.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2480_40x430_2005.phy . Data type : aa . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : WAG . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Amino acid equilibrium frequencies : model . 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... . 399 patterns found. (out of a total of 430 sites) . 44 sites without polymorphism (10.23%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 38Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -28194.2168] [Alpha ][ 0.500960] . ( 2 sec) [ -28112.3243] [ 5702] [depth= 7] . ( 2 sec) [ -28039.5808] [ 5669] [depth= 4] . ( 3 sec) [ -27993.0519] [ 5633] [depth= 12] . ( 3 sec) [ -27958.3193] [ 5609] [depth= 1] . ( 4 sec) [ -27836.5841] [ 5601] [depth= 5] . ( 4 sec) [ -27708.0867] [ 5598] [depth= 2] . ( 5 sec) [ -27633.0146] [ 5588] [depth= 3] . ( 5 sec) [ -27562.8110] [ 5577] [depth= 1] . ( 5 sec) [ -27482.3730] [ 5564] [depth= 2] . ( 6 sec) [ -27479.4471] [ 5549] [depth= 7] . ( 6 sec) [ -27431.9532] [ 5542] [depth= 3] . ( 7 sec) [ -27409.4818] [ 5535] [depth= 1] . ( 7 sec) [ -27326.9198] [ 5526] [depth= 15] . ( 8 sec) [ -27269.7765] [ 5520] [depth= 5] . ( 8 sec) [ -27268.7205] [ 5523] [depth= 1] . ( 9 sec) [ -26985.9060] [ 5503] [depth= 8] . ( 9 sec) [ -26727.5555] [ 5483] [depth= 4] . ( 10 sec) [ -26697.9053] [ 5482] [depth= 1] . ( 10 sec) [ -26585.2690] [ 5466] [depth= 2] . ( 11 sec) [ -26413.4946] [ 5449] [depth= 2] . ( 11 sec) [ -26215.6794] [ 5409] [depth= 12] . ( 12 sec) [ -26195.3597] [ 5407] [depth= 2] . ( 12 sec) [ -26109.5534] [ 5382] [depth= 10] . ( 13 sec) [ -26077.3927] [ 5368] [depth= 5] . ( 13 sec) [ -26063.4614] [ 5367] [depth= 1] . ( 14 sec) [ -25775.2383] [ 5345] [depth= 12] . ( 15 sec) [ -25762.2276] [ 5345] [depth= 1] . ( 15 sec) [ -25694.4239] [ 5327] [depth= 5] . ( 15 sec) [ -25689.3456] [ 5319] [depth= 5] . ( 18 sec) [ -25680.5898] [ 5313] [depth= 1] . ( 19 sec) [ -25675.8690] [ 5316] [depth= 2] . ( 19 sec) [ -25647.7003] [ 5301] [depth= 5] . ( 20 sec) [ -25523.2221] [ 5298] [depth= 2] . ( 20 sec) [ -25499.2684] [ 5300] [depth= 5] . ( 21 sec) [ -25494.0138] [ 5296] [depth= 14] . ( 22 sec) [ -25486.9717] [ 5297] [depth= 1] . ( 22 sec) [ -25481.9198] [ 5294] [depth= 1] . ( 22 sec) [ -25481.1616] [ 5292] [depth= 1] . ( 23 sec) [ -25447.8306] [ 5282] [depth= 1] . ( 23 sec) [ -25445.8975] [ 5283] [depth= 6] . ( 24 sec) [ -25318.6597] [ 5253] [depth= 2] . ( 25 sec) [ -25306.0774] [ 5248] [depth= 1] . ( 25 sec) [ -25160.7419] [ 5224] [depth= 6] . ( 25 sec) [ -25158.7605] [ 5221] [depth= 2] . ( 27 sec) [ -25056.0081] [ 5193] [depth= 12] . ( 28 sec) [ -25048.2880] [ 5187] [depth= 4] . ( 28 sec) [ -25021.4018] [ 5184] [depth= 5] . ( 29 sec) [ -24979.6614] [ 5162] [depth= 7] . ( 29 sec) [ -24971.5649] [ 5165] [depth= 3] . ( 30 sec) [ -24868.7229] [ 5132] [depth= 2] . ( 31 sec) [ -24849.8327] [ 5121] [depth= 2] . ( 31 sec) [ -24838.2622] [ 5118] [depth= 2] . ( 32 sec) [ -24832.9241] [ 5121] [depth= 3] . ( 32 sec) [ -24691.0818] [ 5115] [depth= 2] . ( 33 sec) [ -24680.1711] [ 5113] [depth= 3] . ( 33 sec) [ -24671.5776] [ 5099] [depth= 5] . ( 34 sec) [ -24667.4319] [ 5104] [depth= 2] . ( 35 sec) [ -24665.0366] [ 5104] [depth= 1] . ( 35 sec) [ -24647.4820] [ 5097] [depth= 1] . ( 35 sec) [ -24643.5941] [ 5124] [depth= 1] . ( 36 sec) [ -24614.3067] [ 5114] [depth= 1] . ( 37 sec) [ -24598.1716] [ 5101] [depth= 2] . ( 37 sec) [ -24579.9899] [ 5101] [depth= 1] . ( 38 sec) [ -24571.7973] [ 5099] [depth= 1] . ( 38 sec) [ -24537.1727] [ 5091] [depth= 8] . ( 38 sec) [ -24518.2519] [ 5087] [depth= 2] . ( 39 sec) [ -24504.0379] [ 5080] [depth= 4] . ( 40 sec) [ -24503.8313] [ 5084] [depth= 1] . ( 42 sec) [ -24496.6468] [ 5088] [depth= 1] . ( 42 sec) [ -24486.1038] [ 5083] [depth= 1] . ( 43 sec) [ -24480.0457] [ 5081] [depth= 3] . ( 44 sec) [ -24466.1384] [ 5079] [depth= 1] . ( 44 sec) [ -24453.9558] [ 5071] [depth= 1] . ( 45 sec) [ -24446.6636] [ 5073] [depth= 1] . ( 45 sec) [ -24419.9715] [ 5071] [depth= 1] . ( 46 sec) [ -24417.0656] [ 5069] [depth= 1] . ( 47 sec) [ -24414.1892] [ 5067] [depth= 1] . ( 48 sec) [ -24384.8515] [ 5057] [depth= 4] . ( 49 sec) [ -24384.4567] [ 5062] [depth= 1] . ( 49 sec) [ -24377.9329] [ 5068] [depth= 1] . ( 51 sec) [ -24206.5556] [Branch lengths ] . ( 51 sec) [ -24165.4602] [Alpha ][ 0.766994] . ( 53 sec) [ -24150.6562] [ 5062] [depth= 1] . ( 56 sec) [ -24127.3562] [ 5059] [depth= 1] . ( 58 sec) [ -24125.8623] [ 5057] [depth= 1] . ( 59 sec) [ -24105.6139] [ 5035] [depth= 5] . ( 62 sec) [ -24042.2075] [ 5020] [depth= 1] . ( 63 sec) [ -24041.0764] [ 5022] [depth= 1] . ( 66 sec) [ -24019.9301] [ 5022] [depth= 2] . ( 67 sec) [ -24010.5602] [ 5025] [depth= 1] . ( 67 sec) [ -24005.9136] [ 5024] [depth= 1] . ( 68 sec) [ -23998.2356] [ 5018] [depth= 1] . ( 68 sec) [ -23983.9748] [ 5013] [depth= 1] . ( 73 sec) [ -23973.2014] [ 5009] [depth= 6] . ( 75 sec) [ -23971.6208] [ 5012] [depth= 1] . ( 80 sec) [ -23967.5347] [ 5008] [depth= 3] . ( 84 sec) [ -23965.7035] [ 5006] [depth= 1] . ( 85 sec) [ -23965.2341] [ 5008] [depth= 1] . ( 96 sec) [ -23964.3008] [ 5009] [depth= 1] . ( 97 sec) [ -23962.2666] [ 5014] [depth= 1] . ( 103 sec) [ -23961.4217] [ 5019] [depth= 2] . ( 104 sec) [ -23914.5203] [Branch lengths ] . ( 105 sec) [ -23912.8308] [Alpha ][ 0.845077] . ( 107 sec) [ -23911.5916] [ 5014] [depth= 1] . ( 109 sec) [ -23911.3313] [ 5018] [depth= 1] . ( 116 sec) [ -23907.8056] [ 5017] [depth= 5] . ( 119 sec) [ -23906.9530] [ 5015] [depth= 2] . ( 120 sec) [ -23906.7761] [ 5015] [depth= 1] . ( 124 sec) [ -23903.1895] [ 5018] [depth= 1] . ( 129 sec) [ -23903.1218] [ 5020] [depth= 1] . ( 133 sec) [ -23900.9923] [ 5018] [depth= 2] . ( 134 sec) [ -23899.2360] [ 5019] [depth= 1] . ( 154 sec) [ -23898.6339] [ 5020] [depth= 1] . ( 163 sec) [ -23886.4428] [Branch lengths ] . ( 163 sec) [ -23886.2507] [Alpha ][ 0.874046] . ( 200 sec) [ -23883.1086] [ 5022] [depth= 5] . ( 219 sec) [ -23882.3881] [ 5022] [depth= 1] . ( 240 sec) [ -23878.5223] [Branch lengths ] . ( 241 sec) [ -23878.4846] [Alpha ][ 0.887253] . ( 295 sec) [ -23876.3946] [ 5012] [depth= 3] . ( 298 sec) [ -23875.7295] [ 5014] [depth= 1] . ( 302 sec) [ -23874.5544] [ 5012] [depth= 1] . ( 312 sec) [ -23872.8052] [Branch lengths ] . ( 312 sec) [ -23872.8050] [Alpha ][ 0.886195] . ( 363 sec) [ -23872.6826] [Branch lengths ] . ( 364 sec) [ -23872.6826] [Topology ] . ( 367 sec) [ -23872.6633] [Topology ] . ( 370 sec) [ -23872.6571] [Topology ] . ( 373 sec) [ -23872.6541] [Topology ] . ( 376 sec) [ -23872.6526] [Topology ] . ( 379 sec) [ -23872.6518] [Topology ] . ( 380 sec) [ -23872.6450] [Alpha ][ 0.891842] . ( 380 sec) [ -23872.6450] [Topology ] . ( 383 sec) [ -23872.6436] [Topology ] . ( 387 sec) [ -23872.6429] [Topology ] . ( 387 sec) [ -23872.6429] [Alpha ][ 0.892734] . ( 387 sec) [ -23872.6429] [Topology ] . ( 390 sec) [ -23872.6424] [Topology ] . ( 391 sec) [ -23872.6424] [Alpha ][ 0.892734] . Checking for NNIs, optimizing five branches... . ( 419 sec) [ -23872.4329] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -23872.432879. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -28804.1641] [Alpha ][ 0.509567] . ( 2 sec) [ -28699.9821] [ 5651] [depth= 11] . ( 2 sec) [ -28375.7113] [ 5612] [depth= 10] . ( 3 sec) [ -28253.2895] [ 5592] [depth= 5] . ( 3 sec) [ -28221.6994] [ 5589] [depth= 1] . ( 4 sec) [ -28166.9911] [ 5591] [depth= 2] . ( 4 sec) [ -28124.1649] [ 5587] [depth= 3] . ( 4 sec) [ -28124.0485] [ 5579] [depth= 6] . ( 5 sec) [ -27812.2146] [ 5553] [depth= 3] . ( 5 sec) [ -27736.3607] [ 5573] [depth= 1] . ( 6 sec) [ -27694.9655] [ 5552] [depth= 1] . ( 6 sec) [ -27220.9661] [ 5512] [depth= 14] . ( 7 sec) [ -27078.8144] [ 5502] [depth= 1] . ( 7 sec) [ -27034.3261] [ 5477] [depth= 7] . ( 8 sec) [ -26897.5701] [ 5473] [depth= 1] . ( 8 sec) [ -26896.8670] [ 5468] [depth= 1] . ( 9 sec) [ -26891.8781] [ 5465] [depth= 1] . ( 9 sec) [ -26882.8616] [ 5463] [depth= 3] . ( 10 sec) [ -26882.8287] [ 5462] [depth= 1] . ( 10 sec) [ -26751.1687] [ 5413] [depth= 4] . ( 11 sec) [ -26672.6797] [ 5402] [depth= 7] . ( 11 sec) [ -26540.6227] [ 5401] [depth= 1] . ( 11 sec) [ -26499.0675] [ 5380] [depth= 2] . ( 12 sec) [ -26484.1318] [ 5381] [depth= 1] . ( 12 sec) [ -26471.2723] [ 5381] [depth= 1] . ( 13 sec) [ -26425.6297] [ 5376] [depth= 3] . ( 13 sec) [ -26422.3639] [ 5373] [depth= 1] . ( 14 sec) [ -26207.4207] [ 5345] [depth= 9] . ( 14 sec) [ -26146.7191] [ 5335] [depth= 12] . ( 15 sec) [ -26041.9759] [ 5303] [depth= 9] . ( 15 sec) [ -26002.7590] [ 5295] [depth= 1] . ( 16 sec) [ -25996.3452] [ 5303] [depth= 1] . ( 16 sec) [ -25870.9706] [ 5307] [depth= 6] . ( 17 sec) [ -25858.9390] [ 5308] [depth= 1] . ( 17 sec) [ -25833.2892] [ 5314] [depth= 1] . ( 18 sec) [ -25813.1655] [ 5309] [depth= 2] . ( 18 sec) [ -25805.3029] [ 5307] [depth= 1] . ( 18 sec) [ -25596.2478] [ 5308] [depth= 2] . ( 19 sec) [ -25336.5717] [ 5285] [depth= 1] . ( 19 sec) [ -25266.8825] [ 5269] [depth= 5] . ( 20 sec) [ -25258.4389] [ 5267] [depth= 3] . ( 21 sec) [ -25231.0852] [ 5250] [depth= 12] . ( 21 sec) [ -25176.2367] [ 5231] [depth= 13] . ( 22 sec) [ -25054.5424] [ 5212] [depth= 2] . ( 22 sec) [ -24908.3069] [ 5180] [depth= 11] . ( 23 sec) [ -24903.8022] [ 5189] [depth= 4] . ( 23 sec) [ -24887.5871] [ 5180] [depth= 1] . ( 23 sec) [ -24848.1995] [ 5167] [depth= 5] . ( 24 sec) [ -24840.0729] [ 5169] [depth= 1] . ( 25 sec) [ -24834.8867] [ 5171] [depth= 2] . ( 25 sec) [ -24765.5040] [ 5158] [depth= 3] . ( 25 sec) [ -24712.8416] [ 5157] [depth= 1] . ( 26 sec) [ -24645.8574] [ 5143] [depth= 2] . ( 26 sec) [ -24604.4053] [ 5130] [depth= 3] . ( 28 sec) [ -24568.7299] [ 5114] [depth= 9] . ( 29 sec) [ -24534.5329] [ 5102] [depth= 10] . ( 29 sec) [ -24528.3594] [ 5102] [depth= 2] . ( 30 sec) [ -24491.2740] [ 5092] [depth= 3] . ( 31 sec) [ -24487.6440] [ 5092] [depth= 3] . ( 32 sec) [ -24480.9086] [ 5091] [depth= 2] . ( 32 sec) [ -24479.0453] [ 5093] [depth= 1] . ( 33 sec) [ -24463.3638] [ 5085] [depth= 1] . ( 33 sec) [ -24442.5937] [ 5077] [depth= 1] . ( 34 sec) [ -24376.0568] [ 5067] [depth= 5] . ( 35 sec) [ -24345.5575] [ 5060] [depth= 2] . ( 35 sec) [ -24338.0300] [ 5061] [depth= 1] . ( 36 sec) [ -24324.4630] [ 5051] [depth= 2] . ( 37 sec) [ -24285.8619] [ 5045] [depth= 3] . ( 39 sec) [ -24258.4584] [ 5038] [depth= 1] . ( 39 sec) [ -24214.4271] [ 5026] [depth= 8] . ( 40 sec) [ -24206.0501] [ 5028] [depth= 2] . ( 40 sec) [ -24183.5949] [ 5019] [depth= 3] . ( 41 sec) [ -24152.7996] [ 5016] [depth= 5] . ( 42 sec) [ -24149.5788] [ 5016] [depth= 1] . ( 42 sec) [ -24137.7644] [ 5015] [depth= 1] . ( 44 sec) [ -24122.2173] [ 5012] [depth= 1] . ( 45 sec) [ -24121.1509] [ 5010] [depth= 1] . ( 45 sec) [ -24114.1363] [ 5003] [depth= 1] . ( 47 sec) [ -23992.6549] [Branch lengths ] . ( 47 sec) [ -23954.4456] [Alpha ][ 0.781078] . ( 48 sec) [ -23953.4064] [ 5003] [depth= 1] . ( 51 sec) [ -23952.9552] [ 5008] [depth= 1] . ( 52 sec) [ -23945.8276] [ 5010] [depth= 1] . ( 53 sec) [ -23945.3923] [ 5011] [depth= 1] . ( 55 sec) [ -23944.8611] [ 5013] [depth= 1] . ( 55 sec) [ -23943.8194] [ 5015] [depth= 1] . ( 56 sec) [ -23942.0881] [ 5012] [depth= 1] . ( 62 sec) [ -23941.5613] [ 5012] [depth= 1] . ( 63 sec) [ -23941.1293] [ 5013] [depth= 2] . ( 65 sec) [ -23941.0502] [ 5010] [depth= 1] . ( 102 sec) [ -23938.4361] [ 5015] [depth= 3] . ( 112 sec) [ -23910.2140] [Branch lengths ] . ( 113 sec) [ -23909.2794] [Alpha ][ 0.840523] . ( 118 sec) [ -23908.9607] [ 5015] [depth= 1] . ( 119 sec) [ -23894.0743] [ 5018] [depth= 6] . ( 164 sec) [ -23886.3372] [ 5010] [depth= 4] . ( 165 sec) [ -23885.9333] [ 5011] [depth= 1] . ( 173 sec) [ -23876.6510] [Branch lengths ] . ( 173 sec) [ -23876.0855] [Alpha ][ 0.889691] . ( 242 sec) [ -23874.7312] [Branch lengths ] . ( 243 sec) [ -23874.7312] [Topology ] . ( 246 sec) [ -23874.5774] [Topology ] . ( 249 sec) [ -23874.5235] [Topology ] . ( 252 sec) [ -23874.4978] [Topology ] . ( 256 sec) [ -23874.4849] [Topology ] . ( 259 sec) [ -23874.4783] [Topology ] . ( 262 sec) [ -23874.4749] [Topology ] . ( 263 sec) [ -23874.3735] [Alpha ][ 0.911593] . ( 263 sec) [ -23874.3735] [Topology ] . ( 266 sec) [ -23874.3595] [Topology ] . ( 269 sec) [ -23874.3533] [Topology ] . ( 273 sec) [ -23874.3502] [Topology ] . ( 276 sec) [ -23874.3487] [Topology ] . ( 279 sec) [ -23874.3479] [Topology ] . ( 280 sec) [ -23874.3464] [Alpha ][ 0.914238] . ( 280 sec) [ -23874.3464] [Topology ] . ( 283 sec) [ -23874.3455] [Topology ] . ( 284 sec) [ -23874.3455] [Alpha ][ 0.914238] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -23874.345542. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -29719.7468] [Alpha ][ 0.500960] . ( 2 sec) [ -29534.9060] [ 5660] [depth= 6] . ( 3 sec) [ -29404.4124] [ 5638] [depth= 10] . ( 3 sec) [ -29217.0996] [ 5625] [depth= 3] . ( 4 sec) [ -28765.4652] [ 5627] [depth= 1] . ( 4 sec) [ -28668.8212] [ 5605] [depth= 7] . ( 4 sec) [ -28470.5254] [ 5597] [depth= 5] . ( 5 sec) [ -27694.9231] [ 5581] [depth= 3] . ( 5 sec) [ -27647.3609] [ 5572] [depth= 12] . ( 6 sec) [ -27573.3469] [ 5574] [depth= 1] . ( 7 sec) [ -27564.6854] [ 5574] [depth= 9] . ( 7 sec) [ -27541.6907] [ 5559] [depth= 4] . ( 8 sec) [ -27499.8965] [ 5554] [depth= 9] . ( 8 sec) [ -27413.3125] [ 5535] [depth= 6] . ( 9 sec) [ -27413.1475] [ 5539] [depth= 1] . ( 9 sec) [ -27256.4550] [ 5530] [depth= 5] . ( 9 sec) [ -27182.8153] [ 5525] [depth= 1] . ( 10 sec) [ -27010.7404] [ 5504] [depth= 5] . ( 10 sec) [ -26887.9532] [ 5454] [depth= 11] . ( 11 sec) [ -26513.7222] [ 5424] [depth= 5] . ( 11 sec) [ -26418.9225] [ 5418] [depth= 13] . ( 12 sec) [ -26410.4923] [ 5414] [depth= 3] . ( 12 sec) [ -26367.0060] [ 5409] [depth= 1] . ( 13 sec) [ -26286.5813] [ 5406] [depth= 1] . ( 13 sec) [ -26228.5732] [ 5383] [depth= 6] . ( 14 sec) [ -26193.5568] [ 5387] [depth= 1] . ( 14 sec) [ -26088.7609] [ 5365] [depth= 8] . ( 15 sec) [ -25939.4184] [ 5362] [depth= 10] . ( 15 sec) [ -25897.7236] [ 5352] [depth= 6] . ( 16 sec) [ -25801.5286] [ 5347] [depth= 1] . ( 16 sec) [ -25767.2074] [ 5343] [depth= 1] . ( 16 sec) [ -25736.2204] [ 5344] [depth= 1] . ( 17 sec) [ -25733.7016] [ 5338] [depth= 8] . ( 18 sec) [ -25690.2028] [ 5323] [depth= 6] . ( 18 sec) [ -25651.4451] [ 5299] [depth= 12] . ( 19 sec) [ -25642.8136] [ 5298] [depth= 10] . ( 20 sec) [ -25639.3394] [ 5303] [depth= 1] . ( 20 sec) [ -25635.4088] [ 5294] [depth= 9] . ( 20 sec) [ -25527.6624] [ 5280] [depth= 1] . ( 21 sec) [ -25482.6334] [ 5274] [depth= 4] . ( 21 sec) [ -25464.3736] [ 5275] [depth= 1] . ( 22 sec) [ -25319.5858] [ 5264] [depth= 7] . ( 22 sec) [ -25148.1515] [ 5236] [depth= 1] . ( 23 sec) [ -25122.5813] [ 5213] [depth= 10] . ( 23 sec) [ -25076.3058] [ 5204] [depth= 2] . ( 24 sec) [ -25068.4976] [ 5200] [depth= 1] . ( 24 sec) [ -25042.8065] [ 5205] [depth= 2] . ( 25 sec) [ -25033.2777] [ 5206] [depth= 1] . ( 26 sec) [ -24982.5240] [ 5210] [depth= 5] . ( 26 sec) [ -24974.8893] [ 5205] [depth= 8] . ( 27 sec) [ -24956.2595] [ 5201] [depth= 8] . ( 28 sec) [ -24948.8569] [ 5196] [depth= 1] . ( 30 sec) [ -24927.2722] [ 5193] [depth= 5] . ( 31 sec) [ -24919.8375] [ 5198] [depth= 1] . ( 32 sec) [ -24869.8765] [ 5191] [depth= 2] . ( 32 sec) [ -24860.6219] [ 5191] [depth= 1] . ( 33 sec) [ -24857.1758] [ 5190] [depth= 1] . ( 33 sec) [ -24767.3429] [ 5188] [depth= 5] . ( 34 sec) [ -24747.6624] [ 5184] [depth= 2] . ( 36 sec) [ -24741.7124] [ 5181] [depth= 1] . ( 36 sec) [ -24695.1269] [ 5167] [depth= 7] . ( 37 sec) [ -24694.7053] [ 5166] [depth= 1] . ( 37 sec) [ -24689.4286] [ 5160] [depth= 1] . ( 38 sec) [ -24684.1514] [ 5157] [depth= 4] . ( 38 sec) [ -24682.7418] [ 5156] [depth= 2] . ( 40 sec) [ -24674.1765] [ 5150] [depth= 4] . ( 40 sec) [ -24638.6519] [ 5147] [depth= 2] . ( 42 sec) [ -24621.6508] [ 5138] [depth= 9] . ( 43 sec) [ -24594.6521] [ 5134] [depth= 8] . ( 43 sec) [ -24583.8834] [ 5128] [depth= 2] . ( 44 sec) [ -24575.3595] [ 5122] [depth= 1] . ( 44 sec) [ -24533.9708] [ 5113] [depth= 1] . ( 45 sec) [ -24439.4491] [ 5087] [depth= 1] . ( 46 sec) [ -24433.8016] [ 5086] [depth= 1] . ( 47 sec) [ -24415.1823] [ 5070] [depth= 5] . ( 48 sec) [ -24411.8218] [ 5071] [depth= 6] . ( 49 sec) [ -24386.1577] [ 5036] [depth= 8] . ( 51 sec) [ -24257.6641] [Branch lengths ] . ( 51 sec) [ -24207.0733] [Alpha ][ 0.817087] . ( 53 sec) [ -24205.4550] [ 5034] [depth= 1] . ( 54 sec) [ -24145.7160] [ 5032] [depth= 1] . ( 54 sec) [ -24140.0290] [ 5027] [depth= 2] . ( 54 sec) [ -24136.7516] [ 5022] [depth= 1] . ( 56 sec) [ -24131.3086] [ 5019] [depth= 2] . ( 60 sec) [ -24128.5248] [ 5022] [depth= 1] . ( 61 sec) [ -24128.4814] [ 5017] [depth= 1] . ( 61 sec) [ -24114.3816] [ 5020] [depth= 1] . ( 62 sec) [ -24111.5287] [ 5017] [depth= 3] . ( 70 sec) [ -24077.8229] [ 5018] [depth= 11] . ( 71 sec) [ -24073.9226] [ 5021] [depth= 2] . ( 71 sec) [ -24072.4034] [ 5024] [depth= 1] . ( 73 sec) [ -24055.7383] [ 5022] [depth= 1] . ( 84 sec) [ -24039.6675] [ 5012] [depth= 2] . ( 94 sec) [ -24032.1707] [ 5007] [depth= 2] . ( 95 sec) [ -24031.7914] [ 5005] [depth= 1] . ( 96 sec) [ -24029.9400] [ 5008] [depth= 1] . ( 99 sec) [ -24021.7187] [ 5013] [depth= 1] . ( 99 sec) [ -24020.7405] [ 5012] [depth= 1] . ( 113 sec) [ -23927.1257] [ 5017] [depth= 3] . ( 114 sec) [ -23898.8624] [Branch lengths ] . ( 115 sec) [ -23897.3093] [Alpha ][ 0.896534] . ( 118 sec) [ -23887.7627] [ 5010] [depth= 3] . ( 118 sec) [ -23886.9148] [ 5010] [depth= 1] . ( 130 sec) [ -23883.2429] [ 5011] [depth= 1] . ( 161 sec) [ -23881.6887] [ 5005] [depth= 4] . ( 174 sec) [ -23873.1723] [Branch lengths ] . ( 174 sec) [ -23873.1713] [Alpha ][ 0.894191] . ( 207 sec) [ -23871.7416] [ 5006] [depth= 2] . ( 234 sec) [ -23870.6048] [Branch lengths ] . ( 235 sec) [ -23870.6008] [Alpha ][ 0.898457] . ( 281 sec) [ -23870.5256] [ 5003] [depth= 1] . ( 294 sec) [ -23870.1584] [Branch lengths ] . ( 295 sec) [ -23870.1576] [Alpha ][ 0.900429] . ( 295 sec) [ -23870.1576] [Topology ] . ( 298 sec) [ -23870.1330] [Topology ] . ( 301 sec) [ -23870.1242] [Topology ] . ( 304 sec) [ -23870.1199] [Topology ] . ( 308 sec) [ -23870.1177] [Topology ] . ( 311 sec) [ -23870.1166] [Topology ] . ( 314 sec) [ -23870.1160] [Topology ] . ( 315 sec) [ -23870.1148] [Alpha ][ 0.902835] . ( 315 sec) [ -23870.1148] [Topology ] . ( 318 sec) [ -23870.1141] [Topology ] . ( 319 sec) [ -23870.1141] [Alpha ][ 0.902835] . Checking for NNIs, optimizing five branches... . ( 347 sec) [ -23869.5903] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -23869.590288. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -29133.3881] [Alpha ][ 0.500960] . ( 1 sec) [ -28712.5632] [ 5686] [depth= 9] . ( 2 sec) [ -28433.0804] [ 5645] [depth= 6] . ( 2 sec) [ -28314.7726] [ 5628] [depth= 1] . ( 3 sec) [ -28210.8121] [ 5628] [depth= 8] . ( 3 sec) [ -28189.4953] [ 5605] [depth= 1] . ( 4 sec) [ -28097.7004] [ 5586] [depth= 9] . ( 4 sec) [ -28012.0246] [ 5580] [depth= 1] . ( 4 sec) [ -27980.4521] [ 5569] [depth= 6] . ( 5 sec) [ -27946.5569] [ 5557] [depth= 6] . ( 5 sec) [ -27902.0436] [ 5549] [depth= 3] . ( 6 sec) [ -27585.0685] [ 5532] [depth= 3] . ( 6 sec) [ -27529.3575] [ 5525] [depth= 1] . ( 7 sec) [ -27506.0815] [ 5512] [depth= 6] . ( 7 sec) [ -27392.9259] [ 5508] [depth= 4] . ( 8 sec) [ -27369.1079] [ 5500] [depth= 2] . ( 8 sec) [ -27339.4813] [ 5501] [depth= 2] . ( 8 sec) [ -27098.0553] [ 5488] [depth= 12] . ( 9 sec) [ -27014.0795] [ 5475] [depth= 7] . ( 9 sec) [ -27006.5075] [ 5485] [depth= 1] . ( 10 sec) [ -27005.1427] [ 5484] [depth= 1] . ( 10 sec) [ -26933.9610] [ 5469] [depth= 7] . ( 11 sec) [ -26890.0091] [ 5463] [depth= 3] . ( 11 sec) [ -26841.9953] [ 5454] [depth= 2] . ( 12 sec) [ -26824.8462] [ 5445] [depth= 4] . ( 12 sec) [ -26811.5422] [ 5434] [depth= 13] . ( 13 sec) [ -26799.4426] [ 5416] [depth= 8] . ( 13 sec) [ -26703.9529] [ 5384] [depth= 19] . ( 14 sec) [ -26571.8877] [ 5364] [depth= 9] . ( 15 sec) [ -26085.2848] [ 5363] [depth= 3] . ( 15 sec) [ -25967.0101] [ 5341] [depth= 10] . ( 16 sec) [ -25876.2109] [ 5321] [depth= 3] . ( 16 sec) [ -25820.3004] [ 5312] [depth= 2] . ( 17 sec) [ -25794.8157] [ 5308] [depth= 3] . ( 17 sec) [ -25695.3953] [ 5292] [depth= 1] . ( 18 sec) [ -25669.9586] [ 5290] [depth= 1] . ( 18 sec) [ -25633.3604] [ 5273] [depth= 2] . ( 19 sec) [ -25632.6740] [ 5276] [depth= 1] . ( 20 sec) [ -25628.2042] [ 5273] [depth= 1] . ( 20 sec) [ -25624.2271] [ 5265] [depth= 1] . ( 21 sec) [ -25619.7347] [ 5266] [depth= 5] . ( 21 sec) [ -25569.4265] [ 5248] [depth= 1] . ( 22 sec) [ -25526.1506] [ 5257] [depth= 9] . ( 22 sec) [ -25437.3361] [ 5253] [depth= 6] . ( 23 sec) [ -25421.0688] [ 5250] [depth= 2] . ( 23 sec) [ -25416.5941] [ 5252] [depth= 1] . ( 24 sec) [ -25411.5944] [ 5249] [depth= 1] . ( 24 sec) [ -25343.5871] [ 5247] [depth= 2] . ( 25 sec) [ -25035.4478] [ 5219] [depth= 6] . ( 25 sec) [ -25031.8427] [ 5218] [depth= 3] . ( 26 sec) [ -24955.0816] [ 5195] [depth= 5] . ( 27 sec) [ -24880.7053] [ 5173] [depth= 1] . ( 28 sec) [ -24845.8820] [ 5177] [depth= 2] . ( 28 sec) [ -24827.1806] [ 5173] [depth= 1] . ( 29 sec) [ -24819.7611] [ 5171] [depth= 10] . ( 29 sec) [ -24716.7129] [ 5170] [depth= 3] . ( 30 sec) [ -24711.5454] [ 5165] [depth= 1] . ( 31 sec) [ -24634.7077] [ 5159] [depth= 8] . ( 31 sec) [ -24621.0375] [ 5148] [depth= 1] . ( 32 sec) [ -24611.6751] [ 5142] [depth= 1] . ( 33 sec) [ -24588.2475] [ 5132] [depth= 4] . ( 35 sec) [ -24587.1268] [ 5137] [depth= 3] . ( 35 sec) [ -24546.2197] [ 5138] [depth= 4] . ( 36 sec) [ -24523.4265] [ 5129] [depth= 1] . ( 37 sec) [ -24511.6823] [ 5118] [depth= 3] . ( 37 sec) [ -24490.8013] [ 5118] [depth= 1] . ( 38 sec) [ -24449.2542] [ 5106] [depth= 8] . ( 38 sec) [ -24441.1157] [ 5107] [depth= 1] . ( 39 sec) [ -24422.9792] [ 5110] [depth= 1] . ( 39 sec) [ -24415.8212] [ 5106] [depth= 1] . ( 40 sec) [ -24395.2462] [ 5104] [depth= 8] . ( 40 sec) [ -24380.2232] [ 5098] [depth= 3] . ( 41 sec) [ -24364.0911] [ 5095] [depth= 2] . ( 41 sec) [ -24361.3667] [ 5093] [depth= 1] . ( 43 sec) [ -24340.9563] [ 5091] [depth= 4] . ( 44 sec) [ -24340.4409] [ 5092] [depth= 1] . ( 44 sec) [ -24295.1244] [ 5090] [depth= 9] . ( 45 sec) [ -24263.7284] [ 5077] [depth= 11] . ( 49 sec) [ -24144.6917] [Branch lengths ] . ( 50 sec) [ -24101.4837] [Alpha ][ 0.781380] . ( 51 sec) [ -24099.6999] [ 5083] [depth= 1] . ( 54 sec) [ -24089.9560] [ 5081] [depth= 4] . ( 55 sec) [ -24077.4437] [ 5076] [depth= 1] . ( 56 sec) [ -24074.0304] [ 5072] [depth= 5] . ( 56 sec) [ -24069.9421] [ 5072] [depth= 1] . ( 58 sec) [ -24067.7954] [ 5073] [depth= 1] . ( 59 sec) [ -24064.1557] [ 5071] [depth= 1] . ( 62 sec) [ -24059.1628] [ 5067] [depth= 1] . ( 65 sec) [ -24058.6400] [ 5069] [depth= 1] . ( 71 sec) [ -24051.7525] [ 5073] [depth= 4] . ( 72 sec) [ -24048.9302] [ 5073] [depth= 1] . ( 72 sec) [ -24046.8999] [ 5070] [depth= 6] . ( 74 sec) [ -24044.1489] [ 5072] [depth= 1] . ( 77 sec) [ -24029.1748] [ 5061] [depth= 2] . ( 77 sec) [ -24016.3213] [ 5055] [depth= 5] . ( 78 sec) [ -24008.1902] [ 5038] [depth= 3] . ( 81 sec) [ -24006.6515] [ 5042] [depth= 1] . ( 84 sec) [ -23997.9328] [ 5038] [depth= 1] . ( 87 sec) [ -23997.6250] [ 5038] [depth= 1] . ( 88 sec) [ -23989.2928] [ 5028] [depth= 1] . ( 88 sec) [ -23987.3492] [ 5022] [depth= 4] . ( 89 sec) [ -23986.7872] [ 5027] [depth= 1] . ( 90 sec) [ -23973.8587] [ 5023] [depth= 3] . ( 91 sec) [ -23968.5607] [ 5018] [depth= 1] . ( 93 sec) [ -23968.0508] [ 5015] [depth= 1] . ( 94 sec) [ -23967.5020] [ 5018] [depth= 1] . ( 97 sec) [ -23966.9707] [ 5018] [depth= 1] . ( 99 sec) [ -23965.1723] [ 5015] [depth= 1] . ( 101 sec) [ -23960.4639] [ 5012] [depth= 4] . ( 101 sec) [ -23959.0120] [ 5010] [depth= 1] . ( 104 sec) [ -23956.9079] [ 5008] [depth= 1] . ( 104 sec) [ -23956.3996] [ 5006] [depth= 1] . ( 106 sec) [ -23920.7736] [Branch lengths ] . ( 107 sec) [ -23918.1580] [Alpha ][ 0.885366] . ( 108 sec) [ -23917.6437] [ 5003] [depth= 1] . ( 109 sec) [ -23917.1473] [ 5003] [depth= 1] . ( 114 sec) [ -23913.8904] [ 5006] [depth= 2] . ( 116 sec) [ -23912.1116] [ 5009] [depth= 1] . ( 119 sec) [ -23899.6657] [ 5013] [depth= 1] . ( 119 sec) [ -23897.3534] [ 5014] [depth= 1] . ( 125 sec) [ -23897.2509] [ 5013] [depth= 1] . ( 128 sec) [ -23896.2325] [ 5012] [depth= 1] . ( 139 sec) [ -23895.6566] [ 5006] [depth= 1] . ( 161 sec) [ -23879.6124] [Branch lengths ] . ( 161 sec) [ -23879.5984] [Alpha ][ 0.893514] . ( 214 sec) [ -23878.3372] [Branch lengths ] . ( 215 sec) [ -23878.3372] [Topology ] . ( 218 sec) [ -23878.2162] [Topology ] . ( 221 sec) [ -23878.1851] [Topology ] . ( 224 sec) [ -23878.1710] [Topology ] . ( 228 sec) [ -23878.1640] [Topology ] . ( 231 sec) [ -23878.1604] [Topology ] . ( 234 sec) [ -23878.1586] [Topology ] . ( 235 sec) [ -23878.1050] [Alpha ][ 0.909654] . ( 235 sec) [ -23878.1050] [Topology ] . ( 238 sec) [ -23878.0972] [Topology ] . ( 241 sec) [ -23878.0937] [Topology ] . ( 245 sec) [ -23878.0920] [Topology ] . ( 248 sec) [ -23878.0911] [Topology ] . ( 248 sec) [ -23878.0904] [Alpha ][ 0.911545] . ( 249 sec) [ -23878.0904] [Topology ] . ( 252 sec) [ -23878.0896] [Topology ] . ( 252 sec) [ -23878.0896] [Alpha ][ 0.911545] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -23878.089625. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -27581.3022] [Alpha ][ 0.549303] . ( 2 sec) [ -27515.8998] [ 5618] [depth= 6] . ( 2 sec) [ -27150.6795] [ 5579] [depth= 6] . ( 3 sec) [ -27096.6617] [ 5577] [depth= 1] . ( 3 sec) [ -27091.9857] [ 5560] [depth= 6] . ( 4 sec) [ -27054.8591] [ 5558] [depth= 4] . ( 5 sec) [ -27027.6912] [ 5559] [depth= 3] . ( 6 sec) [ -27008.9899] [ 5554] [depth= 1] . ( 6 sec) [ -26984.0233] [ 5550] [depth= 2] . ( 7 sec) [ -26930.8163] [ 5545] [depth= 5] . ( 8 sec) [ -26802.8270] [ 5537] [depth= 9] . ( 8 sec) [ -26768.9743] [ 5535] [depth= 1] . ( 9 sec) [ -26753.6241] [ 5536] [depth= 3] . ( 9 sec) [ -26646.6377] [ 5534] [depth= 1] . ( 10 sec) [ -26619.6023] [ 5529] [depth= 1] . ( 11 sec) [ -26613.4354] [ 5527] [depth= 1] . ( 11 sec) [ -26564.1197] [ 5510] [depth= 5] . ( 12 sec) [ -26542.6250] [ 5481] [depth= 5] . ( 12 sec) [ -26421.2901] [ 5442] [depth= 17] . ( 13 sec) [ -26414.0448] [ 5444] [depth= 1] . ( 13 sec) [ -26367.4450] [ 5443] [depth= 1] . ( 14 sec) [ -26366.5618] [ 5443] [depth= 1] . ( 14 sec) [ -26365.8254] [ 5448] [depth= 1] . ( 15 sec) [ -26321.9912] [ 5441] [depth= 11] . ( 15 sec) [ -26307.9370] [ 5419] [depth= 9] . ( 16 sec) [ -26290.9019] [ 5422] [depth= 12] . ( 16 sec) [ -26223.0997] [ 5412] [depth= 3] . ( 16 sec) [ -26154.3943] [ 5392] [depth= 8] . ( 17 sec) [ -26121.4142] [ 5385] [depth= 1] . ( 17 sec) [ -26095.2320] [ 5373] [depth= 2] . ( 18 sec) [ -26062.9328] [ 5360] [depth= 11] . ( 18 sec) [ -25961.1044] [ 5317] [depth= 5] . ( 19 sec) [ -25939.1921] [ 5311] [depth= 1] . ( 19 sec) [ -25782.8363] [ 5304] [depth= 6] . ( 20 sec) [ -25702.5332] [ 5264] [depth= 5] . ( 20 sec) [ -25689.1527] [ 5285] [depth= 1] . ( 21 sec) [ -25666.3742] [ 5279] [depth= 1] . ( 22 sec) [ -25567.0523] [ 5240] [depth= 10] . ( 22 sec) [ -25513.3012] [ 5224] [depth= 2] . ( 23 sec) [ -25390.3957] [ 5225] [depth= 1] . ( 23 sec) [ -25318.6261] [ 5216] [depth= 3] . ( 24 sec) [ -25264.4255] [ 5204] [depth= 10] . ( 26 sec) [ -25262.6892] [ 5209] [depth= 2] . ( 26 sec) [ -25211.5074] [ 5208] [depth= 2] . ( 27 sec) [ -25106.3594] [ 5207] [depth= 1] . ( 27 sec) [ -25091.1275] [ 5209] [depth= 1] . ( 27 sec) [ -25069.1827] [ 5209] [depth= 2] . ( 29 sec) [ -25068.8999] [ 5214] [depth= 2] . ( 29 sec) [ -25066.1752] [ 5213] [depth= 1] . ( 30 sec) [ -25025.6682] [ 5206] [depth= 2] . ( 30 sec) [ -24978.7008] [ 5203] [depth= 1] . ( 31 sec) [ -24963.4937] [ 5200] [depth= 5] . ( 31 sec) [ -24846.4447] [ 5169] [depth= 2] . ( 32 sec) [ -24816.1116] [ 5167] [depth= 3] . ( 32 sec) [ -24785.1229] [ 5160] [depth= 1] . ( 33 sec) [ -24782.1146] [ 5164] [depth= 4] . ( 35 sec) [ -24774.4698] [ 5165] [depth= 1] . ( 35 sec) [ -24623.1736] [ 5169] [depth= 2] . ( 36 sec) [ -24622.2029] [ 5164] [depth= 2] . ( 36 sec) [ -24615.0226] [ 5162] [depth= 6] . ( 37 sec) [ -24597.2609] [ 5158] [depth= 6] . ( 38 sec) [ -24553.5967] [ 5161] [depth= 3] . ( 38 sec) [ -24520.7494] [ 5160] [depth= 1] . ( 39 sec) [ -24480.1728] [ 5135] [depth= 10] . ( 39 sec) [ -24366.8777] [ 5088] [depth= 9] . ( 40 sec) [ -24337.8358] [ 5074] [depth= 5] . ( 40 sec) [ -24320.6464] [ 5069] [depth= 1] . ( 42 sec) [ -24311.0412] [ 5067] [depth= 1] . ( 42 sec) [ -24292.3473] [ 5064] [depth= 1] . ( 43 sec) [ -24282.2338] [ 5062] [depth= 2] . ( 43 sec) [ -24277.4913] [ 5062] [depth= 5] . ( 45 sec) [ -24273.8797] [ 5068] [depth= 1] . ( 46 sec) [ -24269.8227] [ 5071] [depth= 1] . ( 46 sec) [ -24239.8718] [ 5066] [depth= 2] . ( 47 sec) [ -24224.7814] [ 5054] [depth= 4] . ( 49 sec) [ -24223.1967] [ 5056] [depth= 1] . ( 50 sec) [ -24212.5790] [ 5055] [depth= 2] . ( 50 sec) [ -24208.2229] [ 5056] [depth= 1] . ( 51 sec) [ -24207.2572] [ 5055] [depth= 1] . ( 52 sec) [ -24186.2333] [ 5060] [depth= 1] . ( 52 sec) [ -24161.9314] [ 5055] [depth= 1] . ( 53 sec) [ -24149.6353] [ 5054] [depth= 3] . ( 54 sec) [ -24138.7462] [ 5055] [depth= 1] . ( 54 sec) [ -24131.8797] [ 5049] [depth= 1] . ( 55 sec) [ -24113.8371] [ 5048] [depth= 2] . ( 56 sec) [ -24040.6160] [Branch lengths ] . ( 57 sec) [ -24006.1448] [Alpha ][ 0.828325] . ( 68 sec) [ -23998.3525] [ 5045] [depth= 1] . ( 68 sec) [ -23995.3272] [ 5042] [depth= 3] . ( 69 sec) [ -23993.0508] [ 5040] [depth= 3] . ( 69 sec) [ -23977.6297] [ 5036] [depth= 3] . ( 72 sec) [ -23974.1636] [ 5035] [depth= 1] . ( 75 sec) [ -23974.1081] [ 5032] [depth= 2] . ( 78 sec) [ -23968.6484] [ 5027] [depth= 2] . ( 87 sec) [ -23966.0088] [ 5028] [depth= 3] . ( 88 sec) [ -23964.7908] [ 5028] [depth= 1] . ( 88 sec) [ -23964.1865] [ 5031] [depth= 1] . ( 89 sec) [ -23945.2511] [ 5024] [depth= 8] . ( 92 sec) [ -23944.8277] [ 5025] [depth= 1] . ( 92 sec) [ -23939.4275] [ 5022] [depth= 1] . ( 95 sec) [ -23938.6025] [ 5023] [depth= 1] . ( 96 sec) [ -23935.7362] [ 5018] [depth= 3] . ( 108 sec) [ -23921.7004] [ 5006] [depth= 7] . ( 115 sec) [ -23898.0094] [Branch lengths ] . ( 116 sec) [ -23897.5031] [Alpha ][ 0.874137] . ( 122 sec) [ -23897.4471] [ 5011] [depth= 1] . ( 126 sec) [ -23895.4175] [ 5007] [depth= 1] . ( 140 sec) [ -23893.2695] [ 5012] [depth= 1] . ( 141 sec) [ -23891.6907] [ 5014] [depth= 1] . ( 149 sec) [ -23886.1836] [ 5015] [depth= 2] . ( 151 sec) [ -23886.1086] [ 5019] [depth= 1] . ( 160 sec) [ -23885.8735] [ 5015] [depth= 1] . ( 174 sec) [ -23878.9527] [Branch lengths ] . ( 174 sec) [ -23878.8658] [Alpha ][ 0.894134] . ( 237 sec) [ -23878.1001] [Branch lengths ] . ( 237 sec) [ -23878.1001] [Topology ] . ( 241 sec) [ -23877.6660] [Topology ] . ( 244 sec) [ -23877.5411] [Topology ] . ( 247 sec) [ -23877.5106] [Topology ] . ( 251 sec) [ -23877.4981] [Topology ] . ( 254 sec) [ -23877.4923] [Topology ] . ( 257 sec) [ -23877.4894] [Topology ] . ( 260 sec) [ -23877.4879] [Topology ] . ( 261 sec) [ -23877.4525] [Alpha ][ 0.906970] . ( 261 sec) [ -23877.4525] [Topology ] . ( 265 sec) [ -23877.4476] [Topology ] . ( 268 sec) [ -23877.4454] [Topology ] . ( 271 sec) [ -23877.4443] [Topology ] . ( 274 sec) [ -23877.4437] [Topology ] . ( 275 sec) [ -23877.4433] [Alpha ][ 0.908332] . ( 275 sec) [ -23877.4433] [Topology ] . ( 279 sec) [ -23877.4428] [Topology ] . ( 279 sec) [ -23877.4428] [Alpha ][ 0.908332] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -23877.442842. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -24093.8919] [Alpha ][ 0.744037] . ( 1 sec) [ -24093.8919] [Topology ] . ( 4 sec) [ -23933.0303] [Topology ] . ( 7 sec) [ -23905.5947] [Topology ] . ( 11 sec) [ -23897.0873] [Topology ] . ( 14 sec) [ -23894.6999] [Topology ] . ( 17 sec) [ -23894.1137] [Topology ] . ( 20 sec) [ -23894.4239] [Topology ] . Moving backward . ( 21 sec) [ -23888.7339] [Topology ] . ( 24 sec) [ -23885.8511] [Topology ] . ( 28 sec) [ -23883.4821] [Topology ] . ( 31 sec) [ -23875.2197] [Alpha ][ 0.893113] . ( 31 sec) [ -23875.2197] [Topology ] . ( 35 sec) [ -23872.7801] [Topology ] . ( 38 sec) [ -23871.6161] [Topology ] . ( 41 sec) [ -23871.4433] [Topology ] . ( 45 sec) [ -23871.3851] [Topology ] . ( 48 sec) [ -23871.3595] [Topology ] . ( 51 sec) [ -23871.3470] [Topology ] . ( 55 sec) [ -23871.3406] [Topology ] . Checking for NNIs, optimizing five branches... . ( 82 sec) [ -23871.3012] [Alpha ][ 0.906587] . ( 82 sec) [ -23871.3012] [Topology ] . ( 86 sec) [ -23871.2910] [Topology ] . ( 89 sec) [ -23871.2860] [Topology ] . ( 92 sec) [ -23871.2835] [Topology ] . ( 96 sec) [ -23871.2821] [Topology ] . ( 99 sec) [ -23871.2814] [Topology ] . Checking for NNIs, optimizing five branches... . ( 127 sec) [ -23871.2804] [Alpha ][ 0.908766] . ( 127 sec) [ -23871.2804] [Topology ] . ( 130 sec) [ -23871.2797] [Topology ] . Checking for NNIs, optimizing five branches... . ( 157 sec) [ -23871.2797] [Alpha ][ 0.908766] . ( 158 sec) [ -23871.2797] [Topology ] . ( 161 sec) [ -23871.2794] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 216 sec) [ -24093.8919] [Alpha ][ 0.744037] . ( 221 sec) [ -24093.1300] [ 5023] [depth= 1] . ( 221 sec) [ -24074.3469] [ 5017] [depth= 1] . ( 226 sec) [ -24074.2184] [ 5018] [depth= 1] . ( 227 sec) [ -24070.3588] [ 5017] [depth= 1] . ( 227 sec) [ -24070.3081] [ 5010] [depth= 1] . ( 228 sec) [ -24059.4258] [ 5017] [depth= 1] . ( 228 sec) [ -24053.8688] [ 5012] [depth= 1] . ( 229 sec) [ -24053.8338] [ 5016] [depth= 1] . ( 230 sec) [ -24044.7092] [ 5012] [depth= 1] . ( 230 sec) [ -24041.4949] [ 5006] [depth= 1] . ( 231 sec) [ -24038.2194] [ 5009] [depth= 1] . ( 231 sec) [ -24037.4616] [ 5006] [depth= 1] . ( 233 sec) [ -24034.8911] [ 5009] [depth= 1] . ( 234 sec) [ -24028.1894] [ 5009] [depth= 2] . ( 234 sec) [ -24027.4720] [ 5011] [depth= 1] . ( 235 sec) [ -24017.8850] [ 5013] [depth= 1] . ( 237 sec) [ -24015.8225] [ 5013] [depth= 1] . ( 237 sec) [ -24010.0331] [ 5012] [depth= 1] . ( 238 sec) [ -23998.2863] [ 5011] [depth= 1] . ( 239 sec) [ -23993.8977] [ 5005] [depth= 3] . ( 239 sec) [ -23993.4091] [ 5007] [depth= 1] . ( 241 sec) [ -23991.7665] [ 5006] [depth= 1] . ( 242 sec) [ -23982.2916] [ 5007] [depth= 1] . ( 243 sec) [ -23978.7872] [ 5007] [depth= 1] . ( 243 sec) [ -23973.4050] [ 5007] [depth= 1] . ( 244 sec) [ -23966.9241] [ 5005] [depth= 1] . ( 244 sec) [ -23964.7344] [ 5007] [depth= 1] . ( 251 sec) [ -23963.0203] [ 5010] [depth= 1] . ( 252 sec) [ -23961.9891] [ 5007] [depth= 1] . ( 255 sec) [ -23892.1227] [Branch lengths ] . ( 256 sec) [ -23887.7439] [Alpha ][ 0.870589] . ( 270 sec) [ -23886.1656] [ 5007] [depth= 1] . ( 297 sec) [ -23880.5868] [Branch lengths ] . ( 297 sec) [ -23880.4813] [Alpha ][ 0.892537] . ( 340 sec) [ -23879.5816] [Branch lengths ] . ( 340 sec) [ -23879.5816] [Topology ] . ( 343 sec) [ -23878.0499] [Topology ] . ( 347 sec) [ -23877.7849] [Topology ] . ( 350 sec) [ -23877.7482] [Topology ] . ( 353 sec) [ -23877.7360] [Topology ] . ( 357 sec) [ -23877.7307] [Topology ] . ( 360 sec) [ -23877.7281] [Topology ] . ( 363 sec) [ -23877.7268] [Topology ] . ( 364 sec) [ -23877.6630] [Alpha ][ 0.909862] . ( 364 sec) [ -23877.6630] [Topology ] . ( 367 sec) [ -23877.6554] [Topology ] . ( 371 sec) [ -23877.6520] [Topology ] . ( 374 sec) [ -23877.6503] [Topology ] . ( 377 sec) [ -23877.6494] [Topology ] . ( 378 sec) [ -23877.6487] [Alpha ][ 0.911614] . ( 378 sec) [ -23877.6487] [Topology ] . ( 381 sec) [ -23877.6480] [Topology ] . ( 382 sec) [ -23877.6480] [Alpha ][ 0.911614] . Checking for NNIs, optimizing five branches... . ( 410 sec) [ -23877.3394] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -23871.279362 . Log likelihood obtained after SPR moves : -23877.339434 . Log likelihood of the current tree: -23871.279362. . Printing the most likely tree in file 'proteic_M2480_40x430_2005.phy_phyml_tree.txt'... . Best log likelihood : -23869.590288 . Time used 0h7m19s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 2161.57user 0.00system 36:06.95elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps