.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2661_66x1027_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 . 9 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 596 patterns found. (out of a total of 1027 sites) . 417 sites without polymorphism (40.60%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 21Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -52927.2558] [GTR parameters ] . ( 2 sec) [ -51780.7785] [Alpha ][ 0.500960] . ( 2 sec) [ -50962.9025] [ 6368] [depth= 11] . ( 2 sec) [ -50024.1989] [ 6236] [depth= 11] . ( 2 sec) [ -49787.6511] [ 6148] [depth= 7] . ( 2 sec) [ -49785.9457] [ 6081] [depth= 1] . ( 2 sec) [ -47487.9024] [ 6068] [depth= 7] . ( 2 sec) [ -47432.3134] [ 6059] [depth= 1] . ( 2 sec) [ -46852.7649] [ 6045] [depth= 2] . ( 3 sec) [ -46514.4187] [ 5945] [depth= 4] . ( 3 sec) [ -46148.6182] [ 5930] [depth= 8] . ( 3 sec) [ -45906.0770] [ 5961] [depth= 2] . ( 3 sec) [ -45550.4653] [ 5903] [depth= 6] . ( 3 sec) [ -45081.4315] [ 5816] [depth= 3] . ( 3 sec) [ -44245.0672] [ 5811] [depth= 9] . ( 3 sec) [ -44068.3121] [ 5785] [depth= 4] . ( 3 sec) [ -43533.1717] [ 5711] [depth= 1] . ( 4 sec) [ -43336.3649] [ 5680] [depth= 7] . ( 4 sec) [ -42475.4167] [ 5546] [depth= 18] . ( 4 sec) [ -42156.8853] [ 5546] [depth= 1] . ( 4 sec) [ -42144.6007] [ 5546] [depth= 13] . ( 4 sec) [ -41848.4135] [ 5499] [depth= 4] . ( 4 sec) [ -40702.7002] [ 5499] [depth= 4] . ( 4 sec) [ -40586.3054] [ 5450] [depth= 13] . ( 4 sec) [ -40265.0878] [ 5435] [depth= 3] . ( 4 sec) [ -40140.5864] [ 5374] [depth= 10] . ( 4 sec) [ -40012.6231] [ 5371] [depth= 1] . ( 5 sec) [ -39310.7119] [ 5330] [depth= 3] . ( 5 sec) [ -36856.4680] [ 5327] [depth= 1] . ( 5 sec) [ -36462.2689] [ 5286] [depth= 10] . ( 5 sec) [ -35716.8199] [ 5141] [depth= 13] . ( 5 sec) [ -34480.8799] [ 5143] [depth= 4] . ( 5 sec) [ -33813.7060] [ 5143] [depth= 12] . ( 5 sec) [ -33810.6841] [ 5143] [depth= 1] . ( 5 sec) [ -33793.0758] [ 5143] [depth= 2] . ( 5 sec) [ -33434.4609] [ 5067] [depth= 1] . ( 5 sec) [ -33419.4927] [ 5062] [depth= 1] . ( 6 sec) [ -33400.3896] [ 5061] [depth= 9] . ( 6 sec) [ -33392.8459] [ 5065] [depth= 2] . ( 6 sec) [ -31891.6248] [ 4926] [depth= 7] . ( 6 sec) [ -31856.9657] [ 4822] [depth= 2] . ( 6 sec) [ -31512.4533] [ 4811] [depth= 3] . ( 6 sec) [ -31386.0718] [ 4864] [depth= 2] . ( 6 sec) [ -31149.6544] [ 4864] [depth= 2] . ( 6 sec) [ -30797.2977] [ 4760] [depth= 2] . ( 6 sec) [ -29943.9968] [ 4592] [depth= 8] . ( 7 sec) [ -29769.4252] [ 4592] [depth= 1] . ( 7 sec) [ -29759.0356] [ 4596] [depth= 1] . ( 7 sec) [ -28907.9024] [ 4446] [depth= 14] . ( 7 sec) [ -28871.1435] [ 4446] [depth= 1] . ( 7 sec) [ -27997.7186] [ 4443] [depth= 1] . ( 7 sec) [ -27954.4918] [ 4373] [depth= 1] . ( 7 sec) [ -27947.4475] [ 4373] [depth= 2] . ( 7 sec) [ -27946.9038] [ 4373] [depth= 3] . ( 7 sec) [ -27446.2864] [ 4359] [depth= 4] . ( 7 sec) [ -27226.5169] [ 4283] [depth= 11] . ( 8 sec) [ -27194.3816] [ 4300] [depth= 1] . ( 8 sec) [ -27194.3444] [ 4300] [depth= 2] . ( 8 sec) [ -27170.6034] [ 4298] [depth= 2] . ( 8 sec) [ -26952.0511] [ 4273] [depth= 4] . ( 8 sec) [ -26947.6291] [ 4273] [depth= 1] . ( 8 sec) [ -26932.6106] [ 4269] [depth= 8] . ( 8 sec) [ -26682.3001] [ 4247] [depth= 8] . ( 8 sec) [ -26032.6923] [ 4230] [depth= 4] . ( 8 sec) [ -24979.1661] [ 4147] [depth= 11] . ( 8 sec) [ -24749.1908] [ 4149] [depth= 5] . ( 8 sec) [ -24681.6888] [ 4104] [depth= 2] . ( 8 sec) [ -24056.4621] [ 4087] [depth= 3] . ( 9 sec) [ -23981.3738] [ 4046] [depth= 9] . ( 9 sec) [ -23770.5409] [ 4018] [depth= 1] . ( 9 sec) [ -23638.7188] [ 4007] [depth= 6] . ( 9 sec) [ -23281.4117] [ 3938] [depth= 6] . ( 9 sec) [ -22964.9965] [ 3852] [depth= 13] . ( 9 sec) [ -22570.0499] [ 3738] [depth= 10] . ( 9 sec) [ -22481.3384] [ 3731] [depth= 1] . ( 9 sec) [ -22459.6106] [ 3719] [depth= 1] . ( 9 sec) [ -22448.7836] [ 3719] [depth= 9] . ( 9 sec) [ -22439.0086] [ 3719] [depth= 1] . ( 10 sec) [ -20168.4334] [ 3718] [depth= 17] . ( 10 sec) [ -19970.1622] [ 3696] [depth= 2] . ( 10 sec) [ -19880.7559] [ 3661] [depth= 11] . ( 10 sec) [ -19837.2853] [ 3646] [depth= 13] . ( 10 sec) [ -19648.3025] [ 3634] [depth= 3] . ( 10 sec) [ -19548.3619] [ 3633] [depth= 1] . ( 10 sec) [ -19359.9570] [ 3525] [depth= 1] . ( 10 sec) [ -19199.3727] [ 3518] [depth= 8] . ( 10 sec) [ -18893.0678] [ 3375] [depth= 7] . ( 10 sec) [ -18717.7024] [ 3375] [depth= 1] . ( 11 sec) [ -18717.6796] [ 3375] [depth= 2] . ( 11 sec) [ -18655.5362] [ 3348] [depth= 1] . ( 11 sec) [ -18425.5691] [ 3319] [depth= 7] . ( 11 sec) [ -18402.1293] [ 3319] [depth= 1] . ( 11 sec) [ -18233.4378] [ 3242] [depth= 6] . ( 11 sec) [ -18231.5701] [ 3245] [depth= 2] . ( 11 sec) [ -18039.1888] [ 3154] [depth= 11] . ( 11 sec) [ -18006.1062] [ 3154] [depth= 1] . ( 11 sec) [ -17737.3064] [ 3155] [depth= 1] . ( 11 sec) [ -17730.9095] [ 3155] [depth= 1] . ( 12 sec) [ -17727.4376] [ 3158] [depth= 13] . ( 12 sec) [ -16939.7880] [ 3158] [depth= 1] . ( 12 sec) [ -16330.4469] [ 3036] [depth= 11] . ( 12 sec) [ -16322.3733] [ 3040] [depth= 2] . ( 12 sec) [ -15354.6358] [ 3041] [depth= 6] . ( 12 sec) [ -14929.5012] [ 3043] [depth= 2] . ( 12 sec) [ -14750.7093] [ 3042] [depth= 4] . ( 12 sec) [ -14650.5725] [ 2920] [depth= 8] . ( 12 sec) [ -14434.0879] [ 2919] [depth= 1] . ( 12 sec) [ -14239.3566] [ 2890] [depth= 1] . ( 13 sec) [ -14017.9899] [ 2820] [depth= 3] . ( 13 sec) [ -13786.6272] [ 2767] [depth= 7] . ( 13 sec) [ -13786.3510] [ 2767] [depth= 1] . ( 13 sec) [ -13774.3518] [ 2766] [depth= 5] . ( 13 sec) [ -13402.4691] [ 2740] [depth= 2] . ( 13 sec) [ -13379.3521] [ 2757] [depth= 3] . ( 13 sec) [ -13339.5684] [ 2739] [depth= 1] . ( 13 sec) [ -12986.4161] [ 2669] [depth= 15] . ( 13 sec) [ -12982.9343] [ 2667] [depth= 1] . ( 13 sec) [ -12656.5226] [ 2666] [depth= 2] . ( 14 sec) [ -12602.1894] [ 2638] [depth= 1] . ( 14 sec) [ -11885.4974] [ 2513] [depth= 10] . ( 14 sec) [ -11877.5765] [ 2512] [depth= 1] . ( 14 sec) [ -11789.0056] [ 2471] [depth= 4] . ( 14 sec) [ -11535.2775] [ 2393] [depth= 15] . ( 14 sec) [ -11503.1838] [ 2393] [depth= 1] . ( 14 sec) [ -11413.5052] [ 2335] [depth= 5] . ( 14 sec) [ -11372.1031] [ 2333] [depth= 4] . ( 14 sec) [ -11369.4015] [ 2333] [depth= 1] . ( 14 sec) [ -11354.7741] [ 2334] [depth= 3] . ( 15 sec) [ -11245.4001] [ 2335] [depth= 3] . ( 15 sec) [ -11217.0553] [ 2332] [depth= 4] . ( 15 sec) [ -11144.6161] [ 2321] [depth= 1] . ( 15 sec) [ -11134.5849] [ 2322] [depth= 1] . ( 15 sec) [ -11133.3319] [ 2322] [depth= 1] . ( 15 sec) [ -10792.1536] [ 2253] [depth= 6] . ( 15 sec) [ -10790.5523] [ 2253] [depth= 1] . ( 15 sec) [ -10736.4465] [ 2253] [depth= 2] . ( 15 sec) [ -10714.6602] [ 2241] [depth= 4] . ( 16 sec) [ -10714.3526] [ 2241] [depth= 2] . ( 16 sec) [ -10704.4008] [ 2240] [depth= 4] . ( 16 sec) [ -10521.2317] [ 2123] [depth= 6] . ( 16 sec) [ -10482.3934] [ 2124] [depth= 1] . ( 16 sec) [ -10327.4632] [ 2095] [depth= 1] . ( 16 sec) [ -10310.4804] [ 2100] [depth= 2] . ( 16 sec) [ -10300.8092] [ 2100] [depth= 1] . ( 16 sec) [ -10297.1039] [ 2099] [depth= 1] . ( 16 sec) [ -10287.1987] [ 2097] [depth= 1] . ( 16 sec) [ -10214.5566] [ 2075] [depth= 1] . ( 17 sec) [ -10208.5251] [ 2080] [depth= 1] . ( 17 sec) [ -10185.4344] [ 2081] [depth= 1] . ( 17 sec) [ -10178.7870] [ 2079] [depth= 1] . ( 17 sec) [ -10178.3736] [ 2078] [depth= 1] . ( 17 sec) [ -10150.8699] [ 2076] [depth= 1] . ( 17 sec) [ -10069.0972] [ 2075] [depth= 5] . ( 17 sec) [ -10049.3463] [ 2055] [depth= 2] . ( 17 sec) [ -10035.1619] [ 2052] [depth= 4] . ( 17 sec) [ -10027.9159] [ 2050] [depth= 1] . ( 17 sec) [ -10011.8910] [ 2050] [depth= 1] . ( 18 sec) [ -9980.3758] [ 2049] [depth= 2] . ( 18 sec) [ -9974.8987] [ 2048] [depth= 1] . ( 18 sec) [ -9974.6765] [ 2048] [depth= 1] . ( 18 sec) [ -9974.3322] [ 2048] [depth= 1] . ( 18 sec) [ -9937.7723] [ 2048] [depth= 2] . ( 18 sec) [ -9937.4962] [ 2048] [depth= 1] . ( 19 sec) [ -9706.3717] [Branch lengths ] . ( 21 sec) [ -9671.6621] [GTR parameters ] . ( 21 sec) [ -9669.4349] [Alpha ][ 0.444451] . ( 22 sec) [ -9669.4008] [ 2048] [depth= 1] . ( 22 sec) [ -9663.1570] [ 2044] [depth= 1] . ( 22 sec) [ -9659.3791] [ 2035] [depth= 1] . ( 22 sec) [ -9623.6255] [ 2019] [depth= 1] . ( 22 sec) [ -9622.7621] [ 2021] [depth= 1] . ( 23 sec) [ -9611.3595] [ 2018] [depth= 1] . ( 23 sec) [ -9600.1607] [ 2000] [depth= 2] . ( 23 sec) [ -9600.1238] [ 2000] [depth= 1] . ( 23 sec) [ -9599.9782] [ 2000] [depth= 1] . ( 24 sec) [ -9595.8246] [ 1999] [depth= 1] . ( 25 sec) [ -9595.0877] [ 1996] [depth= 1] . ( 25 sec) [ -9595.0511] [ 1995] [depth= 1] . ( 25 sec) [ -9594.6423] [ 1995] [depth= 1] . ( 26 sec) [ -9593.8268] [ 1995] [depth= 1] . ( 27 sec) [ -9593.8047] [ 1995] [depth= 2] . ( 27 sec) [ -9591.5318] [ 1995] [depth= 1] . ( 28 sec) [ -9586.9426] [ 1993] [depth= 1] . ( 28 sec) [ -9584.9649] [ 1993] [depth= 3] . ( 28 sec) [ -9583.3750] [ 1991] [depth= 1] . ( 28 sec) [ -9467.3129] [ 1946] [depth= 8] . ( 28 sec) [ -9462.7835] [ 1946] [depth= 1] . ( 29 sec) [ -9461.4402] [ 1947] [depth= 1] . ( 30 sec) [ -9460.3550] [ 1951] [depth= 1] . ( 30 sec) [ -9445.9670] [ 1936] [depth= 1] . ( 30 sec) [ -9445.9294] [ 1938] [depth= 1] . ( 30 sec) [ -9445.9003] [ 1938] [depth= 3] . ( 31 sec) [ -9445.7410] [ 1938] [depth= 1] . ( 31 sec) [ -9442.0959] [ 1938] [depth= 1] . ( 31 sec) [ -9442.0755] [ 1938] [depth= 1] . ( 32 sec) [ -9439.0084] [ 1937] [depth= 1] . ( 32 sec) [ -9437.2338] [ 1935] [depth= 1] . ( 32 sec) [ -9427.5302] [ 1935] [depth= 1] . ( 33 sec) [ -9427.5123] [ 1935] [depth= 2] . ( 33 sec) [ -9401.6087] [ 1907] [depth= 4] . ( 33 sec) [ -9284.1497] [ 1851] [depth= 2] . ( 34 sec) [ -9284.0333] [ 1851] [depth= 1] . ( 35 sec) [ -9284.0163] [ 1851] [depth= 1] . ( 36 sec) [ -9275.6078] [ 1839] [depth= 1] . ( 36 sec) [ -9235.7545] [ 1831] [depth= 1] . ( 36 sec) [ -9234.8210] [ 1842] [depth= 2] . ( 37 sec) [ -9232.5972] [ 1842] [depth= 1] . ( 37 sec) [ -9232.3900] [ 1842] [depth= 2] . ( 37 sec) [ -9230.9536] [ 1842] [depth= 2] . ( 38 sec) [ -9230.7284] [ 1842] [depth= 1] . ( 38 sec) [ -9168.5593] [Branch lengths ] . ( 40 sec) [ -9168.3009] [GTR parameters ] . ( 40 sec) [ -9167.9205] [Alpha ][ 0.467877] . ( 40 sec) [ -9167.8852] [ 1842] [depth= 1] . ( 41 sec) [ -9166.0936] [ 1840] [depth= 1] . ( 42 sec) [ -9163.9314] [ 1829] [depth= 1] . ( 42 sec) [ -9163.0583] [ 1829] [depth= 2] . ( 45 sec) [ -9162.9222] [ 1830] [depth= 2] . ( 47 sec) [ -9161.8694] [ 1830] [depth= 1] . ( 49 sec) [ -9161.8246] [ 1830] [depth= 1] . ( 49 sec) [ -9161.7946] [ 1830] [depth= 1] . ( 51 sec) [ -9161.7742] [ 1830] [depth= 1] . ( 54 sec) [ -9161.6382] [ 1830] [depth= 1] . ( 56 sec) [ -9140.4892] [Branch lengths ] . ( 56 sec) [ -9140.4416] [GTR parameters ] . ( 56 sec) [ -9140.3875] [Alpha ][ 0.477419] . ( 60 sec) [ -9140.3521] [ 1830] [depth= 1] . ( 72 sec) [ -9140.1544] [Branch lengths ] . ( 72 sec) [ -9140.1539] [GTR parameters ] . ( 72 sec) [ -9140.1458] [Alpha ][ 0.481140] . ( 131 sec) [ -9140.0930] [Branch lengths ] . ( 131 sec) [ -9140.0930] [Topology ] . ( 133 sec) [ -9140.0292] [Topology ] . ( 134 sec) [ -9139.6079] [Topology ] . ( 136 sec) [ -9137.4301] [Topology ] . ( 138 sec) [ -9134.8241] [Topology ] . ( 140 sec) [ -9133.2809] [Topology ] . ( 141 sec) [ -9132.5505] [Topology ] . ( 142 sec) [ -9132.5460] [GTR parameters ] . ( 142 sec) [ -9132.5405] [Alpha ][ 0.484229] . ( 142 sec) [ -9132.5405] [Topology ] . ( 144 sec) [ -9132.2102] [Topology ] . ( 145 sec) [ -9132.0670] [Topology ] . ( 147 sec) [ -9132.0108] [Topology ] . ( 149 sec) [ -9131.9895] [Topology ] . ( 150 sec) [ -9131.9819] [Topology ] . ( 152 sec) [ -9131.9790] [Topology ] . ( 153 sec) [ -9131.9784] [GTR parameters ] . ( 153 sec) [ -9131.9782] [Alpha ][ 0.484832] . ( 153 sec) [ -9131.9782] [Topology ] . ( 155 sec) [ -9131.9770] [Topology ] . ( 156 sec) [ -9131.9766] [Topology ] . ( 157 sec) [ -9131.9766] [GTR parameters ] . ( 157 sec) [ -9131.9766] [Alpha ][ 0.484832] . ( 157 sec) [ -9131.9766] [Topology ] . ( 158 sec) [ -9131.9764] [Topology ] . ( 159 sec) [ -9131.9764] [GTR parameters ] . ( 159 sec) [ -9131.9764] [Alpha ][ 0.484832] . Checking for NNIs, optimizing five branches... . ( 170 sec) [ -9131.5822] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9131.582180. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -60403.4107] [GTR parameters ] . ( 2 sec) [ -59257.5546] [Alpha ][ 0.500960] . ( 2 sec) [ -54934.6908] [ 6766] [depth= 7] . ( 2 sec) [ -52330.4085] [ 6687] [depth= 12] . ( 2 sec) [ -49628.4927] [ 6667] [depth= 9] . ( 2 sec) [ -49600.8158] [ 6580] [depth= 1] . ( 2 sec) [ -45865.2181] [ 6555] [depth= 5] . ( 2 sec) [ -45816.8636] [ 6541] [depth= 3] . ( 2 sec) [ -45367.5752] [ 6542] [depth= 5] . ( 2 sec) [ -44763.4668] [ 6462] [depth= 3] . ( 3 sec) [ -44209.0587] [ 6456] [depth= 1] . ( 3 sec) [ -44035.6896] [ 6429] [depth= 13] . ( 3 sec) [ -43733.3925] [ 6421] [depth= 4] . ( 3 sec) [ -42744.9384] [ 6309] [depth= 3] . ( 3 sec) [ -42729.3829] [ 6310] [depth= 1] . ( 3 sec) [ -42503.5965] [ 6277] [depth= 3] . ( 3 sec) [ -41737.5708] [ 6266] [depth= 13] . ( 3 sec) [ -41387.9956] [ 6174] [depth= 19] . ( 3 sec) [ -39832.2808] [ 6125] [depth= 19] . ( 3 sec) [ -38426.2312] [ 6090] [depth= 8] . ( 4 sec) [ -38135.6063] [ 6035] [depth= 14] . ( 4 sec) [ -37216.4941] [ 5926] [depth= 3] . ( 4 sec) [ -36763.1655] [ 5920] [depth= 4] . ( 4 sec) [ -36585.4358] [ 5888] [depth= 1] . ( 4 sec) [ -35762.5692] [ 5884] [depth= 21] . ( 4 sec) [ -35490.2233] [ 5882] [depth= 5] . ( 4 sec) [ -35376.2108] [ 5872] [depth= 1] . ( 4 sec) [ -35008.7333] [ 5815] [depth= 13] . ( 4 sec) [ -34610.6124] [ 5756] [depth= 1] . ( 4 sec) [ -34055.3226] [ 5679] [depth= 15] . ( 4 sec) [ -33642.4344] [ 5566] [depth= 15] . ( 5 sec) [ -33601.8299] [ 5569] [depth= 1] . ( 5 sec) [ -33250.0469] [ 5401] [depth= 5] . ( 5 sec) [ -32666.5675] [ 5401] [depth= 13] . ( 5 sec) [ -31777.7000] [ 5317] [depth= 9] . ( 5 sec) [ -28512.5574] [ 5303] [depth= 12] . ( 5 sec) [ -28440.8565] [ 5299] [depth= 1] . ( 5 sec) [ -28150.9936] [ 5198] [depth= 13] . ( 5 sec) [ -27741.2732] [ 5190] [depth= 3] . ( 5 sec) [ -27576.9614] [ 5167] [depth= 20] . ( 5 sec) [ -26368.9607] [ 5043] [depth= 17] . ( 6 sec) [ -26346.3946] [ 5043] [depth= 22] . ( 6 sec) [ -25179.2403] [ 4938] [depth= 21] . ( 6 sec) [ -24601.6764] [ 4878] [depth= 19] . ( 6 sec) [ -24060.1309] [ 4802] [depth= 1] . ( 6 sec) [ -23707.3096] [ 4723] [depth= 17] . ( 6 sec) [ -22936.2641] [ 4773] [depth= 11] . ( 6 sec) [ -22507.5698] [ 4676] [depth= 14] . ( 6 sec) [ -22476.4399] [ 4677] [depth= 2] . ( 6 sec) [ -22436.7520] [ 4678] [depth= 1] . ( 6 sec) [ -22406.9649] [ 4621] [depth= 1] . ( 7 sec) [ -22190.7909] [ 4592] [depth= 13] . ( 7 sec) [ -21989.1774] [ 4580] [depth= 11] . ( 7 sec) [ -21673.0529] [ 4580] [depth= 1] . ( 7 sec) [ -21551.2925] [ 4492] [depth= 16] . ( 7 sec) [ -21281.0727] [ 4431] [depth= 17] . ( 7 sec) [ -20839.8794] [ 4373] [depth= 4] . ( 7 sec) [ -20512.2740] [ 4373] [depth= 2] . ( 7 sec) [ -20347.1360] [ 4360] [depth= 3] . ( 7 sec) [ -20344.1102] [ 4318] [depth= 20] . ( 7 sec) [ -19830.0291] [ 4161] [depth= 13] . ( 8 sec) [ -19828.4058] [ 4164] [depth= 1] . ( 8 sec) [ -19527.2453] [ 4073] [depth= 10] . ( 8 sec) [ -19412.7634] [ 4053] [depth= 15] . ( 8 sec) [ -19361.0808] [ 4053] [depth= 5] . ( 8 sec) [ -19173.1597] [ 4026] [depth= 12] . ( 8 sec) [ -19170.8047] [ 4026] [depth= 1] . ( 8 sec) [ -19006.2795] [ 4009] [depth= 10] . ( 8 sec) [ -18974.2127] [ 4009] [depth= 2] . ( 8 sec) [ -18572.5878] [ 3888] [depth= 12] . ( 9 sec) [ -18559.5301] [ 3885] [depth= 1] . ( 9 sec) [ -17619.0271] [ 3751] [depth= 6] . ( 9 sec) [ -17615.4285] [ 3751] [depth= 1] . ( 9 sec) [ -17572.1579] [ 3751] [depth= 3] . ( 9 sec) [ -17087.0077] [ 3633] [depth= 7] . ( 9 sec) [ -16978.9138] [ 3634] [depth= 1] . ( 9 sec) [ -16894.0309] [ 3625] [depth= 2] . ( 9 sec) [ -16556.9375] [ 3484] [depth= 7] . ( 9 sec) [ -16460.3670] [ 3477] [depth= 11] . ( 9 sec) [ -16453.0977] [ 3465] [depth= 5] . ( 9 sec) [ -15974.4616] [ 3453] [depth= 4] . ( 10 sec) [ -15937.6151] [ 3451] [depth= 2] . ( 10 sec) [ -15893.8319] [ 3451] [depth= 1] . ( 10 sec) [ -15623.8681] [ 3402] [depth= 13] . ( 10 sec) [ -15623.0901] [ 3402] [depth= 4] . ( 10 sec) [ -15341.7227] [ 3331] [depth= 11] . ( 10 sec) [ -15300.1698] [ 3338] [depth= 1] . ( 10 sec) [ -15004.8283] [ 3219] [depth= 4] . ( 10 sec) [ -14851.5032] [ 3170] [depth= 8] . ( 10 sec) [ -14750.7571] [ 3148] [depth= 2] . ( 10 sec) [ -14556.5324] [ 3074] [depth= 5] . ( 11 sec) [ -14531.7977] [ 3074] [depth= 2] . ( 11 sec) [ -14431.6746] [ 3026] [depth= 9] . ( 11 sec) [ -14332.8603] [ 3018] [depth= 5] . ( 11 sec) [ -14284.7562] [ 3039] [depth= 3] . ( 11 sec) [ -14187.3448] [ 3039] [depth= 1] . ( 11 sec) [ -14179.0405] [ 3039] [depth= 12] . ( 11 sec) [ -14178.9774] [ 3040] [depth= 3] . ( 11 sec) [ -14174.8078] [ 3012] [depth= 1] . ( 11 sec) [ -13837.6862] [ 2946] [depth= 3] . ( 11 sec) [ -13767.7611] [ 2937] [depth= 5] . ( 11 sec) [ -13727.7419] [ 2867] [depth= 1] . ( 12 sec) [ -13727.5136] [ 2809] [depth= 10] . ( 12 sec) [ -13718.7643] [ 2810] [depth= 1] . ( 12 sec) [ -13673.7677] [ 2808] [depth= 3] . ( 12 sec) [ -13567.6177] [ 2792] [depth= 3] . ( 12 sec) [ -13343.3492] [ 2802] [depth= 1] . ( 12 sec) [ -13061.7441] [ 2745] [depth= 1] . ( 12 sec) [ -13007.7172] [ 2735] [depth= 5] . ( 12 sec) [ -12853.9364] [ 2719] [depth= 10] . ( 12 sec) [ -12838.8206] [ 2719] [depth= 1] . ( 12 sec) [ -12835.8427] [ 2718] [depth= 1] . ( 13 sec) [ -12835.2026] [ 2718] [depth= 1] . ( 13 sec) [ -12806.9456] [ 2696] [depth= 1] . ( 13 sec) [ -12497.0091] [ 2608] [depth= 9] . ( 13 sec) [ -12374.2913] [ 2518] [depth= 8] . ( 13 sec) [ -12372.0562] [ 2554] [depth= 2] . ( 13 sec) [ -12368.7991] [ 2554] [depth= 2] . ( 13 sec) [ -12356.0292] [ 2554] [depth= 1] . ( 13 sec) [ -12337.6900] [ 2553] [depth= 2] . ( 13 sec) [ -12042.9356] [ 2470] [depth= 10] . ( 13 sec) [ -12039.6652] [ 2472] [depth= 1] . ( 13 sec) [ -11844.7452] [ 2438] [depth= 5] . ( 14 sec) [ -11834.3942] [ 2401] [depth= 1] . ( 14 sec) [ -11787.6184] [ 2381] [depth= 9] . ( 14 sec) [ -11761.8344] [ 2383] [depth= 1] . ( 14 sec) [ -11760.2946] [ 2384] [depth= 1] . ( 14 sec) [ -11753.4425] [ 2384] [depth= 1] . ( 14 sec) [ -11748.1914] [ 2382] [depth= 2] . ( 14 sec) [ -11622.9558] [ 2345] [depth= 2] . ( 14 sec) [ -11614.6239] [ 2345] [depth= 1] . ( 14 sec) [ -11578.5297] [ 2322] [depth= 1] . ( 14 sec) [ -11576.9780] [ 2322] [depth= 3] . ( 14 sec) [ -11555.9208] [ 2322] [depth= 1] . ( 15 sec) [ -11555.6691] [ 2322] [depth= 2] . ( 15 sec) [ -11494.2778] [ 2275] [depth= 4] . ( 15 sec) [ -11437.0400] [ 2278] [depth= 1] . ( 15 sec) [ -11327.7534] [ 2251] [depth= 4] . ( 15 sec) [ -11003.1387] [ 2160] [depth= 3] . ( 15 sec) [ -10683.4625] [ 2160] [depth= 2] . ( 15 sec) [ -10679.6563] [ 2160] [depth= 1] . ( 15 sec) [ -10541.4297] [ 2144] [depth= 3] . ( 15 sec) [ -10534.7190] [ 2143] [depth= 4] . ( 15 sec) [ -10522.9217] [ 2143] [depth= 2] . ( 16 sec) [ -10520.3909] [ 2143] [depth= 3] . ( 16 sec) [ -10337.9502] [ 2097] [depth= 2] . ( 16 sec) [ -10334.5858] [ 2097] [depth= 1] . ( 16 sec) [ -10332.6472] [ 2097] [depth= 3] . ( 16 sec) [ -10332.2247] [ 2097] [depth= 2] . ( 16 sec) [ -10304.4796] [ 2073] [depth= 2] . ( 16 sec) [ -10255.6463] [ 2041] [depth= 3] . ( 16 sec) [ -10255.0310] [ 2041] [depth= 1] . ( 17 sec) [ -10194.5236] [ 2025] [depth= 1] . ( 17 sec) [ -10194.0366] [ 2025] [depth= 1] . ( 17 sec) [ -10193.1818] [ 2025] [depth= 1] . ( 17 sec) [ -10187.7183] [ 2025] [depth= 1] . ( 17 sec) [ -10152.6432] [ 2028] [depth= 2] . ( 17 sec) [ -10152.6234] [ 2028] [depth= 2] . ( 18 sec) [ -9630.8702] [Branch lengths ] . ( 20 sec) [ -9593.4109] [GTR parameters ] . ( 20 sec) [ -9592.5683] [Alpha ][ 0.466237] . ( 21 sec) [ -9585.0368] [ 2027] [depth= 1] . ( 21 sec) [ -9581.0275] [ 2024] [depth= 2] . ( 21 sec) [ -9573.4411] [ 2017] [depth= 2] . ( 21 sec) [ -9547.1543] [ 2001] [depth= 1] . ( 21 sec) [ -9443.8694] [ 1937] [depth= 5] . ( 21 sec) [ -9346.4092] [ 1905] [depth= 1] . ( 21 sec) [ -9345.7774] [ 1907] [depth= 1] . ( 21 sec) [ -9341.9496] [ 1903] [depth= 1] . ( 21 sec) [ -9339.8537] [ 1901] [depth= 1] . ( 22 sec) [ -9304.8125] [ 1871] [depth= 3] . ( 22 sec) [ -9283.7595] [ 1867] [depth= 1] . ( 22 sec) [ -9283.4526] [ 1867] [depth= 1] . ( 22 sec) [ -9283.4246] [ 1867] [depth= 1] . ( 22 sec) [ -9278.4702] [ 1868] [depth= 1] . ( 23 sec) [ -9274.3250] [ 1867] [depth= 1] . ( 23 sec) [ -9268.8317] [ 1866] [depth= 2] . ( 23 sec) [ -9265.8856] [ 1866] [depth= 1] . ( 23 sec) [ -9248.0366] [ 1861] [depth= 1] . ( 23 sec) [ -9246.7971] [ 1861] [depth= 1] . ( 24 sec) [ -9233.6207] [ 1873] [depth= 1] . ( 24 sec) [ -9233.2649] [ 1873] [depth= 1] . ( 24 sec) [ -9232.4502] [ 1872] [depth= 1] . ( 25 sec) [ -9231.6737] [ 1872] [depth= 1] . ( 25 sec) [ -9206.2932] [ 1857] [depth= 1] . ( 25 sec) [ -9206.2415] [ 1857] [depth= 2] . ( 26 sec) [ -9206.2280] [ 1857] [depth= 1] . ( 26 sec) [ -9201.6933] [ 1845] [depth= 1] . ( 26 sec) [ -9191.9631] [ 1830] [depth= 4] . ( 26 sec) [ -9191.9516] [ 1830] [depth= 1] . ( 26 sec) [ -9187.2324] [ 1835] [depth= 1] . ( 26 sec) [ -9182.7233] [ 1834] [depth= 1] . ( 27 sec) [ -9181.8499] [ 1834] [depth= 1] . ( 28 sec) [ -9181.7765] [ 1834] [depth= 1] . ( 28 sec) [ -9180.2734] [ 1838] [depth= 1] . ( 29 sec) [ -9180.1064] [ 1838] [depth= 1] . ( 29 sec) [ -9171.6937] [ 1843] [depth= 1] . ( 29 sec) [ -9171.0709] [ 1875] [depth= 1] . ( 30 sec) [ -9170.3903] [ 1871] [depth= 1] . ( 30 sec) [ -9170.3797] [ 1875] [depth= 1] . ( 30 sec) [ -9170.0427] [ 1879] [depth= 1] . ( 30 sec) [ -9169.8128] [ 1878] [depth= 1] . ( 31 sec) [ -9169.1453] [ 1878] [depth= 1] . ( 31 sec) [ -9169.0716] [ 1879] [depth= 1] . ( 31 sec) [ -9168.2656] [ 1875] [depth= 1] . ( 32 sec) [ -9168.2311] [ 1875] [depth= 2] . ( 34 sec) [ -9168.2086] [ 1875] [depth= 1] . ( 35 sec) [ -9168.1899] [ 1875] [depth= 1] . ( 36 sec) [ -9146.7328] [Branch lengths ] . ( 37 sec) [ -9146.1396] [GTR parameters ] . ( 37 sec) [ -9146.1328] [Alpha ][ 0.469474] . ( 38 sec) [ -9145.0351] [ 1872] [depth= 1] . ( 39 sec) [ -9144.9845] [ 1871] [depth= 1] . ( 39 sec) [ -9143.1359] [ 1872] [depth= 1] . ( 43 sec) [ -9142.8627] [ 1874] [depth= 2] . ( 43 sec) [ -9142.7837] [ 1874] [depth= 1] . ( 46 sec) [ -9140.2543] [ 1835] [depth= 4] . ( 46 sec) [ -9139.8508] [ 1837] [depth= 1] . ( 52 sec) [ -9133.8291] [Branch lengths ] . ( 53 sec) [ -9133.8214] [GTR parameters ] . ( 53 sec) [ -9133.7049] [Alpha ][ 0.483025] . ( 60 sec) [ -9133.4925] [ 1829] [depth= 1] . ( 70 sec) [ -9131.7337] [Branch lengths ] . ( 71 sec) [ -9131.7249] [GTR parameters ] . ( 72 sec) [ -9131.7198] [Alpha ][ 0.486003] . ( 88 sec) [ -9131.5657] [Branch lengths ] . ( 150 sec) [ -9131.5569] [Branch lengths ] . ( 150 sec) [ -9131.5569] [Topology ] . ( 152 sec) [ -9131.5561] [Topology ] . ( 153 sec) [ -9131.5555] [GTR parameters ] . ( 153 sec) [ -9131.5554] [Alpha ][ 0.486489] . ( 153 sec) [ -9131.5554] [Topology ] . ( 155 sec) [ -9131.5550] [Topology ] . ( 155 sec) [ -9131.5550] [GTR parameters ] . ( 155 sec) [ -9131.5550] [Alpha ][ 0.486489] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9131.555002. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -59425.0970] [GTR parameters ] . ( 2 sec) [ -58301.0113] [Alpha ][ 0.500960] . ( 2 sec) [ -57826.6763] [ 6475] [depth= 3] . ( 2 sec) [ -57805.2710] [ 6479] [depth= 1] . ( 2 sec) [ -56802.4970] [ 6375] [depth= 4] . ( 3 sec) [ -56199.8058] [ 6352] [depth= 3] . ( 3 sec) [ -56142.4973] [ 6340] [depth= 10] . ( 3 sec) [ -55841.8387] [ 6248] [depth= 4] . ( 3 sec) [ -55518.9631] [ 6227] [depth= 2] . ( 3 sec) [ -52206.5876] [ 6224] [depth= 1] . ( 3 sec) [ -51820.4016] [ 6198] [depth= 11] . ( 3 sec) [ -51148.4748] [ 6120] [depth= 8] . ( 3 sec) [ -50543.2228] [ 6125] [depth= 3] . ( 3 sec) [ -50394.0901] [ 6125] [depth= 2] . ( 3 sec) [ -50375.3809] [ 6122] [depth= 1] . ( 4 sec) [ -49495.9532] [ 6042] [depth= 15] . ( 4 sec) [ -49256.1839] [ 5991] [depth= 19] . ( 4 sec) [ -47347.0150] [ 5913] [depth= 15] . ( 4 sec) [ -44810.6437] [ 5824] [depth= 8] . ( 4 sec) [ -44570.8823] [ 5714] [depth= 2] . ( 4 sec) [ -44200.3700] [ 5675] [depth= 11] . ( 4 sec) [ -43628.1346] [ 5667] [depth= 2] . ( 4 sec) [ -43290.9725] [ 5666] [depth= 1] . ( 4 sec) [ -42756.3125] [ 5616] [depth= 3] . ( 4 sec) [ -41951.0326] [ 5612] [depth= 1] . ( 4 sec) [ -41602.4148] [ 5598] [depth= 10] . ( 5 sec) [ -41372.3991] [ 5598] [depth= 1] . ( 5 sec) [ -40869.5821] [ 5519] [depth= 14] . ( 5 sec) [ -40821.9030] [ 5518] [depth= 3] . ( 5 sec) [ -37808.1023] [ 5486] [depth= 5] . ( 5 sec) [ -37139.7113] [ 5517] [depth= 1] . ( 5 sec) [ -36289.2999] [ 5512] [depth= 4] . ( 5 sec) [ -36253.6859] [ 5493] [depth= 21] . ( 5 sec) [ -35867.3369] [ 5434] [depth= 17] . ( 5 sec) [ -35467.1223] [ 5289] [depth= 3] . ( 5 sec) [ -34786.9438] [ 5351] [depth= 1] . ( 6 sec) [ -33969.3252] [ 5303] [depth= 19] . ( 6 sec) [ -33884.5951] [ 5305] [depth= 1] . ( 6 sec) [ -33828.6322] [ 5307] [depth= 8] . ( 6 sec) [ -33513.4523] [ 5161] [depth= 14] . ( 6 sec) [ -32607.6223] [ 5158] [depth= 5] . ( 6 sec) [ -32587.0726] [ 5134] [depth= 7] . ( 6 sec) [ -31908.2204] [ 4989] [depth= 5] . ( 6 sec) [ -31477.3900] [ 4868] [depth= 5] . ( 6 sec) [ -30770.9986] [ 4771] [depth= 3] . ( 6 sec) [ -30504.1487] [ 4771] [depth= 1] . ( 7 sec) [ -30473.6122] [ 4766] [depth= 1] . ( 7 sec) [ -30399.0399] [ 4716] [depth= 10] . ( 7 sec) [ -29741.8528] [ 4707] [depth= 6] . ( 7 sec) [ -29236.0930] [ 4702] [depth= 1] . ( 7 sec) [ -29127.7769] [ 4659] [depth= 9] . ( 7 sec) [ -29105.6432] [ 4643] [depth= 1] . ( 7 sec) [ -28878.5457] [ 4644] [depth= 12] . ( 7 sec) [ -28812.6178] [ 4643] [depth= 1] . ( 7 sec) [ -28673.7221] [ 4581] [depth= 10] . ( 7 sec) [ -28604.7070] [ 4582] [depth= 1] . ( 8 sec) [ -27662.6229] [ 4409] [depth= 12] . ( 8 sec) [ -27497.8812] [ 4293] [depth= 20] . ( 8 sec) [ -27398.7629] [ 4278] [depth= 2] . ( 8 sec) [ -27305.2977] [ 4279] [depth= 2] . ( 8 sec) [ -27097.8839] [ 4200] [depth= 2] . ( 8 sec) [ -27021.7774] [ 4185] [depth= 9] . ( 8 sec) [ -26939.6570] [ 4189] [depth= 1] . ( 8 sec) [ -26929.7603] [ 4189] [depth= 1] . ( 8 sec) [ -26924.2165] [ 4185] [depth= 1] . ( 9 sec) [ -26916.3092] [ 4184] [depth= 1] . ( 9 sec) [ -26721.9932] [ 4126] [depth= 3] . ( 9 sec) [ -25987.7369] [ 4086] [depth= 11] . ( 9 sec) [ -25970.5953] [ 4086] [depth= 1] . ( 9 sec) [ -25952.5828] [ 4086] [depth= 1] . ( 9 sec) [ -25815.9435] [ 4035] [depth= 2] . ( 9 sec) [ -25647.4272] [ 4005] [depth= 9] . ( 9 sec) [ -25497.9957] [ 4005] [depth= 2] . ( 9 sec) [ -24920.3917] [ 3858] [depth= 3] . ( 9 sec) [ -24423.6786] [ 3757] [depth= 1] . ( 10 sec) [ -23911.4069] [ 3667] [depth= 15] . ( 10 sec) [ -23760.5183] [ 3667] [depth= 1] . ( 10 sec) [ -21914.2616] [ 3591] [depth= 10] . ( 10 sec) [ -21691.0810] [ 3521] [depth= 5] . ( 10 sec) [ -21254.9761] [ 3520] [depth= 1] . ( 10 sec) [ -21210.6873] [ 3514] [depth= 1] . ( 10 sec) [ -20281.6799] [ 3442] [depth= 4] . ( 10 sec) [ -20269.8972] [ 3442] [depth= 1] . ( 10 sec) [ -20268.4826] [ 3442] [depth= 1] . ( 11 sec) [ -19927.7208] [ 3395] [depth= 5] . ( 11 sec) [ -19927.3205] [ 3395] [depth= 1] . ( 11 sec) [ -19717.0983] [ 3375] [depth= 5] . ( 11 sec) [ -19696.8930] [ 3339] [depth= 1] . ( 11 sec) [ -19665.5317] [ 3340] [depth= 1] . ( 11 sec) [ -19504.5604] [ 3220] [depth= 7] . ( 11 sec) [ -19280.8437] [ 3220] [depth= 1] . ( 11 sec) [ -19040.1463] [ 3084] [depth= 10] . ( 11 sec) [ -18468.7318] [ 3147] [depth= 7] . ( 12 sec) [ -18339.8271] [ 3147] [depth= 1] . ( 12 sec) [ -18252.0186] [ 3151] [depth= 1] . ( 12 sec) [ -18159.5116] [ 3141] [depth= 3] . ( 12 sec) [ -18148.8567] [ 3141] [depth= 1] . ( 12 sec) [ -17998.4013] [ 3085] [depth= 7] . ( 12 sec) [ -17949.6653] [ 3085] [depth= 1] . ( 12 sec) [ -17075.2792] [ 3085] [depth= 1] . ( 12 sec) [ -16963.3765] [ 3073] [depth= 2] . ( 12 sec) [ -16805.3278] [ 3004] [depth= 6] . ( 13 sec) [ -16750.8506] [ 2978] [depth= 1] . ( 13 sec) [ -16663.2947] [ 2957] [depth= 4] . ( 13 sec) [ -16519.6330] [ 2918] [depth= 1] . ( 13 sec) [ -16494.2784] [ 2910] [depth= 3] . ( 13 sec) [ -16016.5986] [ 2928] [depth= 1] . ( 13 sec) [ -15463.3544] [ 2863] [depth= 3] . ( 13 sec) [ -15371.2728] [ 2870] [depth= 5] . ( 13 sec) [ -15207.0247] [ 2809] [depth= 7] . ( 13 sec) [ -14765.1572] [ 2783] [depth= 6] . ( 13 sec) [ -14590.5899] [ 2781] [depth= 6] . ( 14 sec) [ -14468.3947] [ 2791] [depth= 1] . ( 14 sec) [ -14468.2660] [ 2791] [depth= 4] . ( 14 sec) [ -13577.9488] [ 2702] [depth= 9] . ( 14 sec) [ -13576.1661] [ 2691] [depth= 1] . ( 14 sec) [ -13553.6587] [ 2686] [depth= 4] . ( 14 sec) [ -13497.9107] [ 2665] [depth= 2] . ( 14 sec) [ -13452.8037] [ 2668] [depth= 2] . ( 14 sec) [ -13432.3343] [ 2666] [depth= 1] . ( 14 sec) [ -13405.6929] [ 2675] [depth= 2] . ( 14 sec) [ -13395.4660] [ 2677] [depth= 1] . ( 15 sec) [ -13097.8718] [ 2567] [depth= 6] . ( 15 sec) [ -13084.0890] [ 2566] [depth= 4] . ( 15 sec) [ -12634.7666] [ 2446] [depth= 8] . ( 15 sec) [ -12625.6129] [ 2446] [depth= 2] . ( 15 sec) [ -12615.4674] [ 2446] [depth= 1] . ( 15 sec) [ -12609.8488] [ 2457] [depth= 1] . ( 15 sec) [ -12606.1219] [ 2457] [depth= 2] . ( 15 sec) [ -12545.4762] [ 2396] [depth= 5] . ( 15 sec) [ -12513.0892] [ 2366] [depth= 2] . ( 16 sec) [ -12490.9917] [ 2366] [depth= 1] . ( 16 sec) [ -12485.7188] [ 2363] [depth= 1] . ( 16 sec) [ -12298.3511] [ 2387] [depth= 1] . ( 16 sec) [ -12167.7479] [ 2343] [depth= 2] . ( 16 sec) [ -12164.0513] [ 2345] [depth= 2] . ( 16 sec) [ -12150.4008] [ 2345] [depth= 1] . ( 16 sec) [ -12149.6644] [ 2345] [depth= 2] . ( 16 sec) [ -12149.3637] [ 2345] [depth= 1] . ( 16 sec) [ -12148.5490] [ 2345] [depth= 1] . ( 17 sec) [ -12148.1709] [ 2345] [depth= 1] . ( 17 sec) [ -11990.4854] [ 2345] [depth= 3] . ( 17 sec) [ -11990.3918] [ 2345] [depth= 3] . ( 17 sec) [ -11984.8093] [ 2345] [depth= 1] . ( 17 sec) [ -11388.7711] [ 2349] [depth= 6] . ( 17 sec) [ -11274.9087] [ 2361] [depth= 1] . ( 17 sec) [ -11139.2067] [ 2361] [depth= 1] . ( 17 sec) [ -11137.6115] [ 2361] [depth= 1] . ( 18 sec) [ -10982.8935] [ 2288] [depth= 7] . ( 18 sec) [ -10950.7678] [ 2288] [depth= 2] . ( 18 sec) [ -10950.0029] [ 2288] [depth= 1] . ( 18 sec) [ -10949.9035] [ 2288] [depth= 1] . ( 18 sec) [ -10948.7737] [ 2290] [depth= 1] . ( 18 sec) [ -10935.2820] [ 2238] [depth= 4] . ( 18 sec) [ -10843.4260] [ 2173] [depth= 5] . ( 19 sec) [ -10277.8430] [ 2152] [depth= 2] . ( 19 sec) [ -10187.2556] [ 2152] [depth= 1] . ( 19 sec) [ -10138.0164] [ 2139] [depth= 1] . ( 19 sec) [ -10123.5312] [ 2139] [depth= 2] . ( 19 sec) [ -10110.3131] [ 2139] [depth= 1] . ( 19 sec) [ -10103.4027] [ 2139] [depth= 2] . ( 19 sec) [ -10096.6155] [ 2139] [depth= 1] . ( 19 sec) [ -10093.2020] [ 2139] [depth= 1] . ( 20 sec) [ -10084.9688] [ 2166] [depth= 2] . ( 20 sec) [ -10030.6717] [ 2166] [depth= 1] . ( 20 sec) [ -9811.9240] [Branch lengths ] . ( 22 sec) [ -9764.7902] [GTR parameters ] . ( 23 sec) [ -9761.0012] [Alpha ][ 0.433698] . ( 23 sec) [ -9680.9186] [ 2100] [depth= 7] . ( 23 sec) [ -9669.4925] [ 2108] [depth= 2] . ( 23 sec) [ -9662.3064] [ 2098] [depth= 4] . ( 23 sec) [ -9543.1044] [ 2045] [depth= 5] . ( 24 sec) [ -9543.0777] [ 2036] [depth= 1] . ( 24 sec) [ -9543.0639] [ 2036] [depth= 1] . ( 25 sec) [ -9543.0193] [ 2025] [depth= 1] . ( 25 sec) [ -9541.6150] [ 2025] [depth= 1] . ( 25 sec) [ -9524.5238] [ 2019] [depth= 3] . ( 25 sec) [ -9478.1056] [ 2010] [depth= 1] . ( 25 sec) [ -9431.0396] [ 2000] [depth= 3] . ( 25 sec) [ -9430.5098] [ 1999] [depth= 1] . ( 25 sec) [ -9429.3744] [ 1999] [depth= 3] . ( 26 sec) [ -9426.6454] [ 1997] [depth= 1] . ( 26 sec) [ -9425.7800] [ 1989] [depth= 1] . ( 26 sec) [ -9420.9288] [ 1988] [depth= 2] . ( 26 sec) [ -9413.6381] [ 1988] [depth= 1] . ( 27 sec) [ -9409.0599] [ 1988] [depth= 1] . ( 27 sec) [ -9408.9797] [ 1989] [depth= 1] . ( 27 sec) [ -9406.9622] [ 1988] [depth= 1] . ( 27 sec) [ -9404.8165] [ 1988] [depth= 1] . ( 27 sec) [ -9404.1278] [ 1988] [depth= 1] . ( 27 sec) [ -9403.9249] [ 1988] [depth= 1] . ( 28 sec) [ -9393.4162] [ 1983] [depth= 1] . ( 28 sec) [ -9385.1905] [ 1983] [depth= 1] . ( 28 sec) [ -9381.8806] [ 1985] [depth= 1] . ( 28 sec) [ -9381.7162] [ 1985] [depth= 1] . ( 29 sec) [ -9381.2076] [ 1985] [depth= 1] . ( 29 sec) [ -9381.0740] [ 1985] [depth= 1] . ( 29 sec) [ -9348.5046] [ 1977] [depth= 4] . ( 29 sec) [ -9348.4791] [ 1977] [depth= 1] . ( 30 sec) [ -9325.3843] [ 1965] [depth= 1] . ( 30 sec) [ -9323.0546] [ 1964] [depth= 1] . ( 30 sec) [ -9319.6766] [ 1964] [depth= 1] . ( 30 sec) [ -9308.2979] [ 1952] [depth= 1] . ( 31 sec) [ -9283.8844] [ 1922] [depth= 4] . ( 31 sec) [ -9279.4094] [ 1920] [depth= 1] . ( 32 sec) [ -9270.9930] [ 1914] [depth= 1] . ( 32 sec) [ -9260.6857] [ 1907] [depth= 5] . ( 32 sec) [ -9259.2071] [ 1908] [depth= 1] . ( 32 sec) [ -9259.1965] [ 1908] [depth= 1] . ( 32 sec) [ -9259.1022] [ 1908] [depth= 1] . ( 33 sec) [ -9258.8694] [ 1909] [depth= 3] . ( 33 sec) [ -9252.3136] [ 1915] [depth= 6] . ( 33 sec) [ -9249.8369] [ 1912] [depth= 1] . ( 34 sec) [ -9249.4039] [ 1912] [depth= 1] . ( 34 sec) [ -9249.3666] [ 1912] [depth= 2] . ( 34 sec) [ -9248.7598] [ 1912] [depth= 1] . ( 34 sec) [ -9240.0703] [ 1910] [depth= 1] . ( 34 sec) [ -9235.8050] [ 1911] [depth= 1] . ( 35 sec) [ -9234.4307] [ 1912] [depth= 1] . ( 35 sec) [ -9233.7295] [ 1901] [depth= 2] . ( 35 sec) [ -9233.6207] [ 1901] [depth= 1] . ( 35 sec) [ -9232.6849] [ 1900] [depth= 1] . ( 36 sec) [ -9232.6078] [ 1900] [depth= 1] . ( 36 sec) [ -9232.5934] [ 1900] [depth= 2] . ( 36 sec) [ -9232.5389] [ 1900] [depth= 1] . ( 38 sec) [ -9232.4316] [ 1883] [depth= 7] . ( 38 sec) [ -9232.4090] [ 1883] [depth= 1] . ( 38 sec) [ -9228.0269] [ 1859] [depth= 1] . ( 39 sec) [ -9227.0257] [ 1858] [depth= 6] . ( 39 sec) [ -9227.0151] [ 1858] [depth= 1] . ( 39 sec) [ -9226.9498] [ 1858] [depth= 1] . ( 40 sec) [ -9200.4292] [Branch lengths ] . ( 41 sec) [ -9199.3812] [GTR parameters ] . ( 41 sec) [ -9198.5608] [Alpha ][ 0.466314] . ( 42 sec) [ -9172.6451] [ 1844] [depth= 5] . ( 42 sec) [ -9162.1274] [ 1840] [depth= 2] . ( 42 sec) [ -9159.5450] [ 1839] [depth= 1] . ( 43 sec) [ -9156.6517] [ 1836] [depth= 1] . ( 44 sec) [ -9156.5345] [ 1836] [depth= 1] . ( 45 sec) [ -9155.4429] [ 1836] [depth= 1] . ( 45 sec) [ -9155.4297] [ 1840] [depth= 1] . ( 45 sec) [ -9155.1452] [ 1840] [depth= 1] . ( 46 sec) [ -9149.2520] [ 1837] [depth= 1] . ( 47 sec) [ -9148.9124] [ 1837] [depth= 1] . ( 48 sec) [ -9148.8700] [ 1837] [depth= 1] . ( 48 sec) [ -9148.8269] [ 1837] [depth= 1] . ( 51 sec) [ -9148.3581] [ 1829] [depth= 1] . ( 52 sec) [ -9145.4277] [ 1829] [depth= 1] . ( 54 sec) [ -9145.4157] [ 1829] [depth= 2] . ( 55 sec) [ -9144.8533] [ 1829] [depth= 1] . ( 55 sec) [ -9144.7061] [ 1829] [depth= 1] . ( 56 sec) [ -9133.1866] [Branch lengths ] . ( 57 sec) [ -9132.9515] [GTR parameters ] . ( 57 sec) [ -9132.7354] [Alpha ][ 0.484663] . ( 71 sec) [ -9131.8249] [Branch lengths ] . ( 126 sec) [ -9131.6474] [Branch lengths ] . ( 126 sec) [ -9131.6474] [Topology ] . ( 128 sec) [ -9131.6230] [Topology ] . ( 130 sec) [ -9131.6116] [Topology ] . ( 131 sec) [ -9131.6049] [Topology ] . ( 133 sec) [ -9131.6005] [Topology ] . ( 134 sec) [ -9131.5976] [Topology ] . ( 136 sec) [ -9131.5956] [Topology ] . ( 137 sec) [ -9131.5632] [GTR parameters ] . ( 137 sec) [ -9131.5623] [Alpha ][ 0.485921] . ( 138 sec) [ -9131.5623] [Topology ] . ( 139 sec) [ -9131.5587] [Topology ] . ( 141 sec) [ -9131.5573] [Topology ] . ( 143 sec) [ -9131.5564] [Topology ] . ( 143 sec) [ -9131.5562] [GTR parameters ] . ( 143 sec) [ -9131.5560] [Alpha ][ 0.486517] . ( 143 sec) [ -9131.5560] [Topology ] . ( 145 sec) [ -9131.5554] [Topology ] . ( 145 sec) [ -9131.5554] [GTR parameters ] . ( 145 sec) [ -9131.5554] [Alpha ][ 0.486517] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9131.555381. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -63043.5194] [GTR parameters ] . ( 3 sec) [ -61912.2532] [Alpha ][ 0.500960] . ( 3 sec) [ -61284.3095] [ 6689] [depth= 3] . ( 3 sec) [ -60311.1171] [ 6600] [depth= 14] . ( 3 sec) [ -59099.1962] [ 6584] [depth= 2] . ( 3 sec) [ -58466.8613] [ 6571] [depth= 7] . ( 3 sec) [ -55357.3763] [ 6510] [depth= 3] . ( 3 sec) [ -54586.1892] [ 6504] [depth= 10] . ( 3 sec) [ -54345.7836] [ 6482] [depth= 3] . ( 3 sec) [ -53718.2970] [ 6461] [depth= 3] . ( 3 sec) [ -53391.6647] [ 6412] [depth= 2] . ( 4 sec) [ -50803.2939] [ 6410] [depth= 8] . ( 4 sec) [ -50622.7368] [ 6405] [depth= 4] . ( 4 sec) [ -48035.7984] [ 6396] [depth= 4] . ( 4 sec) [ -47095.9679] [ 6317] [depth= 6] . ( 4 sec) [ -46800.7051] [ 6319] [depth= 7] . ( 4 sec) [ -46435.2717] [ 6288] [depth= 9] . ( 4 sec) [ -46244.4856] [ 6285] [depth= 3] . ( 4 sec) [ -46198.7253] [ 6232] [depth= 1] . ( 4 sec) [ -45923.6931] [ 6226] [depth= 2] . ( 4 sec) [ -45869.3739] [ 6210] [depth= 7] . ( 4 sec) [ -45341.0110] [ 6203] [depth= 1] . ( 4 sec) [ -44989.1644] [ 6161] [depth= 2] . ( 5 sec) [ -44867.6868] [ 6158] [depth= 20] . ( 5 sec) [ -44581.5139] [ 6074] [depth= 3] . ( 5 sec) [ -43751.5390] [ 6003] [depth= 14] . ( 5 sec) [ -43497.0008] [ 5925] [depth= 6] . ( 5 sec) [ -43019.2041] [ 5937] [depth= 1] . ( 5 sec) [ -42874.1976] [ 5937] [depth= 15] . ( 5 sec) [ -42847.0033] [ 5934] [depth= 1] . ( 5 sec) [ -42822.3642] [ 5934] [depth= 1] . ( 5 sec) [ -42708.1786] [ 5886] [depth= 17] . ( 5 sec) [ -42656.7588] [ 5907] [depth= 1] . ( 6 sec) [ -42540.3569] [ 5895] [depth= 13] . ( 6 sec) [ -42357.0815] [ 5830] [depth= 1] . ( 6 sec) [ -42347.1532] [ 5828] [depth= 2] . ( 6 sec) [ -39911.0299] [ 5806] [depth= 14] . ( 6 sec) [ -39476.1977] [ 5756] [depth= 5] . ( 6 sec) [ -38217.6138] [ 5665] [depth= 8] . ( 6 sec) [ -38118.5826] [ 5665] [depth= 8] . ( 6 sec) [ -37605.7446] [ 5655] [depth= 10] . ( 6 sec) [ -37124.1986] [ 5505] [depth= 8] . ( 6 sec) [ -36788.5289] [ 5403] [depth= 6] . ( 7 sec) [ -36728.8308] [ 5394] [depth= 2] . ( 7 sec) [ -36680.3953] [ 5389] [depth= 7] . ( 7 sec) [ -36048.4575] [ 5292] [depth= 16] . ( 7 sec) [ -36004.1504] [ 5293] [depth= 1] . ( 7 sec) [ -35576.3634] [ 5291] [depth= 10] . ( 7 sec) [ -34802.8512] [ 5165] [depth= 6] . ( 7 sec) [ -34198.2438] [ 5095] [depth= 11] . ( 7 sec) [ -33236.1616] [ 4986] [depth= 2] . ( 7 sec) [ -30582.0462] [ 4973] [depth= 3] . ( 7 sec) [ -30492.1222] [ 4969] [depth= 1] . ( 7 sec) [ -29876.8365] [ 4973] [depth= 1] . ( 8 sec) [ -29468.3136] [ 4817] [depth= 7] . ( 8 sec) [ -29465.1457] [ 4815] [depth= 1] . ( 8 sec) [ -29435.5179] [ 4810] [depth= 2] . ( 8 sec) [ -29360.4159] [ 4810] [depth= 4] . ( 8 sec) [ -28904.3644] [ 4796] [depth= 1] . ( 8 sec) [ -28581.1130] [ 4799] [depth= 4] . ( 8 sec) [ -28497.0505] [ 4745] [depth= 13] . ( 8 sec) [ -28408.3946] [ 4731] [depth= 10] . ( 8 sec) [ -28037.0652] [ 4617] [depth= 10] . ( 9 sec) [ -27853.4107] [ 4525] [depth= 4] . ( 9 sec) [ -27782.4575] [ 4525] [depth= 1] . ( 9 sec) [ -27736.1601] [ 4497] [depth= 1] . ( 9 sec) [ -27707.2185] [ 4489] [depth= 9] . ( 9 sec) [ -27705.7893] [ 4489] [depth= 3] . ( 9 sec) [ -27704.8198] [ 4489] [depth= 2] . ( 9 sec) [ -27293.6182] [ 4347] [depth= 20] . ( 9 sec) [ -27284.7119] [ 4348] [depth= 3] . ( 9 sec) [ -26826.1883] [ 4261] [depth= 6] . ( 9 sec) [ -26728.6870] [ 4259] [depth= 3] . ( 10 sec) [ -26728.6449] [ 4259] [depth= 1] . ( 10 sec) [ -26727.2102] [ 4258] [depth= 2] . ( 10 sec) [ -26596.5861] [ 4221] [depth= 1] . ( 10 sec) [ -26528.3570] [ 4192] [depth= 3] . ( 10 sec) [ -26395.2366] [ 4192] [depth= 1] . ( 10 sec) [ -26320.8254] [ 4192] [depth= 2] . ( 10 sec) [ -26276.6581] [ 4229] [depth= 3] . ( 10 sec) [ -25960.3938] [ 4116] [depth= 6] . ( 10 sec) [ -25267.3946] [ 3977] [depth= 9] . ( 10 sec) [ -25011.0405] [ 3919] [depth= 7] . ( 11 sec) [ -24956.7543] [ 3913] [depth= 1] . ( 11 sec) [ -24851.9225] [ 3917] [depth= 2] . ( 11 sec) [ -24807.9758] [ 3903] [depth= 1] . ( 11 sec) [ -24807.2821] [ 3903] [depth= 1] . ( 11 sec) [ -24266.5866] [ 3779] [depth= 6] . ( 11 sec) [ -24264.6557] [ 3779] [depth= 1] . ( 11 sec) [ -24054.7394] [ 3719] [depth= 13] . ( 11 sec) [ -24054.4374] [ 3719] [depth= 3] . ( 11 sec) [ -24054.3923] [ 3719] [depth= 3] . ( 11 sec) [ -23677.2413] [ 3633] [depth= 2] . ( 12 sec) [ -23650.2830] [ 3635] [depth= 6] . ( 12 sec) [ -23573.0569] [ 3635] [depth= 1] . ( 12 sec) [ -23527.5516] [ 3634] [depth= 5] . ( 12 sec) [ -23469.2277] [ 3637] [depth= 1] . ( 12 sec) [ -23469.2141] [ 3637] [depth= 2] . ( 12 sec) [ -23447.5855] [ 3634] [depth= 1] . ( 12 sec) [ -23447.5609] [ 3634] [depth= 3] . ( 12 sec) [ -23431.6796] [ 3611] [depth= 3] . ( 12 sec) [ -22443.7957] [ 3610] [depth= 2] . ( 13 sec) [ -22375.4781] [ 3570] [depth= 5] . ( 13 sec) [ -21977.1446] [ 3433] [depth= 9] . ( 13 sec) [ -21429.7812] [ 3341] [depth= 12] . ( 13 sec) [ -21377.6177] [ 3336] [depth= 7] . ( 13 sec) [ -18194.5129] [ 3339] [depth= 2] . ( 13 sec) [ -17266.1461] [ 3251] [depth= 3] . ( 13 sec) [ -16975.2799] [ 3235] [depth= 9] . ( 13 sec) [ -16961.1263] [ 3247] [depth= 1] . ( 13 sec) [ -16898.7000] [ 3247] [depth= 1] . ( 13 sec) [ -16898.6311] [ 3248] [depth= 1] . ( 14 sec) [ -16829.1717] [ 3241] [depth= 1] . ( 14 sec) [ -16543.2022] [ 3124] [depth= 5] . ( 14 sec) [ -15965.0342] [ 3121] [depth= 2] . ( 14 sec) [ -15311.7352] [ 2927] [depth= 3] . ( 14 sec) [ -14941.1318] [ 2878] [depth= 13] . ( 14 sec) [ -14924.5130] [ 2878] [depth= 1] . ( 14 sec) [ -14768.1967] [ 2878] [depth= 3] . ( 14 sec) [ -14670.4617] [ 2785] [depth= 5] . ( 14 sec) [ -14553.7764] [ 2856] [depth= 16] . ( 14 sec) [ -14553.7589] [ 2901] [depth= 1] . ( 14 sec) [ -13892.8415] [ 2818] [depth= 7] . ( 15 sec) [ -13783.0441] [ 2776] [depth= 2] . ( 15 sec) [ -13427.5955] [ 2746] [depth= 14] . ( 15 sec) [ -13419.0032] [ 2742] [depth= 1] . ( 15 sec) [ -13381.5841] [ 2726] [depth= 1] . ( 15 sec) [ -13008.9389] [ 2627] [depth= 20] . ( 15 sec) [ -12900.6835] [ 2593] [depth= 2] . ( 15 sec) [ -12800.8947] [ 2596] [depth= 3] . ( 15 sec) [ -12786.6182] [ 2596] [depth= 1] . ( 15 sec) [ -12664.6814] [ 2561] [depth= 3] . ( 15 sec) [ -12662.7596] [ 2562] [depth= 1] . ( 16 sec) [ -12021.0224] [ 2562] [depth= 2] . ( 16 sec) [ -11960.8724] [ 2565] [depth= 1] . ( 16 sec) [ -11937.1200] [ 2553] [depth= 1] . ( 16 sec) [ -11864.6826] [ 2545] [depth= 2] . ( 16 sec) [ -11792.0937] [ 2552] [depth= 17] . ( 16 sec) [ -11749.9483] [ 2540] [depth= 2] . ( 17 sec) [ -11696.5403] [ 2534] [depth= 1] . ( 17 sec) [ -11695.8176] [ 2534] [depth= 1] . ( 17 sec) [ -11678.8470] [ 2534] [depth= 23] . ( 17 sec) [ -11677.9324] [ 2535] [depth= 1] . ( 17 sec) [ -11673.9265] [ 2535] [depth= 1] . ( 17 sec) [ -11657.0643] [ 2535] [depth= 2] . ( 17 sec) [ -11654.9805] [ 2538] [depth= 1] . ( 17 sec) [ -11421.4214] [ 2484] [depth= 4] . ( 18 sec) [ -11421.2714] [ 2484] [depth= 1] . ( 18 sec) [ -11289.3326] [ 2420] [depth= 16] . ( 18 sec) [ -11220.0104] [ 2373] [depth= 4] . ( 18 sec) [ -10984.8049] [ 2397] [depth= 1] . ( 18 sec) [ -10983.6835] [ 2397] [depth= 1] . ( 18 sec) [ -10980.4815] [ 2397] [depth= 3] . ( 18 sec) [ -10978.7907] [ 2396] [depth= 2] . ( 18 sec) [ -10945.2633] [ 2398] [depth= 1] . ( 18 sec) [ -10931.8887] [ 2398] [depth= 1] . ( 19 sec) [ -10914.3218] [ 2399] [depth= 2] . ( 19 sec) [ -10257.0371] [Branch lengths ] . ( 22 sec) [ -10214.8620] [GTR parameters ] . ( 22 sec) [ -10198.0996] [Alpha ][ 0.370277] . ( 22 sec) [ -10197.2576] [ 2396] [depth= 1] . ( 22 sec) [ -10168.3087] [ 2396] [depth= 4] . ( 22 sec) [ -10166.3520] [ 2398] [depth= 1] . ( 22 sec) [ -10162.8720] [ 2397] [depth= 2] . ( 22 sec) [ -10101.2484] [ 2386] [depth= 2] . ( 22 sec) [ -10091.7238] [ 2386] [depth= 1] . ( 23 sec) [ -10091.5146] [ 2386] [depth= 1] . ( 23 sec) [ -10045.5406] [ 2351] [depth= 2] . ( 23 sec) [ -10021.9523] [ 2341] [depth= 1] . ( 23 sec) [ -9998.9315] [ 2338] [depth= 1] . ( 24 sec) [ -9997.1254] [ 2336] [depth= 1] . ( 24 sec) [ -9983.8654] [ 2322] [depth= 5] . ( 24 sec) [ -9966.5218] [ 2322] [depth= 1] . ( 24 sec) [ -9918.9198] [ 2291] [depth= 1] . ( 24 sec) [ -9910.2427] [ 2260] [depth= 3] . ( 24 sec) [ -9903.7504] [ 2260] [depth= 1] . ( 24 sec) [ -9759.8070] [ 2162] [depth= 2] . ( 24 sec) [ -9728.3369] [ 2151] [depth= 2] . ( 25 sec) [ -9728.1865] [ 2151] [depth= 2] . ( 25 sec) [ -9718.4158] [ 2155] [depth= 9] . ( 25 sec) [ -9718.3944] [ 2155] [depth= 1] . ( 25 sec) [ -9716.5253] [ 2154] [depth= 1] . ( 25 sec) [ -9684.2335] [ 2125] [depth= 3] . ( 26 sec) [ -9564.2816] [ 2035] [depth= 2] . ( 26 sec) [ -9560.5354] [ 2034] [depth= 1] . ( 26 sec) [ -9559.9570] [ 2034] [depth= 2] . ( 26 sec) [ -9549.9378] [ 2019] [depth= 3] . ( 26 sec) [ -9543.8499] [ 2017] [depth= 1] . ( 26 sec) [ -9542.7040] [ 2017] [depth= 1] . ( 27 sec) [ -9542.6282] [ 2017] [depth= 2] . ( 27 sec) [ -9540.2493] [ 2016] [depth= 3] . ( 27 sec) [ -9539.6299] [ 2016] [depth= 1] . ( 27 sec) [ -9539.6108] [ 2016] [depth= 3] . ( 27 sec) [ -9532.4713] [ 2011] [depth= 2] . ( 27 sec) [ -9532.0257] [ 2011] [depth= 2] . ( 28 sec) [ -9531.4992] [ 2011] [depth= 2] . ( 28 sec) [ -9530.1254] [ 2010] [depth= 2] . ( 28 sec) [ -9525.3151] [ 2010] [depth= 2] . ( 29 sec) [ -9481.5991] [ 2011] [depth= 1] . ( 29 sec) [ -9481.4785] [ 2011] [depth= 1] . ( 29 sec) [ -9480.9521] [ 2007] [depth= 1] . ( 30 sec) [ -9480.1418] [ 2006] [depth= 3] . ( 30 sec) [ -9479.6540] [ 2002] [depth= 1] . ( 31 sec) [ -9466.3391] [ 2002] [depth= 1] . ( 31 sec) [ -9403.0436] [ 1960] [depth= 1] . ( 31 sec) [ -9402.9166] [ 1960] [depth= 1] . ( 31 sec) [ -9402.8747] [ 1960] [depth= 1] . ( 32 sec) [ -9395.9260] [ 1959] [depth= 1] . ( 32 sec) [ -9395.9023] [ 1959] [depth= 1] . ( 32 sec) [ -9386.2231] [ 1939] [depth= 1] . ( 32 sec) [ -9280.3445] [ 1915] [depth= 4] . ( 32 sec) [ -9280.3191] [ 1915] [depth= 1] . ( 32 sec) [ -9278.6818] [ 1915] [depth= 1] . ( 33 sec) [ -9277.1555] [ 1915] [depth= 1] . ( 33 sec) [ -9260.5190] [ 1906] [depth= 1] . ( 33 sec) [ -9260.4715] [ 1906] [depth= 1] . ( 33 sec) [ -9259.9474] [ 1908] [depth= 1] . ( 34 sec) [ -9198.7020] [ 1899] [depth= 2] . ( 34 sec) [ -9198.6059] [ 1899] [depth= 1] . ( 34 sec) [ -9198.5347] [ 1899] [depth= 2] . ( 34 sec) [ -9198.2133] [ 1900] [depth= 1] . ( 34 sec) [ -9194.7615] [ 1899] [depth= 1] . ( 35 sec) [ -9187.9000] [ 1834] [depth= 6] . ( 35 sec) [ -9187.8890] [ 1834] [depth= 1] . ( 36 sec) [ -9187.8171] [ 1834] [depth= 1] . ( 36 sec) [ -9149.6801] [Branch lengths ] . ( 38 sec) [ -9147.9738] [GTR parameters ] . ( 38 sec) [ -9141.3292] [Alpha ][ 0.457066] . ( 40 sec) [ -9139.8587] [ 1832] [depth= 1] . ( 41 sec) [ -9137.7742] [ 1830] [depth= 1] . ( 42 sec) [ -9137.7615] [ 1830] [depth= 1] . ( 43 sec) [ -9137.7491] [ 1830] [depth= 3] . ( 48 sec) [ -9137.7378] [ 1830] [depth= 1] . ( 53 sec) [ -9132.8235] [Branch lengths ] . ( 54 sec) [ -9132.6201] [GTR parameters ] . ( 54 sec) [ -9132.3023] [Alpha ][ 0.479202] . ( 67 sec) [ -9132.2902] [ 1830] [depth= 1] . ( 68 sec) [ -9131.7770] [Branch lengths ] . ( 69 sec) [ -9131.7616] [GTR parameters ] . ( 69 sec) [ -9131.7432] [Alpha ][ 0.484848] . ( 94 sec) [ -9131.7299] [ 1829] [depth= 1] . ( 127 sec) [ -9131.5779] [Branch lengths ] . ( 128 sec) [ -9131.5767] [GTR parameters ] . ( 128 sec) [ -9131.5754] [Alpha ][ 0.486292] . ( 128 sec) [ -9131.5754] [Topology ] . ( 130 sec) [ -9131.5675] [Topology ] . ( 132 sec) [ -9131.5635] [Topology ] . ( 133 sec) [ -9131.5607] [Topology ] . ( 135 sec) [ -9131.5588] [Topology ] . ( 137 sec) [ -9131.5575] [Topology ] . ( 138 sec) [ -9131.5566] [Topology ] . ( 139 sec) [ -9131.5565] [GTR parameters ] . ( 139 sec) [ -9131.5565] [Alpha ][ 0.486779] . ( 139 sec) [ -9131.5565] [Topology ] . ( 140 sec) [ -9131.5558] [Topology ] . ( 141 sec) [ -9131.5557] [GTR parameters ] . ( 141 sec) [ -9131.5557] [Alpha ][ 0.486779] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9131.555748. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -57199.1441] [GTR parameters ] . ( 2 sec) [ -56145.3957] [Alpha ][ 0.500960] . ( 2 sec) [ -54595.6610] [ 6480] [depth= 11] . ( 3 sec) [ -52939.4794] [ 6391] [depth= 6] . ( 3 sec) [ -52677.5704] [ 6367] [depth= 9] . ( 3 sec) [ -52540.3232] [ 6367] [depth= 1] . ( 3 sec) [ -50714.3731] [ 6307] [depth= 5] . ( 3 sec) [ -50065.7771] [ 6279] [depth= 2] . ( 3 sec) [ -50040.8951] [ 6267] [depth= 7] . ( 3 sec) [ -49919.3921] [ 6267] [depth= 1] . ( 3 sec) [ -49746.0000] [ 6269] [depth= 8] . ( 3 sec) [ -49242.2603] [ 6271] [depth= 1] . ( 3 sec) [ -49122.0007] [ 6248] [depth= 7] . ( 3 sec) [ -48839.8674] [ 6166] [depth= 2] . ( 4 sec) [ -48632.0550] [ 6164] [depth= 8] . ( 4 sec) [ -45687.7870] [ 6149] [depth= 2] . ( 4 sec) [ -45493.6188] [ 6135] [depth= 4] . ( 4 sec) [ -44773.7154] [ 6078] [depth= 7] . ( 4 sec) [ -44368.1460] [ 6075] [depth= 8] . ( 4 sec) [ -44253.0166] [ 6040] [depth= 9] . ( 4 sec) [ -43507.1217] [ 6042] [depth= 5] . ( 4 sec) [ -43214.7867] [ 5996] [depth= 9] . ( 4 sec) [ -42738.9975] [ 5929] [depth= 21] . ( 4 sec) [ -39535.4814] [ 5848] [depth= 6] . ( 5 sec) [ -39518.2630] [ 5848] [depth= 4] . ( 5 sec) [ -38860.1100] [ 5761] [depth= 3] . ( 5 sec) [ -37874.3432] [ 5578] [depth= 9] . ( 5 sec) [ -37380.7794] [ 5567] [depth= 15] . ( 5 sec) [ -37147.0002] [ 5490] [depth= 21] . ( 5 sec) [ -36903.1479] [ 5491] [depth= 3] . ( 5 sec) [ -36386.5315] [ 5415] [depth= 13] . ( 5 sec) [ -32887.0595] [ 5372] [depth= 1] . ( 5 sec) [ -32526.5757] [ 5240] [depth= 13] . ( 5 sec) [ -32392.5268] [ 5239] [depth= 2] . ( 6 sec) [ -32390.1724] [ 5239] [depth= 1] . ( 6 sec) [ -32390.1445] [ 5239] [depth= 1] . ( 6 sec) [ -32314.7144] [ 5238] [depth= 5] . ( 6 sec) [ -32089.1429] [ 5195] [depth= 5] . ( 6 sec) [ -32079.8694] [ 5158] [depth= 8] . ( 6 sec) [ -31856.6168] [ 5035] [depth= 5] . ( 6 sec) [ -31779.4299] [ 5034] [depth= 2] . ( 6 sec) [ -31407.5824] [ 4966] [depth= 8] . ( 6 sec) [ -31404.9858] [ 4966] [depth= 2] . ( 6 sec) [ -31168.1816] [ 4881] [depth= 8] . ( 7 sec) [ -30911.1691] [ 4863] [depth= 8] . ( 7 sec) [ -30721.0128] [ 4836] [depth= 13] . ( 7 sec) [ -30690.2685] [ 4836] [depth= 2] . ( 7 sec) [ -30402.0390] [ 4705] [depth= 10] . ( 7 sec) [ -27841.7760] [ 4705] [depth= 9] . ( 7 sec) [ -27555.4348] [ 4580] [depth= 10] . ( 7 sec) [ -27472.3601] [ 4580] [depth= 2] . ( 7 sec) [ -27394.7640] [ 4580] [depth= 1] . ( 7 sec) [ -27234.6996] [ 4621] [depth= 15] . ( 7 sec) [ -27194.2537] [ 4616] [depth= 4] . ( 8 sec) [ -24607.0455] [ 4607] [depth= 2] . ( 8 sec) [ -24201.8802] [ 4491] [depth= 7] . ( 8 sec) [ -22960.9530] [ 4433] [depth= 9] . ( 8 sec) [ -22209.7842] [ 4360] [depth= 19] . ( 8 sec) [ -21853.5832] [ 4362] [depth= 1] . ( 8 sec) [ -21502.6466] [ 4301] [depth= 5] . ( 8 sec) [ -21281.8345] [ 4290] [depth= 1] . ( 8 sec) [ -21210.0677] [ 4208] [depth= 2] . ( 8 sec) [ -20871.4419] [ 4119] [depth= 11] . ( 9 sec) [ -20835.5122] [ 4119] [depth= 1] . ( 9 sec) [ -20797.8804] [ 4105] [depth= 17] . ( 9 sec) [ -20114.7402] [ 4027] [depth= 20] . ( 9 sec) [ -20067.3483] [ 4036] [depth= 1] . ( 9 sec) [ -19903.8077] [ 3990] [depth= 7] . ( 9 sec) [ -19778.8238] [ 3945] [depth= 5] . ( 9 sec) [ -18401.3609] [ 3826] [depth= 9] . ( 9 sec) [ -18396.3726] [ 3826] [depth= 1] . ( 9 sec) [ -18198.3533] [ 3838] [depth= 1] . ( 9 sec) [ -17820.5425] [ 3703] [depth= 4] . ( 10 sec) [ -17228.0251] [ 3608] [depth= 8] . ( 10 sec) [ -17074.2888] [ 3611] [depth= 2] . ( 10 sec) [ -16366.1882] [ 3594] [depth= 7] . ( 10 sec) [ -16359.3725] [ 3594] [depth= 1] . ( 10 sec) [ -16319.0031] [ 3594] [depth= 2] . ( 10 sec) [ -15952.6659] [ 3501] [depth= 1] . ( 10 sec) [ -15942.0494] [ 3500] [depth= 1] . ( 10 sec) [ -15788.1614] [ 3461] [depth= 5] . ( 10 sec) [ -15715.3083] [ 3460] [depth= 1] . ( 10 sec) [ -15715.2426] [ 3460] [depth= 8] . ( 10 sec) [ -15715.1502] [ 3464] [depth= 1] . ( 11 sec) [ -15692.7202] [ 3464] [depth= 3] . ( 11 sec) [ -15380.5938] [ 3437] [depth= 14] . ( 11 sec) [ -15150.5749] [ 3337] [depth= 8] . ( 11 sec) [ -14880.9697] [ 3356] [depth= 12] . ( 11 sec) [ -14880.1156] [ 3318] [depth= 6] . ( 11 sec) [ -14673.0160] [ 3280] [depth= 8] . ( 11 sec) [ -14663.1048] [ 3280] [depth= 1] . ( 11 sec) [ -14332.3006] [ 3253] [depth= 1] . ( 12 sec) [ -14211.2918] [ 3239] [depth= 3] . ( 12 sec) [ -14054.3337] [ 3239] [depth= 1] . ( 12 sec) [ -13910.4050] [ 3195] [depth= 2] . ( 12 sec) [ -13590.1112] [ 3027] [depth= 8] . ( 12 sec) [ -13294.7460] [ 2914] [depth= 8] . ( 12 sec) [ -13284.6671] [ 2883] [depth= 1] . ( 12 sec) [ -13261.3316] [ 2886] [depth= 1] . ( 12 sec) [ -13261.1813] [ 2886] [depth= 1] . ( 12 sec) [ -12873.8521] [ 2788] [depth= 7] . ( 13 sec) [ -12779.1281] [ 2752] [depth= 3] . ( 13 sec) [ -12757.1022] [ 2752] [depth= 1] . ( 13 sec) [ -12744.9275] [ 2749] [depth= 1] . ( 13 sec) [ -12728.6401] [ 2749] [depth= 1] . ( 13 sec) [ -12605.5848] [ 2724] [depth= 3] . ( 13 sec) [ -12490.2727] [ 2720] [depth= 2] . ( 13 sec) [ -12348.8713] [ 2656] [depth= 10] . ( 13 sec) [ -12331.7162] [ 2656] [depth= 1] . ( 13 sec) [ -12326.8621] [ 2651] [depth= 1] . ( 13 sec) [ -12215.2176] [ 2649] [depth= 1] . ( 13 sec) [ -12207.5819] [ 2648] [depth= 1] . ( 14 sec) [ -12202.0644] [ 2646] [depth= 1] . ( 14 sec) [ -12159.7150] [ 2646] [depth= 5] . ( 14 sec) [ -12134.9038] [ 2636] [depth= 1] . ( 14 sec) [ -12133.5337] [ 2636] [depth= 1] . ( 14 sec) [ -12130.8069] [ 2636] [depth= 1] . ( 14 sec) [ -12130.5940] [ 2636] [depth= 3] . ( 14 sec) [ -12130.5370] [ 2636] [depth= 4] . ( 14 sec) [ -11955.1254] [ 2623] [depth= 2] . ( 15 sec) [ -11903.7099] [ 2623] [depth= 1] . ( 15 sec) [ -11896.7719] [ 2623] [depth= 2] . ( 15 sec) [ -11814.6946] [ 2600] [depth= 1] . ( 15 sec) [ -11785.7699] [ 2561] [depth= 3] . ( 15 sec) [ -11766.9969] [ 2561] [depth= 1] . ( 15 sec) [ -11751.9002] [ 2560] [depth= 1] . ( 15 sec) [ -11631.0078] [ 2500] [depth= 3] . ( 15 sec) [ -11491.5929] [ 2490] [depth= 1] . ( 15 sec) [ -11431.8053] [ 2481] [depth= 2] . ( 15 sec) [ -11329.6603] [ 2432] [depth= 5] . ( 16 sec) [ -11326.2866] [ 2435] [depth= 1] . ( 16 sec) [ -11322.4763] [ 2435] [depth= 1] . ( 16 sec) [ -11321.8486] [ 2435] [depth= 1] . ( 16 sec) [ -11300.0348] [ 2422] [depth= 1] . ( 16 sec) [ -11297.6627] [ 2422] [depth= 1] . ( 16 sec) [ -11283.4648] [ 2432] [depth= 1] . ( 16 sec) [ -11063.0464] [ 2349] [depth= 2] . ( 16 sec) [ -10706.3948] [ 2279] [depth= 7] . ( 16 sec) [ -10677.9061] [ 2281] [depth= 9] . ( 17 sec) [ -10650.8088] [ 2252] [depth= 6] . ( 17 sec) [ -10620.2905] [ 2252] [depth= 1] . ( 17 sec) [ -10620.1842] [ 2252] [depth= 1] . ( 17 sec) [ -10619.3842] [ 2252] [depth= 1] . ( 17 sec) [ -10619.2392] [ 2252] [depth= 1] . ( 17 sec) [ -10606.3266] [ 2251] [depth= 1] . ( 17 sec) [ -10469.8353] [ 2251] [depth= 2] . ( 17 sec) [ -10455.1892] [ 2253] [depth= 4] . ( 18 sec) [ -10444.9306] [ 2253] [depth= 1] . ( 18 sec) [ -10433.9324] [ 2252] [depth= 3] . ( 19 sec) [ -9863.5832] [Branch lengths ] . ( 21 sec) [ -9817.8861] [GTR parameters ] . ( 21 sec) [ -9809.9799] [Alpha ][ 0.406724] . ( 21 sec) [ -9809.8793] [ 2251] [depth= 1] . ( 22 sec) [ -9809.1001] [ 2251] [depth= 2] . ( 22 sec) [ -9808.7556] [ 2249] [depth= 1] . ( 22 sec) [ -9808.3437] [ 2243] [depth= 1] . ( 22 sec) [ -9808.3305] [ 2242] [depth= 2] . ( 22 sec) [ -9808.0324] [ 2227] [depth= 8] . ( 22 sec) [ -9805.1444] [ 2221] [depth= 11] . ( 23 sec) [ -9779.7649] [ 2215] [depth= 1] . ( 23 sec) [ -9778.5067] [ 2215] [depth= 1] . ( 23 sec) [ -9700.8747] [ 2161] [depth= 10] . ( 23 sec) [ -9668.3590] [ 2141] [depth= 1] . ( 23 sec) [ -9661.3399] [ 2139] [depth= 1] . ( 23 sec) [ -9661.2749] [ 2139] [depth= 1] . ( 23 sec) [ -9658.3437] [ 2141] [depth= 4] . ( 24 sec) [ -9649.5778] [ 2066] [depth= 8] . ( 24 sec) [ -9648.4604] [ 2066] [depth= 1] . ( 24 sec) [ -9645.7421] [ 2064] [depth= 1] . ( 24 sec) [ -9645.1256] [ 2059] [depth= 1] . ( 25 sec) [ -9645.0852] [ 2059] [depth= 2] . ( 25 sec) [ -9644.3579] [ 2057] [depth= 4] . ( 25 sec) [ -9469.6226] [ 1984] [depth= 10] . ( 25 sec) [ -9465.5799] [ 1983] [depth= 1] . ( 25 sec) [ -9462.3231] [ 1985] [depth= 1] . ( 26 sec) [ -9462.2079] [ 1985] [depth= 1] . ( 26 sec) [ -9433.6355] [ 1966] [depth= 2] . ( 26 sec) [ -9433.1376] [ 1966] [depth= 1] . ( 27 sec) [ -9433.1072] [ 1965] [depth= 1] . ( 27 sec) [ -9399.1864] [ 1921] [depth= 3] . ( 27 sec) [ -9392.1648] [ 1921] [depth= 1] . ( 28 sec) [ -9382.7958] [ 1917] [depth= 1] . ( 28 sec) [ -9378.8179] [ 1916] [depth= 1] . ( 29 sec) [ -9377.4268] [ 1914] [depth= 1] . ( 29 sec) [ -9375.6261] [ 1914] [depth= 1] . ( 29 sec) [ -9363.1032] [ 1914] [depth= 1] . ( 29 sec) [ -9363.0898] [ 1914] [depth= 1] . ( 30 sec) [ -9363.0796] [ 1914] [depth= 1] . ( 30 sec) [ -9362.6351] [ 1914] [depth= 1] . ( 31 sec) [ -9346.8650] [ 1912] [depth= 1] . ( 31 sec) [ -9346.7151] [ 1912] [depth= 1] . ( 31 sec) [ -9346.3806] [ 1914] [depth= 1] . ( 32 sec) [ -9344.7572] [ 1912] [depth= 1] . ( 32 sec) [ -9344.6832] [ 1912] [depth= 2] . ( 33 sec) [ -9344.6348] [ 1912] [depth= 1] . ( 33 sec) [ -9340.0416] [ 1913] [depth= 1] . ( 33 sec) [ -9338.3147] [ 1912] [depth= 1] . ( 33 sec) [ -9337.2931] [ 1908] [depth= 1] . ( 35 sec) [ -9247.5244] [ 1860] [depth= 2] . ( 35 sec) [ -9245.7954] [ 1859] [depth= 1] . ( 35 sec) [ -9200.9734] [ 1831] [depth= 3] . ( 35 sec) [ -9187.7307] [ 1836] [depth= 1] . ( 35 sec) [ -9173.6970] [ 1831] [depth= 1] . ( 36 sec) [ -9173.5181] [ 1831] [depth= 1] . ( 37 sec) [ -9173.5070] [ 1831] [depth= 1] . ( 37 sec) [ -9167.8705] [ 1830] [depth= 2] . ( 38 sec) [ -9144.2594] [Branch lengths ] . ( 40 sec) [ -9143.3403] [GTR parameters ] . ( 40 sec) [ -9140.4264] [Alpha ][ 0.467999] . ( 42 sec) [ -9139.7967] [ 1829] [depth= 1] . ( 44 sec) [ -9136.2549] [ 1829] [depth= 1] . ( 46 sec) [ -9135.8691] [ 1829] [depth= 1] . ( 49 sec) [ -9135.8535] [ 1829] [depth= 1] . ( 51 sec) [ -9135.7211] [ 1829] [depth= 1] . ( 57 sec) [ -9132.1868] [Branch lengths ] . ( 58 sec) [ -9132.1137] [GTR parameters ] . ( 58 sec) [ -9131.9815] [Alpha ][ 0.482361] . ( 75 sec) [ -9131.6183] [Branch lengths ] . ( 138 sec) [ -9131.5869] [Branch lengths ] . ( 138 sec) [ -9131.5869] [Topology ] . ( 140 sec) [ -9131.5835] [Topology ] . ( 141 sec) [ -9131.5819] [Topology ] . ( 143 sec) [ -9131.5808] [Topology ] . ( 145 sec) [ -9131.5801] [Topology ] . ( 146 sec) [ -9131.5655] [GTR parameters ] . ( 146 sec) [ -9131.5599] [Alpha ][ 0.485486] . ( 146 sec) [ -9131.5599] [Topology ] . ( 148 sec) [ -9131.5567] [Topology ] . ( 149 sec) [ -9131.5561] [Topology ] . ( 150 sec) [ -9131.5559] [GTR parameters ] . ( 150 sec) [ -9131.5555] [Alpha ][ 0.486327] . ( 150 sec) [ -9131.5555] [Topology ] . ( 152 sec) [ -9131.5550] [Topology ] . ( 152 sec) [ -9131.5550] [GTR parameters ] . ( 152 sec) [ -9131.5550] [Alpha ][ 0.486814] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9131.554990. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 4 sec) [ -9359.5522] [GTR parameters ] . ( 4 sec) [ -9317.1831] [Alpha ][ 0.504181] . ( 4 sec) [ -9317.1831] [Topology ] . ( 6 sec) [ -9164.4237] [Topology ] . ( 8 sec) [ -9148.3480] [Topology ] . ( 9 sec) [ -9145.2237] [Topology ] . ( 11 sec) [ -9144.2204] [Topology ] . ( 13 sec) [ -9143.8194] [Topology ] . ( 15 sec) [ -9143.4921] [Topology ] . ( 16 sec) [ -9142.5506] [Topology ] . ( 18 sec) [ -9140.3922] [Topology ] . Checking for NNIs, optimizing five branches... . ( 30 sec) [ -9139.8066] [Topology ] . ( 33 sec) [ -9133.7956] [GTR parameters ] . ( 33 sec) [ -9133.7578] [Alpha ][ 0.496003] . ( 33 sec) [ -9133.7578] [Topology ] . ( 35 sec) [ -9132.4617] [Topology ] . ( 36 sec) [ -9132.3132] [Topology ] . ( 38 sec) [ -9132.2662] [Topology ] . ( 40 sec) [ -9132.2468] [Topology ] . ( 41 sec) [ -9132.2379] [Topology ] . ( 43 sec) [ -9132.2334] [Topology ] . Checking for NNIs, optimizing five branches... . ( 55 sec) [ -9131.6484] [Topology ] . ( 57 sec) [ -9131.6026] [GTR parameters ] . ( 57 sec) [ -9131.5779] [Alpha ][ 0.489167] . ( 57 sec) [ -9131.5779] [Topology ] . ( 59 sec) [ -9131.5633] [Topology ] . ( 60 sec) [ -9131.5605] [Topology ] . ( 62 sec) [ -9131.5593] [Topology ] . ( 64 sec) [ -9131.5585] [Topology ] . Checking for NNIs, optimizing five branches... . ( 76 sec) [ -9131.5572] [GTR parameters ] . ( 76 sec) [ -9131.5554] [Alpha ][ 0.487312] . ( 76 sec) [ -9131.5554] [Topology ] . ( 78 sec) [ -9131.5542] [Topology ] . ( 79 sec) [ -9131.5538] [Topology ] . Checking for NNIs, optimizing five branches... . ( 92 sec) [ -9131.5537] [GTR parameters ] . ( 92 sec) [ -9131.5536] [Alpha ][ 0.486824] . ( 92 sec) [ -9131.5536] [Topology ] . ( 93 sec) [ -9131.5533] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 120 sec) [ -9359.5522] [GTR parameters ] . ( 120 sec) [ -9317.1831] [Alpha ][ 0.504181] . ( 121 sec) [ -9317.1645] [ 1834] [depth= 1] . ( 121 sec) [ -9315.6040] [ 1834] [depth= 1] . ( 121 sec) [ -9315.1052] [ 1833] [depth= 1] . ( 122 sec) [ -9315.0255] [ 1833] [depth= 1] . ( 122 sec) [ -9314.3793] [ 1833] [depth= 1] . ( 122 sec) [ -9314.2353] [ 1833] [depth= 1] . ( 123 sec) [ -9262.9945] [ 1860] [depth= 1] . ( 123 sec) [ -9248.7438] [ 1833] [depth= 1] . ( 123 sec) [ -9247.9524] [ 1833] [depth= 1] . ( 123 sec) [ -9247.8331] [ 1833] [depth= 1] . ( 124 sec) [ -9247.8211] [ 1833] [depth= 1] . ( 124 sec) [ -9247.8078] [ 1833] [depth= 1] . ( 124 sec) [ -9235.3607] [ 1830] [depth= 1] . ( 124 sec) [ -9234.3904] [ 1833] [depth= 1] . ( 124 sec) [ -9233.9232] [ 1830] [depth= 1] . ( 125 sec) [ -9233.1588] [ 1830] [depth= 2] . ( 125 sec) [ -9233.0346] [ 1830] [depth= 1] . ( 125 sec) [ -9232.9893] [ 1830] [depth= 1] . ( 125 sec) [ -9232.9739] [ 1830] [depth= 1] . ( 126 sec) [ -9232.9450] [ 1830] [depth= 3] . ( 128 sec) [ -9231.8949] [ 1832] [depth= 1] . ( 128 sec) [ -9229.6619] [ 1830] [depth= 1] . ( 129 sec) [ -9215.3303] [ 1835] [depth= 1] . ( 129 sec) [ -9204.6040] [ 1830] [depth= 1] . ( 129 sec) [ -9188.8289] [ 1829] [depth= 1] . ( 130 sec) [ -9188.7212] [ 1829] [depth= 1] . ( 130 sec) [ -9187.8323] [ 1829] [depth= 1] . ( 130 sec) [ -9187.7954] [ 1829] [depth= 1] . ( 131 sec) [ -9184.3888] [ 1829] [depth= 1] . ( 131 sec) [ -9179.3403] [ 1840] [depth= 1] . ( 132 sec) [ -9177.1602] [ 1829] [depth= 1] . ( 132 sec) [ -9174.3976] [ 1832] [depth= 1] . ( 133 sec) [ -9174.2815] [ 1832] [depth= 1] . ( 133 sec) [ -9173.9300] [ 1832] [depth= 1] . ( 133 sec) [ -9173.6882] [ 1832] [depth= 1] . ( 135 sec) [ -9171.2726] [ 1835] [depth= 1] . ( 135 sec) [ -9170.1518] [ 1832] [depth= 1] . ( 135 sec) [ -9170.1235] [ 1832] [depth= 1] . ( 135 sec) [ -9170.0995] [ 1832] [depth= 1] . ( 137 sec) [ -9149.5675] [Branch lengths ] . ( 139 sec) [ -9144.1259] [GTR parameters ] . ( 139 sec) [ -9144.1055] [Alpha ][ 0.497716] . ( 142 sec) [ -9144.0484] [ 1832] [depth= 1] . ( 143 sec) [ -9143.1183] [ 1829] [depth= 1] . ( 149 sec) [ -9143.0920] [ 1829] [depth= 1] . ( 155 sec) [ -9136.8309] [Branch lengths ] . ( 158 sec) [ -9136.7563] [GTR parameters ] . ( 158 sec) [ -9136.7065] [Alpha ][ 0.488466] . ( 166 sec) [ -9136.6799] [ 1829] [depth= 1] . ( 171 sec) [ -9136.0985] [Branch lengths ] . ( 172 sec) [ -9136.0933] [GTR parameters ] . ( 172 sec) [ -9136.0920] [Alpha ][ 0.486910] . ( 227 sec) [ -9135.9733] [Branch lengths ] . ( 227 sec) [ -9135.9733] [Topology ] . ( 229 sec) [ -9135.8505] [Topology ] . ( 230 sec) [ -9135.2320] [Topology ] . ( 232 sec) [ -9133.1923] [Topology ] . ( 234 sec) [ -9131.6586] [Topology ] . ( 235 sec) [ -9131.5822] [Topology ] . ( 237 sec) [ -9131.5678] [Topology ] . ( 238 sec) [ -9131.5600] [GTR parameters ] . ( 238 sec) [ -9131.5600] [Alpha ][ 0.486910] . ( 238 sec) [ -9131.5600] [Topology ] . ( 240 sec) [ -9131.5560] [Topology ] . ( 241 sec) [ -9131.5546] [Topology ] . ( 243 sec) [ -9131.5540] [Topology ] . ( 243 sec) [ -9131.5539] [GTR parameters ] . ( 243 sec) [ -9131.5539] [Alpha ][ 0.486910] . ( 244 sec) [ -9131.5539] [Topology ] . ( 245 sec) [ -9131.5535] [Topology ] . ( 245 sec) [ -9131.5535] [GTR parameters ] . ( 246 sec) [ -9131.5535] [Alpha ][ 0.486910] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9131.553329 . Log likelihood obtained after SPR moves : -9131.553478 . Log likelihood of the current tree: -9131.553329. . Printing the most likely tree in file 'nucleic_M2661_66x1027_2006.phy_phyml_tree.txt'... . Best log likelihood : -9131.553329 . Time used 0h4m18s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1068.96user 0.00system 18:03.44elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps