.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2476_30x719_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... . 620 patterns found. (out of a total of 719 sites) . 115 sites without polymorphism (15.99%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 44Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -32813.6705] [Alpha ][ 0.500960] . ( 3 sec) [ -32682.8510] [ 5452] [depth= 11] . ( 3 sec) [ -32352.6334] [ 5440] [depth= 10] . ( 4 sec) [ -32309.3180] [ 5441] [depth= 1] . ( 4 sec) [ -28956.4316] [ 5430] [depth= 6] . ( 5 sec) [ -28467.5726] [ 5429] [depth= 2] . ( 5 sec) [ -28419.6173] [ 5426] [depth= 1] . ( 6 sec) [ -27979.1336] [ 5361] [depth= 5] . ( 6 sec) [ -27829.3792] [ 5328] [depth= 1] . ( 7 sec) [ -27711.1799] [ 5313] [depth= 4] . ( 8 sec) [ -27421.0109] [ 5273] [depth= 8] . ( 8 sec) [ -27372.3693] [ 5279] [depth= 1] . ( 9 sec) [ -27290.3712] [ 5264] [depth= 10] . ( 9 sec) [ -27274.1004] [ 5264] [depth= 2] . ( 10 sec) [ -27199.5781] [ 5242] [depth= 3] . ( 10 sec) [ -27182.4120] [ 5235] [depth= 3] . ( 11 sec) [ -27143.1867] [ 5226] [depth= 1] . ( 11 sec) [ -26870.3216] [ 5193] [depth= 4] . ( 12 sec) [ -26761.2978] [ 5162] [depth= 6] . ( 13 sec) [ -26056.0634] [ 5137] [depth= 4] . ( 14 sec) [ -26047.6808] [ 5140] [depth= 4] . ( 15 sec) [ -25950.6578] [ 5130] [depth= 1] . ( 15 sec) [ -25868.2201] [ 5120] [depth= 4] . ( 16 sec) [ -25842.2280] [ 5111] [depth= 1] . ( 16 sec) [ -25837.9693] [ 5112] [depth= 3] . ( 18 sec) [ -25803.2243] [ 5090] [depth= 7] . ( 19 sec) [ -25763.6145] [ 5074] [depth= 1] . ( 20 sec) [ -25748.2933] [ 5070] [depth= 1] . ( 21 sec) [ -25681.9563] [ 5066] [depth= 1] . ( 21 sec) [ -25662.1265] [ 5056] [depth= 4] . ( 22 sec) [ -25660.4168] [ 5056] [depth= 1] . ( 23 sec) [ -25652.8218] [ 5060] [depth= 1] . ( 24 sec) [ -25651.1327] [ 5056] [depth= 1] . ( 25 sec) [ -25586.8373] [ 5040] [depth= 2] . ( 25 sec) [ -25324.9138] [ 5036] [depth= 1] . ( 26 sec) [ -25322.8719] [ 5039] [depth= 1] . ( 27 sec) [ -25294.6144] [ 5035] [depth= 3] . ( 27 sec) [ -25289.3996] [ 5033] [depth= 1] . ( 28 sec) [ -25240.3497] [ 5025] [depth= 1] . ( 28 sec) [ -25173.4694] [ 4992] [depth= 3] . ( 29 sec) [ -24880.1961] [ 4948] [depth= 1] . ( 30 sec) [ -24879.7623] [ 4944] [depth= 1] . ( 30 sec) [ -24874.9350] [ 4942] [depth= 1] . ( 31 sec) [ -24860.3664] [ 4940] [depth= 1] . ( 32 sec) [ -24783.6788] [ 4934] [depth= 1] . ( 33 sec) [ -24773.7057] [ 4932] [depth= 1] . ( 33 sec) [ -24767.4136] [ 4935] [depth= 2] . ( 34 sec) [ -24766.1109] [ 4932] [depth= 1] . ( 34 sec) [ -24760.4615] [ 4931] [depth= 1] . ( 35 sec) [ -24748.8470] [ 4931] [depth= 3] . ( 37 sec) [ -24747.8606] [ 4933] [depth= 2] . ( 37 sec) [ -24734.1154] [ 4932] [depth= 2] . ( 38 sec) [ -24725.7948] [ 4929] [depth= 3] . ( 40 sec) [ -24716.2488] [ 4928] [depth= 2] . ( 41 sec) [ -24628.8377] [Branch lengths ] . ( 42 sec) [ -24609.0363] [Alpha ][ 0.668788] . ( 47 sec) [ -24601.1582] [ 4925] [depth= 1] . ( 48 sec) [ -24596.5052] [ 4912] [depth= 1] . ( 49 sec) [ -24595.7415] [ 4907] [depth= 2] . ( 58 sec) [ -24595.0409] [ 4923] [depth= 1] . ( 69 sec) [ -24593.2116] [ 4915] [depth= 5] . ( 71 sec) [ -24592.3227] [ 4914] [depth= 5] . ( 72 sec) [ -24590.4479] [ 4913] [depth= 1] . ( 86 sec) [ -24563.7573] [Branch lengths ] . ( 86 sec) [ -24563.5857] [Alpha ][ 0.686970] . ( 112 sec) [ -24558.4048] [ 4919] [depth= 1] . ( 129 sec) [ -24548.2439] [Branch lengths ] . ( 130 sec) [ -24548.2386] [Alpha ][ 0.690295] . ( 178 sec) [ -24546.2267] [Branch lengths ] . ( 178 sec) [ -24546.2267] [Topology ] . ( 182 sec) [ -24545.8939] [Topology ] . ( 185 sec) [ -24545.7600] [Topology ] . ( 189 sec) [ -24545.6831] [Topology ] . ( 193 sec) [ -24545.6373] [Topology ] . ( 197 sec) [ -24545.6098] [Topology ] . ( 200 sec) [ -24545.5931] [Topology ] . ( 201 sec) [ -24545.5556] [Alpha ][ 0.699179] . ( 201 sec) [ -24545.5556] [Topology ] . ( 205 sec) [ -24545.5409] [Topology ] . ( 209 sec) [ -24545.5327] [Topology ] . ( 213 sec) [ -24545.5277] [Topology ] . ( 216 sec) [ -24545.5247] [Topology ] . ( 220 sec) [ -24545.5228] [Topology ] . ( 224 sec) [ -24545.5217] [Topology ] . ( 225 sec) [ -24545.5213] [Alpha ][ 0.700066] . ( 225 sec) [ -24545.5213] [Topology ] . ( 229 sec) [ -24545.5205] [Topology ] . ( 229 sec) [ -24545.5205] [Alpha ][ 0.700066] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -24545.520482. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -29032.3917] [Alpha ][ 0.500960] . ( 3 sec) [ -28833.9353] [ 5541] [depth= 9] . ( 3 sec) [ -28789.1554] [ 5539] [depth= 8] . ( 4 sec) [ -28787.7294] [ 5520] [depth= 6] . ( 5 sec) [ -28781.6436] [ 5521] [depth= 1] . ( 5 sec) [ -28595.3752] [ 5506] [depth= 5] . ( 6 sec) [ -28563.7419] [ 5502] [depth= 2] . ( 6 sec) [ -28552.4682] [ 5498] [depth= 3] . ( 7 sec) [ -28483.7668] [ 5492] [depth= 2] . ( 8 sec) [ -28323.4347] [ 5480] [depth= 3] . ( 8 sec) [ -28270.1553] [ 5465] [depth= 1] . ( 9 sec) [ -28128.1383] [ 5454] [depth= 2] . ( 9 sec) [ -27998.8005] [ 5426] [depth= 5] . ( 10 sec) [ -27528.9410] [ 5377] [depth= 6] . ( 11 sec) [ -27390.6776] [ 5373] [depth= 5] . ( 11 sec) [ -27190.4376] [ 5367] [depth= 4] . ( 12 sec) [ -27190.1823] [ 5376] [depth= 2] . ( 13 sec) [ -27076.0023] [ 5381] [depth= 10] . ( 13 sec) [ -27070.3525] [ 5381] [depth= 1] . ( 14 sec) [ -27002.2721] [ 5350] [depth= 13] . ( 14 sec) [ -26792.8203] [ 5302] [depth= 1] . ( 15 sec) [ -26670.9700] [ 5283] [depth= 4] . ( 16 sec) [ -26642.0827] [ 5276] [depth= 3] . ( 16 sec) [ -26616.6175] [ 5270] [depth= 3] . ( 17 sec) [ -26602.1382] [ 5269] [depth= 3] . ( 17 sec) [ -26527.6814] [ 5275] [depth= 2] . ( 18 sec) [ -26412.7053] [ 5244] [depth= 3] . ( 19 sec) [ -26384.8684] [ 5224] [depth= 4] . ( 19 sec) [ -26364.7756] [ 5207] [depth= 2] . ( 20 sec) [ -26360.4039] [ 5200] [depth= 2] . ( 21 sec) [ -26233.9403] [ 5165] [depth= 5] . ( 21 sec) [ -26206.4072] [ 5170] [depth= 1] . ( 22 sec) [ -26135.0452] [ 5150] [depth= 3] . ( 22 sec) [ -26032.8753] [ 5133] [depth= 5] . ( 23 sec) [ -25989.0907] [ 5117] [depth= 1] . ( 24 sec) [ -25965.6164] [ 5112] [depth= 1] . ( 24 sec) [ -25927.1542] [ 5096] [depth= 2] . ( 25 sec) [ -25880.3043] [ 5081] [depth= 3] . ( 25 sec) [ -25830.9842] [ 5072] [depth= 1] . ( 26 sec) [ -25247.8277] [ 5014] [depth= 6] . ( 27 sec) [ -25149.7074] [ 5006] [depth= 1] . ( 27 sec) [ -25129.8553] [ 5010] [depth= 6] . ( 28 sec) [ -25093.8507] [ 4995] [depth= 6] . ( 28 sec) [ -25088.6519] [ 4989] [depth= 1] . ( 29 sec) [ -25042.8300] [ 4979] [depth= 2] . ( 30 sec) [ -24945.1182] [ 4978] [depth= 3] . ( 31 sec) [ -24929.7007] [ 4970] [depth= 4] . ( 32 sec) [ -24922.8900] [ 4968] [depth= 2] . ( 32 sec) [ -24908.4837] [ 4962] [depth= 1] . ( 33 sec) [ -24901.6692] [ 4959] [depth= 1] . ( 35 sec) [ -24892.3118] [ 4960] [depth= 1] . ( 36 sec) [ -24890.1836] [ 4963] [depth= 3] . ( 37 sec) [ -24883.4957] [ 4963] [depth= 1] . ( 38 sec) [ -24877.7948] [ 4947] [depth= 1] . ( 38 sec) [ -24831.0634] [ 4946] [depth= 1] . ( 39 sec) [ -24822.0594] [ 4941] [depth= 1] . ( 40 sec) [ -24809.6479] [ 4948] [depth= 1] . ( 41 sec) [ -24804.2508] [ 4953] [depth= 1] . ( 42 sec) [ -24801.0101] [ 4953] [depth= 2] . ( 43 sec) [ -24785.1197] [ 4951] [depth= 1] . ( 44 sec) [ -24784.8146] [ 4936] [depth= 6] . ( 45 sec) [ -24777.2939] [ 4926] [depth= 3] . ( 46 sec) [ -24670.7318] [Branch lengths ] . ( 47 sec) [ -24654.1145] [Alpha ][ 0.652194] . ( 49 sec) [ -24652.3166] [ 4931] [depth= 1] . ( 50 sec) [ -24648.9234] [ 4930] [depth= 2] . ( 54 sec) [ -24641.5690] [ 4932] [depth= 1] . ( 57 sec) [ -24641.1810] [ 4930] [depth= 1] . ( 57 sec) [ -24640.1906] [ 4930] [depth= 1] . ( 60 sec) [ -24638.6669] [ 4930] [depth= 7] . ( 61 sec) [ -24636.7299] [ 4928] [depth= 1] . ( 62 sec) [ -24624.5146] [ 4928] [depth= 1] . ( 65 sec) [ -24609.5862] [ 4922] [depth= 2] . ( 66 sec) [ -24603.6729] [ 4916] [depth= 1] . ( 67 sec) [ -24593.9361] [ 4910] [depth= 1] . ( 70 sec) [ -24592.5763] [ 4912] [depth= 1] . ( 72 sec) [ -24589.9824] [ 4905] [depth= 1] . ( 75 sec) [ -24589.3863] [ 4909] [depth= 1] . ( 88 sec) [ -24586.8350] [ 4910] [depth= 2] . ( 89 sec) [ -24586.3770] [ 4912] [depth= 1] . ( 90 sec) [ -24549.4990] [Branch lengths ] . ( 91 sec) [ -24549.0472] [Alpha ][ 0.681992] . ( 93 sec) [ -24548.5898] [ 4910] [depth= 1] . ( 98 sec) [ -24548.3287] [ 4902] [depth= 1] . ( 105 sec) [ -24546.6227] [ 4903] [depth= 1] . ( 123 sec) [ -24542.7961] [ 4909] [depth= 1] . ( 133 sec) [ -24532.8137] [Branch lengths ] . ( 133 sec) [ -24532.7259] [Alpha ][ 0.695662] . ( 186 sec) [ -24530.6668] [Branch lengths ] . ( 186 sec) [ -24530.6668] [Topology ] . ( 189 sec) [ -24530.2522] [Topology ] . ( 193 sec) [ -24530.0820] [Topology ] . ( 197 sec) [ -24529.9786] [Topology ] . ( 200 sec) [ -24529.9130] [Topology ] . ( 204 sec) [ -24529.8713] [Topology ] . ( 208 sec) [ -24529.8447] [Topology ] . ( 208 sec) [ -24529.8247] [Alpha ][ 0.702187] . ( 209 sec) [ -24529.8247] [Topology ] . ( 212 sec) [ -24529.8046] [Topology ] . ( 216 sec) [ -24529.7922] [Topology ] . ( 219 sec) [ -24529.7842] [Topology ] . ( 223 sec) [ -24529.7791] [Topology ] . ( 227 sec) [ -24529.7758] [Topology ] . ( 230 sec) [ -24529.7737] [Topology ] . ( 231 sec) [ -24529.7733] [Alpha ][ 0.703049] . ( 231 sec) [ -24529.7733] [Topology ] . ( 235 sec) [ -24529.7718] [Topology ] . ( 238 sec) [ -24529.7709] [Topology ] . ( 239 sec) [ -24529.7709] [Alpha ][ 0.703049] . ( 239 sec) [ -24529.7709] [Topology ] . ( 243 sec) [ -24529.7703] [Topology ] . ( 243 sec) [ -24529.7703] [Alpha ][ 0.703049] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -24529.770277. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -29204.9401] [Alpha ][ 0.500960] . ( 2 sec) [ -28954.0909] [ 5537] [depth= 7] . ( 3 sec) [ -28687.7482] [ 5525] [depth= 1] . ( 3 sec) [ -27750.9641] [ 5517] [depth= 4] . ( 4 sec) [ -27698.3921] [ 5510] [depth= 1] . ( 4 sec) [ -27680.4746] [ 5509] [depth= 1] . ( 5 sec) [ -27668.6364] [ 5471] [depth= 1] . ( 5 sec) [ -27484.0730] [ 5431] [depth= 11] . ( 6 sec) [ -27452.0126] [ 5423] [depth= 1] . ( 6 sec) [ -27297.5660] [ 5401] [depth= 4] . ( 7 sec) [ -27141.1138] [ 5390] [depth= 1] . ( 7 sec) [ -27132.1788] [ 5388] [depth= 1] . ( 8 sec) [ -26968.3136] [ 5356] [depth= 7] . ( 8 sec) [ -26967.5614] [ 5348] [depth= 5] . ( 9 sec) [ -26956.1721] [ 5336] [depth= 4] . ( 10 sec) [ -26804.2883] [ 5330] [depth= 2] . ( 11 sec) [ -26611.0295] [ 5305] [depth= 6] . ( 11 sec) [ -26477.3751] [ 5280] [depth= 5] . ( 12 sec) [ -26446.0575] [ 5276] [depth= 10] . ( 13 sec) [ -26439.7269] [ 5278] [depth= 9] . ( 13 sec) [ -26109.0135] [ 5269] [depth= 3] . ( 14 sec) [ -26102.0863] [ 5265] [depth= 1] . ( 15 sec) [ -26082.7177] [ 5253] [depth= 2] . ( 15 sec) [ -25983.9556] [ 5216] [depth= 3] . ( 16 sec) [ -25958.9893] [ 5195] [depth= 3] . ( 16 sec) [ -25935.5563] [ 5194] [depth= 3] . ( 17 sec) [ -25922.9681] [ 5197] [depth= 2] . ( 19 sec) [ -25921.7482] [ 5202] [depth= 1] . ( 19 sec) [ -25905.1669] [ 5195] [depth= 1] . ( 20 sec) [ -25811.5910] [ 5162] [depth= 5] . ( 21 sec) [ -25687.8018] [ 5153] [depth= 1] . ( 22 sec) [ -25687.7366] [ 5154] [depth= 2] . ( 22 sec) [ -25673.3589] [ 5149] [depth= 2] . ( 24 sec) [ -25639.7347] [ 5140] [depth= 1] . ( 24 sec) [ -25369.5261] [ 5063] [depth= 6] . ( 25 sec) [ -25343.3960] [ 5037] [depth= 4] . ( 26 sec) [ -25336.3635] [ 5028] [depth= 2] . ( 27 sec) [ -25239.4627] [ 5017] [depth= 3] . ( 30 sec) [ -25234.8780] [ 5017] [depth= 1] . ( 31 sec) [ -25205.4559] [ 5017] [depth= 1] . ( 32 sec) [ -25198.5007] [ 5012] [depth= 2] . ( 32 sec) [ -25191.8597] [ 5016] [depth= 2] . ( 33 sec) [ -25187.4621] [ 4999] [depth= 5] . ( 34 sec) [ -25083.3412] [ 4999] [depth= 2] . ( 35 sec) [ -25045.8748] [ 4988] [depth= 13] . ( 35 sec) [ -25017.6764] [ 4982] [depth= 1] . ( 36 sec) [ -24897.2889] [ 4952] [depth= 1] . ( 36 sec) [ -24889.8016] [ 4947] [depth= 1] . ( 37 sec) [ -24889.4204] [ 4949] [depth= 2] . ( 38 sec) [ -24885.9254] [ 4945] [depth= 1] . ( 38 sec) [ -24849.5676] [ 4940] [depth= 11] . ( 39 sec) [ -24816.3757] [ 4944] [depth= 12] . ( 40 sec) [ -24805.6220] [ 4933] [depth= 1] . ( 41 sec) [ -24796.2664] [ 4935] [depth= 1] . ( 44 sec) [ -24674.4206] [Branch lengths ] . ( 45 sec) [ -24658.9845] [Alpha ][ 0.644432] . ( 47 sec) [ -24655.4648] [ 4934] [depth= 3] . ( 48 sec) [ -24651.2377] [ 4935] [depth= 1] . ( 49 sec) [ -24650.6618] [ 4936] [depth= 1] . ( 50 sec) [ -24649.8717] [ 4936] [depth= 2] . ( 51 sec) [ -24649.3500] [ 4938] [depth= 1] . ( 52 sec) [ -24645.9239] [ 4938] [depth= 1] . ( 53 sec) [ -24640.6615] [ 4936] [depth= 1] . ( 54 sec) [ -24635.9286] [ 4934] [depth= 1] . ( 55 sec) [ -24634.7563] [ 4928] [depth= 1] . ( 61 sec) [ -24627.7038] [ 4926] [depth= 2] . ( 68 sec) [ -24626.9261] [ 4925] [depth= 1] . ( 70 sec) [ -24624.4380] [ 4926] [depth= 1] . ( 70 sec) [ -24610.8728] [ 4925] [depth= 1] . ( 72 sec) [ -24605.2985] [ 4928] [depth= 2] . ( 78 sec) [ -24600.9263] [ 4933] [depth= 1] . ( 78 sec) [ -24599.4285] [ 4947] [depth= 5] . ( 83 sec) [ -24597.8121] [ 4951] [depth= 1] . ( 84 sec) [ -24595.3726] [ 4914] [depth= 9] . ( 86 sec) [ -24592.4741] [ 4918] [depth= 2] . ( 88 sec) [ -24559.9007] [Branch lengths ] . ( 89 sec) [ -24559.1269] [Alpha ][ 0.682433] . ( 96 sec) [ -24558.8163] [ 4913] [depth= 1] . ( 123 sec) [ -24557.7521] [ 4914] [depth= 1] . ( 127 sec) [ -24551.5636] [ 4921] [depth= 1] . ( 142 sec) [ -24550.5721] [ 4920] [depth= 1] . ( 144 sec) [ -24542.8312] [Branch lengths ] . ( 145 sec) [ -24542.7931] [Alpha ][ 0.691311] . ( 152 sec) [ -24541.7554] [ 4909] [depth= 1] . ( 197 sec) [ -24531.1872] [Branch lengths ] . ( 198 sec) [ -24531.1687] [Alpha ][ 0.697572] . ( 251 sec) [ -24529.9856] [Branch lengths ] . ( 251 sec) [ -24529.9856] [Topology ] . ( 255 sec) [ -24529.8908] [Topology ] . ( 258 sec) [ -24529.8508] [Topology ] . ( 262 sec) [ -24529.8268] [Topology ] . ( 266 sec) [ -24529.8117] [Topology ] . ( 269 sec) [ -24529.8021] [Topology ] . ( 273 sec) [ -24529.7960] [Topology ] . ( 274 sec) [ -24529.7834] [Alpha ][ 0.702746] . ( 274 sec) [ -24529.7834] [Topology ] . ( 277 sec) [ -24529.7781] [Topology ] . ( 281 sec) [ -24529.7749] [Topology ] . ( 285 sec) [ -24529.7729] [Topology ] . ( 288 sec) [ -24529.7717] [Topology ] . ( 292 sec) [ -24529.7708] [Topology ] . ( 293 sec) [ -24529.7708] [Alpha ][ 0.703448] . ( 293 sec) [ -24529.7708] [Topology ] . ( 296 sec) [ -24529.7702] [Topology ] . ( 297 sec) [ -24529.7702] [Alpha ][ 0.703448] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -24529.770174. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -29625.2599] [Alpha ][ 0.500960] . ( 2 sec) [ -29531.3034] [ 5516] [depth= 6] . ( 3 sec) [ -29394.5682] [ 5499] [depth= 7] . ( 4 sec) [ -29153.8466] [ 5489] [depth= 3] . ( 4 sec) [ -29144.6548] [ 5502] [depth= 1] . ( 5 sec) [ -28921.5144] [ 5482] [depth= 4] . ( 6 sec) [ -28902.2445] [ 5484] [depth= 1] . ( 6 sec) [ -28703.1118] [ 5465] [depth= 4] . ( 7 sec) [ -28624.0328] [ 5431] [depth= 2] . ( 7 sec) [ -28362.3620] [ 5420] [depth= 2] . ( 8 sec) [ -28308.8973] [ 5409] [depth= 5] . ( 8 sec) [ -28193.7713] [ 5405] [depth= 1] . ( 9 sec) [ -28175.4035] [ 5387] [depth= 2] . ( 9 sec) [ -28145.4153] [ 5401] [depth= 1] . ( 10 sec) [ -28091.2538] [ 5387] [depth= 1] . ( 10 sec) [ -27796.3267] [ 5304] [depth= 8] . ( 11 sec) [ -27582.4933] [ 5280] [depth= 8] . ( 11 sec) [ -27580.5964] [ 5280] [depth= 1] . ( 12 sec) [ -27490.0165] [ 5245] [depth= 1] . ( 13 sec) [ -26583.7750] [ 5234] [depth= 4] . ( 13 sec) [ -26578.0430] [ 5220] [depth= 4] . ( 14 sec) [ -26500.0508] [ 5208] [depth= 1] . ( 14 sec) [ -26495.4138] [ 5199] [depth= 1] . ( 15 sec) [ -26366.8159] [ 5166] [depth= 5] . ( 16 sec) [ -26300.0284] [ 5144] [depth= 6] . ( 17 sec) [ -26213.6003] [ 5128] [depth= 4] . ( 17 sec) [ -26146.2300] [ 5114] [depth= 1] . ( 18 sec) [ -26043.5503] [ 5085] [depth= 2] . ( 19 sec) [ -25854.7470] [ 5049] [depth= 4] . ( 19 sec) [ -25833.0471] [ 5043] [depth= 1] . ( 20 sec) [ -25832.4463] [ 5044] [depth= 1] . ( 21 sec) [ -25791.5534] [ 5049] [depth= 9] . ( 22 sec) [ -25776.9512] [ 5048] [depth= 1] . ( 22 sec) [ -25666.3077] [ 5032] [depth= 4] . ( 23 sec) [ -25295.0449] [ 5005] [depth= 3] . ( 24 sec) [ -25153.1736] [ 4989] [depth= 1] . ( 25 sec) [ -25142.8128] [ 4991] [depth= 2] . ( 26 sec) [ -25133.6279] [ 4988] [depth= 2] . ( 27 sec) [ -25101.5942] [ 4975] [depth= 3] . ( 28 sec) [ -25097.8460] [ 4979] [depth= 2] . ( 29 sec) [ -25089.7109] [ 4978] [depth= 1] . ( 29 sec) [ -25068.2542] [ 4977] [depth= 1] . ( 30 sec) [ -25063.8025] [ 4977] [depth= 1] . ( 30 sec) [ -25052.8692] [ 4985] [depth= 7] . ( 31 sec) [ -25017.0106] [ 4983] [depth= 2] . ( 32 sec) [ -25002.5520] [ 4982] [depth= 2] . ( 33 sec) [ -24998.8883] [ 4977] [depth= 3] . ( 35 sec) [ -24995.7737] [ 4979] [depth= 3] . ( 36 sec) [ -24991.8147] [ 4974] [depth= 1] . ( 36 sec) [ -24987.7419] [ 4983] [depth= 1] . ( 40 sec) [ -24982.3856] [ 4971] [depth= 2] . ( 41 sec) [ -24956.7728] [ 4963] [depth= 5] . ( 42 sec) [ -24943.0361] [ 4966] [depth= 1] . ( 43 sec) [ -24935.0482] [ 4967] [depth= 4] . ( 44 sec) [ -24933.8345] [ 4969] [depth= 2] . ( 46 sec) [ -24932.1798] [ 4966] [depth= 4] . ( 46 sec) [ -24834.1622] [ 4957] [depth= 1] . ( 47 sec) [ -24824.4101] [ 4960] [depth= 1] . ( 48 sec) [ -24679.6161] [Branch lengths ] . ( 49 sec) [ -24660.1188] [Alpha ][ 0.666138] . ( 50 sec) [ -24655.3806] [ 4953] [depth= 2] . ( 51 sec) [ -24652.2595] [ 4957] [depth= 1] . ( 58 sec) [ -24651.3798] [ 4946] [depth= 4] . ( 60 sec) [ -24646.8869] [ 4942] [depth= 1] . ( 61 sec) [ -24644.7248] [ 4946] [depth= 1] . ( 68 sec) [ -24628.6561] [ 4948] [depth= 4] . ( 74 sec) [ -24621.7023] [ 4944] [depth= 1] . ( 76 sec) [ -24618.9149] [ 4933] [depth= 1] . ( 77 sec) [ -24608.6561] [ 4929] [depth= 5] . ( 78 sec) [ -24588.3809] [ 4934] [depth= 6] . ( 80 sec) [ -24587.1739] [ 4933] [depth= 1] . ( 85 sec) [ -24584.2789] [ 4931] [depth= 2] . ( 94 sec) [ -24582.4907] [ 4929] [depth= 2] . ( 97 sec) [ -24582.0059] [ 4926] [depth= 1] . ( 112 sec) [ -24545.3519] [Branch lengths ] . ( 113 sec) [ -24544.7637] [Alpha ][ 0.699873] . ( 118 sec) [ -24543.4484] [ 4929] [depth= 1] . ( 130 sec) [ -24541.9197] [ 4930] [depth= 2] . ( 145 sec) [ -24534.4889] [ 4929] [depth= 2] . ( 152 sec) [ -24533.6105] [ 4921] [depth= 1] . ( 173 sec) [ -24527.6897] [Branch lengths ] . ( 173 sec) [ -24527.6865] [Alpha ][ 0.697182] . ( 225 sec) [ -24526.7517] [Branch lengths ] . ( 226 sec) [ -24526.7517] [Topology ] . ( 229 sec) [ -24526.5875] [Topology ] . ( 233 sec) [ -24526.5136] [Topology ] . ( 237 sec) [ -24526.4681] [Topology ] . ( 240 sec) [ -24526.4390] [Topology ] . ( 244 sec) [ -24526.4202] [Topology ] . ( 248 sec) [ -24526.4080] [Topology ] . ( 248 sec) [ -24526.3940] [Alpha ][ 0.702621] . ( 248 sec) [ -24526.3940] [Topology ] . ( 252 sec) [ -24526.3842] [Topology ] . ( 256 sec) [ -24526.3780] [Topology ] . ( 259 sec) [ -24526.3740] [Topology ] . ( 263 sec) [ -24526.3714] [Topology ] . ( 267 sec) [ -24526.3697] [Topology ] . ( 270 sec) [ -24526.3686] [Topology ] . ( 271 sec) [ -24526.3684] [Alpha ][ 0.703324] . ( 271 sec) [ -24526.3684] [Topology ] . ( 275 sec) [ -24526.3676] [Topology ] . ( 276 sec) [ -24526.3676] [Alpha ][ 0.703324] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -24526.367571. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -31693.2878] [Alpha ][ 0.500960] . ( 2 sec) [ -31097.8991] [ 5537] [depth= 6] . ( 2 sec) [ -30740.4251] [ 5518] [depth= 8] . ( 3 sec) [ -30460.2105] [ 5511] [depth= 2] . ( 3 sec) [ -29092.0732] [ 5510] [depth= 1] . ( 4 sec) [ -28900.9921] [ 5493] [depth= 7] . ( 4 sec) [ -28469.6742] [ 5503] [depth= 1] . ( 5 sec) [ -28345.7369] [ 5491] [depth= 1] . ( 6 sec) [ -28209.1916] [ 5446] [depth= 10] . ( 6 sec) [ -28058.5249] [ 5408] [depth= 4] . ( 7 sec) [ -27856.2415] [ 5353] [depth= 4] . ( 8 sec) [ -27736.8841] [ 5377] [depth= 10] . ( 8 sec) [ -27572.8865] [ 5346] [depth= 7] . ( 9 sec) [ -27437.2225] [ 5344] [depth= 6] . ( 9 sec) [ -27405.1349] [ 5338] [depth= 2] . ( 10 sec) [ -26497.7750] [ 5296] [depth= 3] . ( 11 sec) [ -26334.3324] [ 5242] [depth= 9] . ( 11 sec) [ -26232.5718] [ 5223] [depth= 1] . ( 12 sec) [ -26203.4763] [ 5228] [depth= 5] . ( 13 sec) [ -26156.0101] [ 5198] [depth= 4] . ( 13 sec) [ -26053.0517] [ 5153] [depth= 1] . ( 14 sec) [ -25969.3777] [ 5135] [depth= 9] . ( 15 sec) [ -25843.9988] [ 5119] [depth= 7] . ( 15 sec) [ -25718.5031] [ 5112] [depth= 3] . ( 16 sec) [ -25686.9334] [ 5113] [depth= 1] . ( 17 sec) [ -25679.0297] [ 5107] [depth= 5] . ( 17 sec) [ -25671.6286] [ 5104] [depth= 1] . ( 18 sec) [ -25647.1149] [ 5097] [depth= 4] . ( 18 sec) [ -25612.7950] [ 5096] [depth= 3] . ( 19 sec) [ -25591.1540] [ 5093] [depth= 5] . ( 19 sec) [ -25577.3204] [ 5093] [depth= 1] . ( 20 sec) [ -25576.0120] [ 5094] [depth= 2] . ( 21 sec) [ -25521.9634] [ 5096] [depth= 1] . ( 21 sec) [ -25324.2032] [ 5088] [depth= 2] . ( 22 sec) [ -25157.5828] [ 5078] [depth= 2] . ( 23 sec) [ -25107.6409] [ 5062] [depth= 1] . ( 24 sec) [ -25100.0400] [ 5062] [depth= 2] . ( 25 sec) [ -25092.9241] [ 5055] [depth= 3] . ( 25 sec) [ -25068.1053] [ 5066] [depth= 6] . ( 27 sec) [ -25064.7838] [ 5067] [depth= 2] . ( 28 sec) [ -25021.0563] [ 5067] [depth= 7] . ( 28 sec) [ -24992.9043] [ 5062] [depth= 1] . ( 29 sec) [ -24982.5600] [ 5055] [depth= 3] . ( 30 sec) [ -24976.1048] [ 5039] [depth= 2] . ( 30 sec) [ -24974.9563] [ 5041] [depth= 1] . ( 31 sec) [ -24966.3048] [ 5038] [depth= 2] . ( 31 sec) [ -24926.2196] [ 5024] [depth= 1] . ( 32 sec) [ -24879.5408] [ 5012] [depth= 1] . ( 33 sec) [ -24869.4158] [ 5007] [depth= 4] . ( 33 sec) [ -24866.0458] [ 5000] [depth= 1] . ( 35 sec) [ -24855.2691] [ 4995] [depth= 3] . ( 41 sec) [ -24848.9038] [ 5000] [depth= 5] . ( 42 sec) [ -24842.8789] [ 4987] [depth= 1] . ( 44 sec) [ -24839.7678] [ 4991] [depth= 1] . ( 45 sec) [ -24836.4277] [ 4986] [depth= 2] . ( 46 sec) [ -24835.5089] [ 4988] [depth= 2] . ( 47 sec) [ -24795.0185] [ 4977] [depth= 1] . ( 49 sec) [ -24677.7606] [Branch lengths ] . ( 50 sec) [ -24659.9552] [Alpha ][ 0.655653] . ( 51 sec) [ -24651.2096] [ 4974] [depth= 1] . ( 51 sec) [ -24639.6736] [ 4955] [depth= 6] . ( 52 sec) [ -24631.2936] [ 4952] [depth= 1] . ( 53 sec) [ -24630.7736] [ 4949] [depth= 2] . ( 54 sec) [ -24624.2909] [ 4953] [depth= 1] . ( 56 sec) [ -24616.4804] [ 4945] [depth= 1] . ( 58 sec) [ -24616.0630] [ 4950] [depth= 1] . ( 59 sec) [ -24613.5921] [ 4948] [depth= 1] . ( 62 sec) [ -24597.9286] [ 4936] [depth= 5] . ( 65 sec) [ -24590.5546] [ 4934] [depth= 1] . ( 80 sec) [ -24588.5201] [ 4930] [depth= 1] . ( 84 sec) [ -24586.0625] [ 4917] [depth= 4] . ( 89 sec) [ -24582.2171] [ 4919] [depth= 2] . ( 91 sec) [ -24550.0262] [Branch lengths ] . ( 92 sec) [ -24549.5480] [Alpha ][ 0.686337] . ( 97 sec) [ -24547.9361] [ 4924] [depth= 1] . ( 103 sec) [ -24546.9642] [ 4924] [depth= 1] . ( 127 sec) [ -24545.7801] [ 4924] [depth= 1] . ( 134 sec) [ -24543.9935] [ 4929] [depth= 3] . ( 136 sec) [ -24543.6769] [ 4925] [depth= 1] . ( 148 sec) [ -24541.6988] [ 4923] [depth= 2] . ( 150 sec) [ -24530.1052] [Branch lengths ] . ( 151 sec) [ -24530.0254] [Alpha ][ 0.699442] . ( 215 sec) [ -24528.3177] [Branch lengths ] . ( 215 sec) [ -24528.3177] [Topology ] . ( 219 sec) [ -24528.0493] [Topology ] . ( 223 sec) [ -24527.9307] [Topology ] . ( 226 sec) [ -24527.8569] [Topology ] . ( 230 sec) [ -24527.8094] [Topology ] . ( 234 sec) [ -24527.7786] [Topology ] . ( 237 sec) [ -24527.7585] [Topology ] . ( 238 sec) [ -24527.7466] [Alpha ][ 0.704480] . ( 238 sec) [ -24527.7466] [Topology ] . ( 242 sec) [ -24527.7315] [Topology ] . ( 245 sec) [ -24527.7217] [Topology ] . ( 249 sec) [ -24527.7153] [Topology ] . ( 253 sec) [ -24527.7111] [Topology ] . ( 256 sec) [ -24527.7083] [Topology ] . ( 260 sec) [ -24527.7065] [Topology ] . ( 260 sec) [ -24527.7062] [Alpha ][ 0.705237] . ( 261 sec) [ -24527.7062] [Topology ] . ( 264 sec) [ -24527.7049] [Topology ] . ( 268 sec) [ -24527.7041] [Topology ] . ( 269 sec) [ -24527.7041] [Alpha ][ 0.705237] . ( 269 sec) [ -24527.7041] [Topology ] . ( 272 sec) [ -24527.7035] [Topology ] . ( 273 sec) [ -24527.7035] [Alpha ][ 0.705237] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -24527.703506. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 2 sec) [ -24774.5534] [Alpha ][ 0.568788] . ( 2 sec) [ -24774.5534] [Topology ] . ( 5 sec) [ -24604.5727] [Topology ] . ( 9 sec) [ -24577.4142] [Topology ] . ( 12 sec) [ -24569.8172] [Topology ] . ( 16 sec) [ -24566.0500] [Topology ] . ( 19 sec) [ -24563.8019] [Topology ] . ( 23 sec) [ -24562.4009] [Topology ] . ( 27 sec) [ -24561.5110] [Topology ] . ( 30 sec) [ -24560.9388] [Topology ] . Checking for NNIs, optimizing five branches... . ( 62 sec) [ -24551.4355] [Alpha ][ 0.694186] . ( 62 sec) [ -24551.4355] [Topology ] . ( 65 sec) [ -24550.1640] [Topology ] . ( 69 sec) [ -24549.5953] [Topology ] . ( 72 sec) [ -24549.2553] [Topology ] . ( 76 sec) [ -24549.0455] [Topology ] . ( 80 sec) [ -24548.9148] [Topology ] . ( 83 sec) [ -24548.8327] [Topology ] . Checking for NNIs, optimizing five branches... . ( 114 sec) [ -24548.7536] [Alpha ][ 0.707150] . ( 114 sec) [ -24548.7536] [Topology ] . ( 118 sec) [ -24548.6901] [Topology ] . ( 121 sec) [ -24548.6518] [Topology ] . ( 125 sec) [ -24548.6279] [Topology ] . ( 128 sec) [ -24548.6128] [Topology ] . ( 132 sec) [ -24548.6033] [Topology ] . ( 135 sec) [ -24548.5973] [Topology ] . Checking for NNIs, optimizing five branches... . ( 166 sec) [ -24548.5961] [Alpha ][ 0.708722] . ( 166 sec) [ -24548.5961] [Topology ] . ( 170 sec) [ -24548.5920] [Topology ] . ( 173 sec) [ -24548.5894] [Topology ] . ( 177 sec) [ -24548.5878] [Topology ] . ( 180 sec) [ -24548.5867] [Topology ] . ( 184 sec) [ -24548.5861] [Topology ] . Checking for NNIs, optimizing five branches... . ( 215 sec) [ -24548.5861] [Alpha ][ 0.709431] . ( 215 sec) [ -24548.5861] [Topology ] . ( 218 sec) [ -24548.5856] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 279 sec) [ -24774.5534] [Alpha ][ 0.568788] . ( 281 sec) [ -24770.6356] [ 4912] [depth= 2] . ( 282 sec) [ -24754.7924] [ 4911] [depth= 1] . ( 283 sec) [ -24750.8991] [ 4912] [depth= 1] . ( 286 sec) [ -24750.3251] [ 4917] [depth= 1] . ( 287 sec) [ -24749.7088] [ 4922] [depth= 1] . ( 288 sec) [ -24749.1434] [ 4918] [depth= 3] . ( 290 sec) [ -24745.1957] [ 4935] [depth= 1] . ( 291 sec) [ -24735.6770] [ 4918] [depth= 1] . ( 291 sec) [ -24725.4325] [ 4918] [depth= 2] . ( 293 sec) [ -24722.7390] [ 4922] [depth= 1] . ( 294 sec) [ -24720.7531] [ 4918] [depth= 1] . ( 295 sec) [ -24719.3563] [ 4921] [depth= 2] . ( 296 sec) [ -24711.0539] [ 4914] [depth= 2] . ( 297 sec) [ -24709.7604] [ 4917] [depth= 1] . ( 297 sec) [ -24703.2458] [ 4921] [depth= 1] . ( 298 sec) [ -24691.7815] [ 4925] [depth= 1] . ( 300 sec) [ -24682.0022] [ 4926] [depth= 1] . ( 300 sec) [ -24677.6305] [ 4925] [depth= 1] . ( 301 sec) [ -24677.2427] [ 4921] [depth= 1] . ( 302 sec) [ -24666.3676] [ 4923] [depth= 4] . ( 305 sec) [ -24665.7809] [ 4926] [depth= 1] . ( 308 sec) [ -24658.7862] [ 4923] [depth= 1] . ( 309 sec) [ -24658.5416] [ 4926] [depth= 1] . ( 309 sec) [ -24658.1349] [ 4922] [depth= 1] . ( 310 sec) [ -24655.6356] [ 4926] [depth= 1] . ( 311 sec) [ -24655.5104] [ 4925] [depth= 1] . ( 312 sec) [ -24648.1249] [ 4920] [depth= 1] . ( 313 sec) [ -24647.2387] [ 4923] [depth= 1] . ( 314 sec) [ -24643.6939] [ 4927] [depth= 2] . ( 318 sec) [ -24641.3313] [ 4923] [depth= 1] . ( 320 sec) [ -24638.6431] [ 4926] [depth= 2] . ( 322 sec) [ -24581.3651] [Branch lengths ] . ( 323 sec) [ -24573.5916] [Alpha ][ 0.682758] . ( 328 sec) [ -24567.1512] [ 4919] [depth= 1] . ( 339 sec) [ -24558.3976] [ 4921] [depth= 3] . ( 375 sec) [ -24545.7546] [Branch lengths ] . ( 375 sec) [ -24545.6295] [Alpha ][ 0.698976] . ( 378 sec) [ -24544.1948] [ 4920] [depth= 6] . ( 427 sec) [ -24540.7976] [Branch lengths ] . ( 427 sec) [ -24540.7971] [Alpha ][ 0.697836] . ( 479 sec) [ -24539.9444] [Branch lengths ] . ( 479 sec) [ -24539.9444] [Topology ] . ( 483 sec) [ -24534.6494] [Topology ] . ( 486 sec) [ -24530.5271] [Topology ] . ( 490 sec) [ -24529.9490] [Topology ] . ( 493 sec) [ -24529.8280] [Topology ] . ( 497 sec) [ -24529.7965] [Topology ] . ( 501 sec) [ -24529.7876] [Topology ] . ( 504 sec) [ -24529.7850] [Topology ] . ( 505 sec) [ -24529.7722] [Alpha ][ 0.703045] . ( 505 sec) [ -24529.7722] [Topology ] . ( 509 sec) [ -24529.7704] [Topology ] . ( 513 sec) [ -24529.7698] [Topology ] . ( 513 sec) [ -24529.7698] [Alpha ][ 0.703045] . ( 514 sec) [ -24529.7698] [Topology ] . ( 517 sec) [ -24529.7695] [Topology ] . ( 518 sec) [ -24529.7695] [Alpha ][ 0.703045] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -24548.585605 . Log likelihood obtained after SPR moves : -24529.769532 . Log likelihood of the current tree: -24529.769532. . Printing the most likely tree in file 'proteic_M2476_30x719_2005.phy_phyml_tree.txt'... . Best log likelihood : -24526.367571 . Time used 0h9m11s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 2019.07user 0.00system 33:52.77elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps