec) [ -17170.2910] [ 3954] [depth= 1] . ( 230 sec) [ -17170.1443] [ 3954] [depth= 1] . ( 231 sec) [ -17168.6264] [ 3957] [depth= 1] . ( 231 sec) [ -17161.6293] [ 3955] [depth= 1] . ( 231 sec) [ -17161.6041] [ 3955] [depth= 1] . ( 231 sec) [ -17159.9143] [ 3957] [depth= 1] . ( 232 sec) [ -17140.6645] [ 3974] [depth= 2] . ( 232 sec) [ -17103.7654] [ 3959] [depth= 2] . ( 232 sec) [ -17095.7780] [ 3972] [depth= 1] . ( 232 sec) [ -17081.8023] [ 3959] [depth= 1] . ( 232 sec) [ -17079.8526] [ 3952] [depth= 1] . ( 232 sec) [ -17070.9245] [ 3951] [depth= 1] . ( 232 sec) [ -17069.8324] [ 3952] [depth= 1] . ( 233 sec) [ -17066.5519] [ 3957] [depth= 1] . ( 233 sec) [ -17063.8078] [ 3954] [depth= 2] . ( 233 sec) [ -17055.2804] [ 3952] [depth= 2] . ( 233 sec) [ -17046.1616] [ 3956] [depth= 1] . ( 233 sec) [ -17044.4079] [ 3955] [depth= 1] . ( 233 sec) [ -17025.4110] [ 3953] [depth= 1] . ( 233 sec) [ -17015.1784] [ 3953] [depth= 1] . ( 233 sec) [ -16989.7343] [ 3948] [depth= 1] . ( 233 sec) [ -16988.5808] [ 3946] [depth= 1] . ( 234 sec) [ -16988.4308] [ 3948] [depth= 1] . ( 234 sec) [ -16985.2922] [ 3952] [depth= 1] . ( 234 sec) [ -16977.0947] [ 3954] [depth= 2] . ( 235 sec) [ -16913.0865] [Branch lengths ] . ( 238 sec) [ -16443.4134] [GTR parameters ] . ( 239 sec) [ -16372.1845] [Alpha ][ 0.306024] . ( 239 sec) [ -16371.6719] [ 3954] [depth= 1] . ( 239 sec) [ -16371.6338] [ 3956] [depth= 1] . ( 239 sec) [ -16371.3508] [ 3956] [depth= 2] . ( 240 sec) [ -16370.9277] [ 3959] [depth= 1] . ( 240 sec) [ -16370.5992] [ 3954] [depth= 1] . ( 240 sec) [ -16369.5120] [ 3948] [depth= 1] . ( 241 sec) [ -16369.4212] [ 3949] [depth= 1] . ( 241 sec) [ -16369.3971] [ 3949] [depth= 1] . ( 242 sec) [ -16369.3846] [ 3949] [depth= 1] . ( 242 sec) [ -16369.3197] [ 3949] [depth= 1] . ( 243 sec) [ -16361.3214] [ 3944] [depth= 1] . ( 245 sec) [ -16360.7520] [ 3947] [depth= 1] . ( 245 sec) [ -16358.8862] [ 3949] [depth= 1] . ( 246 sec) [ -16358.8613] [ 3955] [depth= 3] . ( 246 sec) [ -16346.7839] [ 3943] [depth= 2] . ( 246 sec) [ -16334.5016] [ 3944] [depth= 1] . ( 247 sec) [ -16300.4734] [Branch lengths ] . ( 251 sec) [ -16281.9168] [GTR parameters ] . ( 251 sec) [ -16281.2715] [Alpha ][ 0.292982] . ( 252 sec) [ -16280.6311] [ 3945] [depth= 1] . ( 260 sec) [ -16268.6402] [Branch lengths ] . ( 263 sec) [ -16266.1326] [GTR parameters ] . ( 263 sec) [ -16266.1321] [Alpha ][ 0.292554] . ( 272 sec) [ -16259.8282] [Branch lengths ] . ( 316 sec) [ -16258.3282] [Branch lengths ] . ( 316 sec) [ -16258.3282] [Topology ] . ( 317 sec) [ -16257.0357] [Topology ] . ( 318 sec) [ -16256.8731] [Topology ] . ( 320 sec) [ -16256.8272] [Topology ] . ( 321 sec) [ -16256.8093] [Topology ] . ( 322 sec) [ -16256.8012] [Topology ] . ( 324 sec) [ -16256.7973] [Topology ] . ( 325 sec) [ -16256.7954] [Topology ] . ( 328 sec) [ -16254.4858] [GTR parameters ] . ( 328 sec) [ -16254.4846] [Alpha ][ 0.291936] . ( 328 sec) [ -16254.4846] [Topology ] . ( 330 sec) [ -16253.9978] [Topology ] . ( 331 sec) [ -16253.8230] [Topology ] . ( 332 sec) [ -16253.7375] [Topology ] . ( 334 sec) [ -16253.6934] [Topology ] . ( 335 sec) [ -16253.6700] [Topology ] . ( 336 sec) [ -16253.6576] [Topology ] . ( 340 sec) [ -16253.4004] [GTR parameters ] . ( 340 sec) [ -16253.3884] [Alpha ][ 0.290462] . ( 340 sec) [ -16253.3884] [Topology ] . ( 341 sec) [ -16253.2950] [Topology ] . ( 343 sec) [ -16253.2583] [Topology ] . ( 344 sec) [ -16253.2394] [Topology ] . ( 345 sec) [ -16253.2294] [Topology ] . ( 347 sec) [ -16253.2240] [Topology ] . ( 348 sec) [ -16253.2211] [Topology ] . ( 351 sec) [ -16253.1616] [GTR parameters ] . ( 351 sec) [ -16253.1566] [Alpha ][ 0.289296] . ( 351 sec) [ -16253.1566] [Topology ] . ( 353 sec) [ -16253.1348] [Topology ] . ( 354 sec) [ -16253.1265] [Topology ] . ( 355 sec) [ -16253.1222] [Topology ] . ( 357 sec) [ -16253.1199] [Topology ] . ( 358 sec) [ -16253.1186] [Topology ] . ( 359 sec) [ -16253.1179] [Topology ] . ( 362 sec) [ -16253.1019] [GTR parameters ] . ( 363 sec) [ -16253.1013] [Alpha ][ 0.288818] . ( 363 sec) [ -16253.1013] [Topology ] . ( 364 sec) [ -16253.0958] [Topology ] . ( 365 sec) [ -16253.0937] [Topology ] . ( 367 sec) [ -16253.0926] [Topology ] . ( 368 sec) [ -16253.0920] [Topology ] . ( 369 sec) [ -16253.0887] [GTR parameters ] . ( 369 sec) [ -16253.0887] [Alpha ][ 0.288530] . ( 369 sec) [ -16253.0887] [Topology ] . ( 370 sec) [ -16253.0870] [Topology ] . ( 372 sec) [ -16253.0862] [Topology ] . ( 372 sec) [ -16253.0855] [GTR parameters ] . ( 372 sec) [ -16253.0855] [Alpha ][ 0.288530] . ( 372 sec) [ -16253.0855] [Topology ] . ( 374 sec) [ -16253.0846] [Topology ] . ( 374 sec) [ -16253.0845] [GTR parameters ] . ( 374 sec) [ -16253.0845] [Alpha ][ 0.288530] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -16253.084612 . Log likelihood obtained after SPR moves : -16253.084546 . Log likelihood of the current tree: -16253.084546. . Printing the most likely tree in file 'nucleic_M2862_54x1011_2006.phy_phyml_tree.txt'... . Best log likelihood : -16253.083940 . Time used 0h6m28s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1171.97user 0.00system 19:38.61elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps