.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2627_54x1915_2006.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . Optimise tree topology : yes . Tree topology search : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : yes . Number of random starting trees : 5 . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 1299 patterns found. (out of a total of 1915 sites) . 625 sites without polymorphism (32.64%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 36Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 4 sec) [ -70233.6820] [GTR parameters ] . ( 5 sec) [ -68828.0694] [Alpha ][ 0.500960] . ( 5 sec) [ -68268.8659] [14172] [depth= 15] . ( 5 sec) [ -67897.0178] [14085] [depth= 15] . ( 6 sec) [ -67542.8218] [14039] [depth= 11] . ( 6 sec) [ -67012.5383] [13876] [depth= 1] . ( 6 sec) [ -66607.2311] [13840] [depth= 6] . ( 6 sec) [ -66304.8549] [13806] [depth= 1] . ( 6 sec) [ -65415.8181] [13805] [depth= 12] . ( 6 sec) [ -64847.8923] [13667] [depth= 3] . ( 7 sec) [ -64823.2912] [13667] [depth= 1] . ( 7 sec) [ -64721.9426] [13638] [depth= 1] . ( 7 sec) [ -64085.4412] [13643] [depth= 4] . ( 7 sec) [ -64042.4867] [13574] [depth= 1] . ( 7 sec) [ -63795.6209] [13498] [depth= 10] . ( 7 sec) [ -63130.8380] [13440] [depth= 2] . ( 8 sec) [ -63056.5545] [13413] [depth= 6] . ( 8 sec) [ -62823.3396] [13219] [depth= 3] . ( 8 sec) [ -62660.5377] [13216] [depth= 3] . ( 8 sec) [ -62531.8410] [13164] [depth= 3] . ( 8 sec) [ -61471.7586] [12927] [depth= 13] . ( 8 sec) [ -61184.0487] [12938] [depth= 4] . ( 9 sec) [ -61043.5370] [12945] [depth= 1] . ( 9 sec) [ -60905.6441] [12930] [depth= 2] . ( 9 sec) [ -60720.2776] [12833] [depth= 3] . ( 9 sec) [ -60087.9967] [12814] [depth= 2] . ( 9 sec) [ -59170.7069] [12678] [depth= 24] . ( 9 sec) [ -58928.2918] [12557] [depth= 7] . ( 10 sec) [ -58752.0541] [12519] [depth= 1] . ( 10 sec) [ -58478.6822] [12490] [depth= 17] . ( 10 sec) [ -58024.4682] [12381] [depth= 17] . ( 10 sec) [ -51619.8756] [12143] [depth= 5] . ( 10 sec) [ -51246.5092] [12136] [depth= 17] . ( 11 sec) [ -51031.6744] [12080] [depth= 2] . ( 11 sec) [ -51011.7585] [12071] [depth= 1] . ( 11 sec) [ -49628.6710] [11784] [depth= 11] . ( 11 sec) [ -49444.0577] [11706] [depth= 1] . ( 11 sec) [ -48650.1047] [11622] [depth= 23] . ( 11 sec) [ -48584.1725] [11621] [depth= 12] . ( 12 sec) [ -47840.7990] [11506] [depth= 2] . ( 12 sec) [ -47818.2090] [11505] [depth= 17] . ( 12 sec) [ -47131.2240] [11295] [depth= 17] . ( 12 sec) [ -47124.6844] [11296] [depth= 1] . ( 12 sec) [ -47084.4378] [11289] [depth= 2] . ( 12 sec) [ -46796.3526] [11264] [depth= 2] . ( 13 sec) [ -46541.4096] [11226] [depth= 2] . ( 13 sec) [ -46389.7343] [11135] [depth= 1] . ( 13 sec) [ -45748.1638] [11078] [depth= 10] . ( 13 sec) [ -45206.5355] [11090] [depth= 14] . ( 13 sec) [ -44584.2084] [10911] [depth= 11] . ( 14 sec) [ -44538.6753] [10881] [depth= 1] . ( 14 sec) [ -44347.1364] [10843] [depth= 1] . ( 14 sec) [ -44193.2435] [10831] [depth= 4] . ( 14 sec) [ -44178.6543] [10827] [depth= 6] . ( 14 sec) [ -44160.4142] [10798] [depth= 10] . ( 14 sec) [ -44148.8272] [10795] [depth= 1] . ( 15 sec) [ -44026.6147] [10791] [depth= 1] . ( 15 sec) [ -43842.4762] [10654] [depth= 4] . ( 15 sec) [ -43819.1486] [10644] [depth= 1] . ( 15 sec) [ -43712.9349] [10623] [depth= 12] . ( 15 sec) [ -43700.6391] [10620] [depth= 2] . ( 15 sec) [ -43380.1426] [10545] [depth= 3] . ( 16 sec) [ -43378.8511] [10554] [depth= 1] . ( 16 sec) [ -42907.1975] [10418] [depth= 9] . ( 16 sec) [ -42658.3773] [10242] [depth= 4] . ( 16 sec) [ -42549.0735] [10206] [depth= 3] . ( 16 sec) [ -42474.2359] [10154] [depth= 1] . ( 16 sec) [ -42406.1857] [10157] [depth= 2] . ( 17 sec) [ -42162.3620] [10062] [depth= 7] . ( 17 sec) [ -41909.1915] [ 9929] [depth= 1] . ( 17 sec) [ -41487.4617] [ 9813] [depth= 8] . ( 17 sec) [ -41279.3076] [ 9794] [depth= 16] . ( 17 sec) [ -40992.6176] [ 9725] [depth= 3] . ( 18 sec) [ -40901.8866] [ 9726] [depth= 2] . ( 18 sec) [ -40892.2249] [ 9718] [depth= 1] . ( 18 sec) [ -40838.6994] [ 9706] [depth= 4] . ( 18 sec) [ -40387.9768] [ 9648] [depth= 12] . ( 18 sec) [ -40286.0066] [ 9657] [depth= 2] . ( 18 sec) [ -40229.4553] [ 9641] [depth= 1] . ( 19 sec) [ -40141.0847] [ 9596] [depth= 1] . ( 19 sec) [ -40130.4782] [ 9562] [depth= 1] . ( 19 sec) [ -39737.7171] [ 9411] [depth= 10] . ( 19 sec) [ -39714.5950] [ 9401] [depth= 2] . ( 19 sec) [ -39709.4488] [ 9404] [depth= 1] . ( 20 sec) [ -39418.8909] [ 9330] [depth= 10] . ( 20 sec) [ -39369.7773] [ 9312] [depth= 2] . ( 20 sec) [ -39334.2795] [ 9292] [depth= 1] . ( 20 sec) [ -39086.9149] [ 9199] [depth= 2] . ( 20 sec) [ -39061.2589] [ 9195] [depth= 1] . ( 20 sec) [ -39059.3962] [ 9192] [depth= 1] . ( 21 sec) [ -39020.6377] [ 9151] [depth= 1] . ( 21 sec) [ -38882.5069] [ 9173] [depth= 1] . ( 21 sec) [ -38684.5857] [ 9031] [depth= 10] . ( 21 sec) [ -38563.4782] [ 9011] [depth= 1] . ( 22 sec) [ -38438.1137] [ 8953] [depth= 3] . ( 22 sec) [ -38309.0045] [ 8890] [depth= 1] . ( 22 sec) [ -38233.9883] [ 8864] [depth= 11] . ( 22 sec) [ -38201.2984] [ 8854] [depth= 3] . ( 22 sec) [ -37970.3496] [ 8851] [depth= 2] . ( 23 sec) [ -37956.9307] [ 8851] [depth= 1] . ( 23 sec) [ -37776.6167] [ 8761] [depth= 5] . ( 24 sec) [ -37724.5232] [ 8742] [depth= 1] . ( 24 sec) [ -37672.1645] [ 8725] [depth= 1] . ( 24 sec) [ -37583.8603] [ 8708] [depth= 5] . ( 24 sec) [ -37498.1157] [ 8696] [depth= 1] . ( 24 sec) [ -37490.1294] [ 8702] [depth= 1] . ( 24 sec) [ -37473.6125] [ 8696] [depth= 1] . ( 25 sec) [ -37460.6724] [ 8692] [depth= 1] . ( 25 sec) [ -37347.2307] [ 8648] [depth= 1] . ( 25 sec) [ -37330.4227] [ 8605] [depth= 1] . ( 25 sec) [ -37301.6894] [ 8587] [depth= 1] . ( 25 sec) [ -37159.2901] [ 8510] [depth= 3] . ( 26 sec) [ -37127.5059] [ 8504] [depth= 1] . ( 26 sec) [ -37114.1238] [ 8500] [depth= 1] . ( 26 sec) [ -36886.5619] [ 8424] [depth= 2] . ( 27 sec) [ -36885.1780] [ 8436] [depth= 1] . ( 28 sec) [ -36412.2694] [Branch lengths ] . ( 31 sec) [ -35645.9244] [GTR parameters ] . ( 31 sec) [ -35644.7009] [Alpha ][ 0.476957] . ( 32 sec) [ -35625.7594] [ 8426] [depth= 1] . ( 32 sec) [ -35613.6326] [ 8420] [depth= 1] . ( 32 sec) [ -35601.1117] [ 8414] [depth= 1] . ( 33 sec) [ -35601.0716] [ 8414] [depth= 1] . ( 34 sec) [ -35588.1802] [ 8405] [depth= 2] . ( 34 sec) [ -35416.6679] [ 8293] [depth= 7] . ( 35 sec) [ -35401.8427] [ 8281] [depth= 1] . ( 35 sec) [ -35398.1231] [ 8277] [depth= 2] . ( 36 sec) [ -35397.5659] [ 8277] [depth= 1] . ( 36 sec) [ -35392.2187] [ 8275] [depth= 1] . ( 37 sec) [ -35391.7181] [ 8279] [depth= 1] . ( 38 sec) [ -35390.0400] [ 8275] [depth= 1] . ( 39 sec) [ -35376.2229] [ 8257] [depth= 1] . ( 39 sec) [ -35364.8677] [ 8238] [depth= 1] . ( 40 sec) [ -35363.9617] [ 8237] [depth= 1] . ( 40 sec) [ -35355.8849] [ 8232] [depth= 1] . ( 42 sec) [ -35354.4731] [ 8236] [depth= 1] . ( 42 sec) [ -35354.0583] [ 8240] [depth= 1] . ( 42 sec) [ -35353.8889] [ 8243] [depth= 1] . ( 43 sec) [ -35346.1662] [ 8246] [depth= 1] . ( 43 sec) [ -35342.4177] [ 8239] [depth= 1] . ( 43 sec) [ -35335.3998] [ 8239] [depth= 1] . ( 45 sec) [ -35333.7004] [ 8236] [depth= 1] . ( 45 sec) [ -35332.7841] [ 8239] [depth= 1] . ( 47 sec) [ -35274.6441] [Branch lengths ] . ( 49 sec) [ -35272.3216] [GTR parameters ] . ( 49 sec) [ -35271.9359] [Alpha ][ 0.489998] . ( 58 sec) [ -35270.6609] [ 8231] [depth= 2] . ( 64 sec) [ -35260.6411] [Branch lengths ] . ( 65 sec) [ -35260.2857] [GTR parameters ] . ( 65 sec) [ -35260.2366] [Alpha ][ 0.494821] . ( 81 sec) [ -35256.9021] [Branch lengths ] . ( 166 sec) [ -35255.6316] [Branch lengths ] . ( 166 sec) [ -35255.6316] [Topology ] . ( 169 sec) [ -35255.3437] [Topology ] . ( 171 sec) [ -35255.1956] [Topology ] . ( 174 sec) [ -35255.0912] [Topology ] . ( 177 sec) [ -35255.0155] [Topology ] . ( 180 sec) [ -35254.9601] [Topology ] . ( 183 sec) [ -35254.9192] [Topology ] . ( 185 sec) [ -35254.1419] [GTR parameters ] . ( 185 sec) [ -35254.0880] [Alpha ][ 0.499813] . ( 185 sec) [ -35254.0880] [Topology ] . ( 188 sec) [ -35253.8884] [Topology ] . ( 191 sec) [ -35253.7553] [Topology ] . ( 194 sec) [ -35253.6578] [Topology ] . ( 196 sec) [ -35253.5860] [Topology ] . ( 199 sec) [ -35253.5329] [Topology ] . ( 202 sec) [ -35253.4934] [Topology ] . ( 203 sec) [ -35253.4381] [GTR parameters ] . ( 203 sec) [ -35253.4381] [Alpha ][ 0.499813] . ( 203 sec) [ -35253.4381] [Topology ] . ( 206 sec) [ -35253.3825] [Topology ] . ( 209 sec) [ -35253.3424] [Topology ] . ( 212 sec) [ -35253.3126] [Topology ] . ( 215 sec) [ -35253.2902] [Topology ] . ( 218 sec) [ -35253.2734] [Topology ] . ( 221 sec) [ -35253.2608] [Topology ] . ( 221 sec) [ -35253.2370] [GTR parameters ] . ( 221 sec) [ -35253.2370] [Alpha ][ 0.499813] . ( 221 sec) [ -35253.2370] [Topology ] . ( 224 sec) [ -35253.2176] [Topology ] . ( 227 sec) [ -35253.2036] [Topology ] . ( 230 sec) [ -35253.1931] [Topology ] . ( 233 sec) [ -35253.1852] [Topology ] . ( 236 sec) [ -35253.1792] [Topology ] . ( 239 sec) [ -35253.1746] [Topology ] . ( 239 sec) [ -35253.1659] [GTR parameters ] . ( 239 sec) [ -35253.1655] [Alpha ][ 0.499308] . ( 239 sec) [ -35253.1655] [Topology ] . ( 242 sec) [ -35253.1585] [Topology ] . ( 245 sec) [ -35253.1534] [Topology ] . ( 248 sec) [ -35253.1497] [Topology ] . ( 251 sec) [ -35253.1468] [Topology ] . ( 254 sec) [ -35253.1446] [Topology ] . ( 257 sec) [ -35253.1430] [Topology ] . ( 257 sec) [ -35253.1392] [GTR parameters ] . ( 258 sec) [ -35253.1392] [Alpha ][ 0.499308] . ( 258 sec) [ -35253.1392] [Topology ] . ( 261 sec) [ -35253.1365] [Topology ] . ( 263 sec) [ -35253.1345] [Topology ] . ( 266 sec) [ -35253.1331] [Topology ] . ( 269 sec) [ -35253.1320] [Topology ] . ( 272 sec) [ -35253.1311] [Topology ] . ( 273 sec) [ -35253.1302] [GTR parameters ] . ( 273 sec) [ -35253.1302] [Alpha ][ 0.499308] . ( 273 sec) [ -35253.1302] [Topology ] . ( 276 sec) [ -35253.1291] [Topology ] . ( 279 sec) [ -35253.1283] [Topology ] . ( 279 sec) [ -35253.1281] [GTR parameters ] . ( 280 sec) [ -35253.1281] [Alpha ][ 0.499308] . ( 280 sec) [ -35253.1281] [Topology ] . ( 283 sec) [ -35253.1273] [Topology ] . ( 283 sec) [ -35253.1272] [GTR parameters ] . ( 283 sec) [ -35253.1272] [Alpha ][ 0.498809] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -35253.127208. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 7 sec) [ -71651.8242] [GTR parameters ] . ( 8 sec) [ -70212.1399] [Alpha ][ 0.500960] . ( 8 sec) [ -69846.5892] [13878] [depth= 15] . ( 8 sec) [ -69626.8627] [13788] [depth= 12] . ( 8 sec) [ -68964.3326] [13655] [depth= 11] . ( 8 sec) [ -68555.6011] [13538] [depth= 1] . ( 9 sec) [ -67874.2509] [13409] [depth= 12] . ( 9 sec) [ -67503.9674] [13346] [depth= 8] . ( 9 sec) [ -67347.4818] [13280] [depth= 1] . ( 9 sec) [ -67332.0568] [13271] [depth= 1] . ( 9 sec) [ -67179.7200] [13265] [depth= 1] . ( 9 sec) [ -66947.9260] [13247] [depth= 9] . ( 10 sec) [ -66866.4343] [13235] [depth= 3] . ( 10 sec) [ -66476.0425] [13271] [depth= 1] . ( 10 sec) [ -66383.3070] [13244] [depth= 14] . ( 10 sec) [ -65765.1458] [13026] [depth= 2] . ( 10 sec) [ -65017.1116] [12849] [depth= 10] . ( 10 sec) [ -64859.8254] [12842] [depth= 13] . ( 11 sec) [ -64149.4419] [12833] [depth= 2] . ( 11 sec) [ -63958.2922] [12824] [depth= 9] . ( 11 sec) [ -63425.2645] [12772] [depth= 6] . ( 11 sec) [ -63248.6486] [12744] [depth= 1] . ( 11 sec) [ -62923.3981] [12624] [depth= 9] . ( 11 sec) [ -62539.4400] [12617] [depth= 2] . ( 12 sec) [ -61722.1008] [12423] [depth= 9] . ( 12 sec) [ -61139.3105] [12152] [depth= 9] . ( 12 sec) [ -61097.4221] [12145] [depth= 8] . ( 12 sec) [ -61063.7134] [12144] [depth= 4] . ( 12 sec) [ -60707.7755] [12093] [depth= 4] . ( 13 sec) [ -60608.6804] [12063] [depth= 1] . ( 13 sec) [ -60185.9211] [12012] [depth= 6] . ( 13 sec) [ -60163.3240] [12019] [depth= 9] . ( 13 sec) [ -60138.8907] [12011] [depth= 1] . ( 13 sec) [ -59797.6151] [11940] [depth= 12] . ( 13 sec) [ -59781.8771] [11943] [depth= 1] . ( 14 sec) [ -59516.1761] [11838] [depth= 4] . ( 14 sec) [ -58323.6271] [11830] [depth= 1] . ( 14 sec) [ -58291.8662] [11757] [depth= 1] . ( 14 sec) [ -58172.4424] [11752] [depth= 3] . ( 14 sec) [ -58098.4509] [11742] [depth= 4] . ( 14 sec) [ -57201.0032] [11340] [depth= 9] . ( 15 sec) [ -57166.7845] [11262] [depth= 1] . ( 15 sec) [ -57161.5563] [11248] [depth= 1] . ( 15 sec) [ -57063.9913] [11240] [depth= 2] . ( 15 sec) [ -56829.8471] [11127] [depth= 8] . ( 15 sec) [ -56446.6022] [11067] [depth= 9] . ( 15 sec) [ -56383.8236] [11028] [depth= 9] . ( 15 sec) [ -56282.8760] [10994] [depth= 1] . ( 16 sec) [ -56012.8249] [10855] [depth= 11] . ( 16 sec) [ -55809.0866] [10848] [depth= 2] . ( 16 sec) [ -55746.8881] [10818] [depth= 3] . ( 16 sec) [ -55499.1139] [10722] [depth= 1] . ( 16 sec) [ -55308.3577] [10650] [depth= 1] . ( 17 sec) [ -55091.4511] [10659] [depth= 1] . ( 17 sec) [ -55056.3367] [10561] [depth= 9] . ( 17 sec) [ -55015.3657] [10561] [depth= 9] . ( 17 sec) [ -54992.1463] [10562] [depth= 1] . ( 17 sec) [ -54832.4897] [10533] [depth= 9] . ( 18 sec) [ -54814.7132] [10511] [depth= 1] . ( 18 sec) [ -54645.6801] [10515] [depth= 2] . ( 18 sec) [ -54236.2603] [10456] [depth= 7] . ( 18 sec) [ -53167.2337] [10313] [depth= 3] . ( 18 sec) [ -52884.8976] [10304] [depth= 2] . ( 18 sec) [ -52865.6048] [10280] [depth= 1] . ( 19 sec) [ -52274.8777] [10263] [depth= 1] . ( 19 sec) [ -51999.1179] [10188] [depth= 16] . ( 19 sec) [ -51826.2236] [10122] [depth= 9] . ( 19 sec) [ -51792.1641] [10088] [depth= 1] . ( 19 sec) [ -51461.5746] [ 9986] [depth= 11] . ( 20 sec) [ -51323.2543] [ 9936] [depth= 6] . ( 20 sec) [ -41624.3090] [ 9869] [depth= 6] . ( 20 sec) [ -41520.8441] [ 9824] [depth= 1] . ( 20 sec) [ -41201.0476] [ 9730] [depth= 3] . ( 20 sec) [ -40890.3105] [ 9809] [depth= 1] . ( 21 sec) [ -40501.8935] [ 9696] [depth= 8] . ( 21 sec) [ -40424.0722] [ 9664] [depth= 6] . ( 21 sec) [ -40332.5162] [ 9615] [depth= 1] . ( 21 sec) [ -39989.0031] [ 9497] [depth= 5] . ( 21 sec) [ -39718.4309] [ 9407] [depth= 4] . ( 22 sec) [ -39622.8845] [ 9284] [depth= 3] . ( 22 sec) [ -39439.2502] [ 9250] [depth= 2] . ( 22 sec) [ -39286.8393] [ 9238] [depth= 6] . ( 22 sec) [ -39229.4568] [ 9233] [depth= 1] . ( 22 sec) [ -39057.4274] [ 9220] [depth= 5] . ( 22 sec) [ -38775.6845] [ 9105] [depth= 3] . ( 23 sec) [ -38752.1584] [ 9096] [depth= 2] . ( 23 sec) [ -37987.1100] [ 8962] [depth= 8] . ( 23 sec) [ -37829.1489] [ 8921] [depth= 4] . ( 23 sec) [ -37794.9687] [ 8959] [depth= 8] . ( 23 sec) [ -37740.3178] [ 8949] [depth= 3] . ( 23 sec) [ -37724.5568] [ 8946] [depth= 1] . ( 24 sec) [ -37639.4606] [ 8931] [depth= 2] . ( 24 sec) [ -37613.8705] [ 8932] [depth= 5] . ( 24 sec) [ -37501.7219] [ 8922] [depth= 7] . ( 24 sec) [ -37467.2388] [ 8894] [depth= 2] . ( 25 sec) [ -37416.7160] [ 8870] [depth= 1] . ( 25 sec) [ -37401.0301] [ 8872] [depth= 1] . ( 25 sec) [ -37394.3236] [ 8836] [depth= 10] . ( 25 sec) [ -37384.0936] [ 8852] [depth= 1] . ( 26 sec) [ -37333.6655] [ 8839] [depth= 1] . ( 26 sec) [ -37216.5576] [ 8781] [depth= 1] . ( 26 sec) [ -37084.9171] [ 8796] [depth= 1] . ( 26 sec) [ -37027.7823] [ 8781] [depth= 1] . ( 27 sec) [ -37004.0249] [ 8780] [depth= 1] . ( 27 sec) [ -36909.4263] [ 8759] [depth= 2] . ( 27 sec) [ -36805.1056] [ 8723] [depth= 2] . ( 27 sec) [ -36787.9717] [ 8719] [depth= 2] . ( 27 sec) [ -36769.4410] [ 8717] [depth= 1] . ( 28 sec) [ -36672.2595] [ 8596] [depth= 1] . ( 28 sec) [ -36554.9750] [ 8565] [depth= 2] . ( 28 sec) [ -36501.4260] [ 8557] [depth= 3] . ( 28 sec) [ -36455.2761] [ 8516] [depth= 2] . ( 29 sec) [ -36451.8319] [ 8519] [depth= 1] . ( 30 sec) [ -36088.8211] [Branch lengths ] . ( 34 sec) [ -35936.8330] [GTR parameters ] . ( 35 sec) [ -35935.6348] [Alpha ][ 0.477678] . ( 35 sec) [ -35929.9961] [ 8508] [depth= 1] . ( 35 sec) [ -35754.6645] [ 8408] [depth= 3] . ( 35 sec) [ -35730.8918] [ 8408] [depth= 1] . ( 36 sec) [ -35672.8439] [ 8391] [depth= 3] . ( 36 sec) [ -35671.4236] [ 8395] [depth= 1] . ( 36 sec) [ -35556.1803] [ 8329] [depth= 2] . ( 36 sec) [ -35551.2164] [ 8328] [depth= 1] . ( 37 sec) [ -35475.7530] [ 8289] [depth= 4] . ( 38 sec) [ -35448.6027] [ 8285] [depth= 2] . ( 38 sec) [ -35446.5816] [ 8286] [depth= 1] . ( 39 sec) [ -35403.4379] [ 8265] [depth= 1] . ( 39 sec) [ -35402.9345] [ 8266] [depth= 1] . ( 40 sec) [ -35371.4544] [ 8254] [depth= 1] . ( 41 sec) [ -35366.8263] [ 8249] [depth= 1] . ( 41 sec) [ -35365.6473] [ 8248] [depth= 1] . ( 42 sec) [ -35352.0920] [ 8255] [depth= 1] . ( 43 sec) [ -35339.4352] [ 8251] [depth= 2] . ( 43 sec) [ -35338.5842] [ 8256] [depth= 1] . ( 43 sec) [ -35335.1229] [ 8251] [depth= 1] . ( 43 sec) [ -35332.9219] [ 8249] [depth= 1] . ( 44 sec) [ -35326.0842] [ 8245] [depth= 1] . ( 44 sec) [ -35326.0396] [ 8248] [depth= 1] . ( 47 sec) [ -35325.3522] [ 8248] [depth= 1] . ( 48 sec) [ -35323.0984] [ 8247] [depth= 1] . ( 48 sec) [ -35319.6994] [ 8243] [depth= 1] . ( 50 sec) [ -35273.8336] [Branch lengths ] . ( 53 sec) [ -35271.9443] [GTR parameters ] . ( 53 sec) [ -35271.2919] [Alpha ][ 0.494984] . ( 54 sec) [ -35270.7890] [ 8248] [depth= 1] . ( 56 sec) [ -35270.1643] [ 8241] [depth= 1] . ( 58 sec) [ -35270.0996] [ 8242] [depth= 1] . ( 69 sec) [ -35265.4038] [Branch lengths ] . ( 72 sec) [ -35265.3065] [GTR parameters ] . ( 72 sec) [ -35265.3007] [Alpha ][ 0.496608] . ( 72 sec) [ -35265.1508] [ 8238] [depth= 3] . ( 73 sec) [ -35263.2937] [ 8233] [depth= 1] . ( 76 sec) [ -35262.0244] [ 8231] [depth= 1] . ( 85 sec) [ -35256.4777] [Branch lengths ] . ( 88 sec) [ -35256.3431] [GTR parameters ] . ( 88 sec) [ -35256.3281] [Alpha ][ 0.499247] . ( 102 sec) [ -35254.8477] [Branch lengths ] . ( 184 sec) [ -35254.2700] [Branch lengths ] . ( 184 sec) [ -35254.2700] [Topology ] . ( 187 sec) [ -35254.1364] [Topology ] . ( 189 sec) [ -35254.0661] [Topology ] . ( 192 sec) [ -35254.0160] [Topology ] . ( 195 sec) [ -35253.9791] [Topology ] . ( 198 sec) [ -35253.9518] [Topology ] . ( 201 sec) [ -35253.9315] [Topology ] . ( 203 sec) [ -35253.5837] [GTR parameters ] . ( 203 sec) [ -35253.5823] [Alpha ][ 0.499999] . ( 203 sec) [ -35253.5823] [Topology ] . ( 206 sec) [ -35253.4929] [Topology ] . ( 209 sec) [ -35253.4346] [Topology ] . ( 212 sec) [ -35253.3916] [Topology ] . ( 215 sec) [ -35253.3595] [Topology ] . ( 218 sec) [ -35253.3355] [Topology ] . ( 221 sec) [ -35253.3175] [Topology ] . ( 223 sec) [ -35253.2835] [GTR parameters ] . ( 223 sec) [ -35253.2833] [Alpha ][ 0.499499] . ( 223 sec) [ -35253.2833] [Topology ] . ( 226 sec) [ -35253.2552] [Topology ] . ( 229 sec) [ -35253.2352] [Topology ] . ( 232 sec) [ -35253.2202] [Topology ] . ( 234 sec) [ -35253.2089] [Topology ] . ( 237 sec) [ -35253.2004] [Topology ] . ( 240 sec) [ -35253.1940] [Topology ] . ( 241 sec) [ -35253.1816] [GTR parameters ] . ( 241 sec) [ -35253.1816] [Alpha ][ 0.499499] . ( 241 sec) [ -35253.1816] [Topology ] . ( 244 sec) [ -35253.1713] [Topology ] . ( 247 sec) [ -35253.1639] [Topology ] . ( 250 sec) [ -35253.1584] [Topology ] . ( 253 sec) [ -35253.1542] [Topology ] . ( 256 sec) [ -35253.1510] [Topology ] . ( 259 sec) [ -35253.1486] [Topology ] . ( 260 sec) [ -35253.1447] [GTR parameters ] . ( 260 sec) [ -35253.1446] [Alpha ][ 0.498999] . ( 260 sec) [ -35253.1446] [Topology ] . ( 263 sec) [ -35253.1410] [Topology ] . ( 266 sec) [ -35253.1385] [Topology ] . ( 269 sec) [ -35253.1366] [Topology ] . ( 271 sec) [ -35253.1351] [Topology ] . ( 274 sec) [ -35253.1340] [Topology ] . ( 277 sec) [ -35253.1331] [Topology ] . ( 278 sec) [ -35253.1313] [GTR parameters ] . ( 278 sec) [ -35253.1313] [Alpha ][ 0.498999] . ( 278 sec) [ -35253.1313] [Topology ] . ( 281 sec) [ -35253.1299] [Topology ] . ( 284 sec) [ -35253.1289] [Topology ] . ( 284 sec) [ -35253.1288] [GTR parameters ] . ( 285 sec) [ -35253.1288] [Alpha ][ 0.498999] . ( 285 sec) [ -35253.1288] [Topology ] . ( 288 sec) [ -35253.1279] [Topology ] . ( 288 sec) [ -35253.1278] [GTR parameters ] . ( 288 sec) [ -35253.1278] [Alpha ][ 0.498999] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -35253.127832. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 7 sec) [ -68283.1350] [GTR parameters ] . ( 8 sec) [ -66704.4366] [Alpha ][ 0.500960] . ( 8 sec) [ -66316.1156] [14002] [depth= 12] . ( 8 sec) [ -65964.5561] [13964] [depth= 8] . ( 8 sec) [ -64469.3343] [13926] [depth= 1] . ( 8 sec) [ -64234.2587] [13901] [depth= 4] . ( 8 sec) [ -64105.8600] [13839] [depth= 1] . ( 9 sec) [ -63722.9196] [13810] [depth= 2] . ( 9 sec) [ -63655.9331] [13756] [depth= 1] . ( 9 sec) [ -62818.5917] [13714] [depth= 6] . ( 9 sec) [ -62679.8948] [13647] [depth= 1] . ( 9 sec) [ -61529.0840] [13591] [depth= 9] . ( 9 sec) [ -61033.7915] [13505] [depth= 5] . ( 10 sec) [ -59782.4863] [13483] [depth= 4] . ( 10 sec) [ -59729.3193] [13425] [depth= 1] . ( 10 sec) [ -59536.8235] [13421] [depth= 2] . ( 10 sec) [ -56035.7874] [13406] [depth= 3] . ( 10 sec) [ -55517.8142] [13195] [depth= 4] . ( 10 sec) [ -54886.3976] [12916] [depth= 2] . ( 11 sec) [ -54575.3197] [12898] [depth= 12] . ( 11 sec) [ -54464.1203] [12892] [depth= 4] . ( 11 sec) [ -53680.1694] [12805] [depth= 2] . ( 11 sec) [ -53512.9000] [12808] [depth= 1] . ( 11 sec) [ -53482.2354] [12805] [depth= 1] . ( 11 sec) [ -52911.7641] [12748] [depth= 5] . ( 12 sec) [ -52693.8461] [12715] [depth= 6] . ( 12 sec) [ -52428.8860] [12589] [depth= 10] . ( 12 sec) [ -52247.8943] [12523] [depth= 9] . ( 12 sec) [ -52080.6220] [12486] [depth= 5] . ( 12 sec) [ -51748.2306] [12475] [depth= 11] . ( 13 sec) [ -51714.8716] [12483] [depth= 12] . ( 13 sec) [ -50544.5267] [12334] [depth= 9] . ( 13 sec) [ -50239.6135] [12286] [depth= 10] . ( 13 sec) [ -49811.7346] [12210] [depth= 8] . ( 13 sec) [ -49623.2989] [12225] [depth= 2] . ( 13 sec) [ -49590.4458] [12221] [depth= 1] . ( 14 sec) [ -49411.1614] [12124] [depth= 7] . ( 14 sec) [ -48632.3748] [11968] [depth= 1] . ( 14 sec) [ -48380.9948] [11681] [depth= 15] . ( 15 sec) [ -48238.3590] [11583] [depth= 8] . ( 15 sec) [ -48073.5818] [11574] [depth= 8] . ( 15 sec) [ -48064.1884] [11587] [depth= 1] . ( 15 sec) [ -48056.0243] [11586] [depth= 2] . ( 15 sec) [ -47949.3911] [11547] [depth= 2] . ( 15 sec) [ -47718.9805] [11368] [depth= 6] . ( 15 sec) [ -47394.0762] [11261] [depth= 6] . ( 16 sec) [ -47219.2496] [11227] [depth= 6] . ( 16 sec) [ -46963.6446] [11204] [depth= 1] . ( 16 sec) [ -46792.8641] [11188] [depth= 2] . ( 16 sec) [ -46615.2054] [11104] [depth= 1] . ( 16 sec) [ -46562.1923] [11071] [depth= 4] . ( 16 sec) [ -46183.7385] [10981] [depth= 2] . ( 17 sec) [ -46052.9546] [10943] [depth= 2] . ( 17 sec) [ -45853.2393] [10960] [depth= 1] . ( 17 sec) [ -45621.6611] [10880] [depth= 2] . ( 17 sec) [ -45608.2257] [10842] [depth= 8] . ( 17 sec) [ -45318.2702] [10727] [depth= 5] . ( 17 sec) [ -44937.8824] [10612] [depth= 4] . ( 18 sec) [ -44710.9887] [10567] [depth= 4] . ( 18 sec) [ -44191.0182] [10431] [depth= 1] . ( 18 sec) [ -43733.2033] [10297] [depth= 11] . ( 18 sec) [ -43703.9436] [10329] [depth= 8] . ( 18 sec) [ -43243.9881] [10198] [depth= 4] . ( 19 sec) [ -42696.3798] [10018] [depth= 5] . ( 19 sec) [ -42652.3329] [ 9991] [depth= 1] . ( 19 sec) [ -42617.6433] [ 9982] [depth= 1] . ( 19 sec) [ -42523.5713] [ 9970] [depth= 4] . ( 19 sec) [ -42410.1276] [ 9946] [depth= 17] . ( 20 sec) [ -42392.2684] [ 9960] [depth= 1] . ( 20 sec) [ -42125.0781] [ 9810] [depth= 11] . ( 20 sec) [ -42108.0595] [ 9828] [depth= 1] . ( 20 sec) [ -42094.5643] [ 9816] [depth= 1] . ( 20 sec) [ -42069.2453] [ 9816] [depth= 2] . ( 20 sec) [ -42046.5922] [ 9821] [depth= 1] . ( 21 sec) [ -41985.7187] [ 9816] [depth= 1] . ( 21 sec) [ -41923.5224] [ 9811] [depth= 1] . ( 21 sec) [ -41864.4068] [ 9842] [depth= 3] . ( 21 sec) [ -41537.4279] [ 9680] [depth= 19] . ( 21 sec) [ -41518.4211] [ 9683] [depth= 1] . ( 22 sec) [ -41474.2879] [ 9666] [depth= 1] . ( 22 sec) [ -41302.6244] [ 9613] [depth= 3] . ( 22 sec) [ -40692.5288] [ 9413] [depth= 9] . ( 22 sec) [ -39767.1224] [ 9404] [depth= 1] . ( 22 sec) [ -39518.7286] [ 9279] [depth= 3] . ( 23 sec) [ -39443.9514] [ 9256] [depth= 2] . ( 23 sec) [ -39384.3352] [ 9206] [depth= 1] . ( 23 sec) [ -39291.4489] [ 9176] [depth= 1] . ( 23 sec) [ -39281.4433] [ 9158] [depth= 1] . ( 23 sec) [ -39228.7246] [ 9158] [depth= 3] . ( 24 sec) [ -39204.1276] [ 9134] [depth= 1] . ( 24 sec) [ -38435.2983] [ 9163] [depth= 1] . ( 24 sec) [ -38199.5921] [ 8930] [depth= 8] . ( 24 sec) [ -38199.4963] [ 8927] [depth= 1] . ( 24 sec) [ -38197.0421] [ 8937] [depth= 1] . ( 24 sec) [ -38169.3527] [ 8922] [depth= 1] . ( 25 sec) [ -38168.6129] [ 8922] [depth= 15] . ( 25 sec) [ -38148.0053] [ 8905] [depth= 1] . ( 25 sec) [ -38137.5433] [ 8926] [depth= 1] . ( 25 sec) [ -38017.3877] [ 8855] [depth= 2] . ( 25 sec) [ -37967.2679] [ 8844] [depth= 4] . ( 25 sec) [ -37784.4160] [ 8774] [depth= 5] . ( 26 sec) [ -37732.6882] [ 8757] [depth= 1] . ( 26 sec) [ -37626.8207] [ 8685] [depth= 1] . ( 26 sec) [ -37409.1636] [ 8640] [depth= 4] . ( 26 sec) [ -37260.5686] [ 8550] [depth= 7] . ( 26 sec) [ -37255.1719] [ 8549] [depth= 1] . ( 27 sec) [ -37235.0035] [ 8536] [depth= 1] . ( 27 sec) [ -37230.9608] [ 8541] [depth= 1] . ( 27 sec) [ -37229.1236] [ 8547] [depth= 3] . ( 27 sec) [ -37226.3397] [ 8547] [depth= 1] . ( 27 sec) [ -37218.0542] [ 8546] [depth= 1] . ( 28 sec) [ -37183.5480] [ 8554] [depth= 1] . ( 28 sec) [ -37170.7463] [ 8549] [depth= 1] . ( 28 sec) [ -37110.8940] [ 8527] [depth= 1] . ( 28 sec) [ -37040.3236] [ 8521] [depth= 3] . ( 28 sec) [ -36913.2036] [ 8520] [depth= 1] . ( 29 sec) [ -36904.0584] [ 8520] [depth= 1] . ( 29 sec) [ -36858.5784] [ 8513] [depth= 2] . ( 30 sec) [ -36492.0056] [Branch lengths ] . ( 37 sec) [ -35943.8859] [GTR parameters ] . ( 37 sec) [ -35939.8372] [Alpha ][ 0.458318] . ( 37 sec) [ -35869.3692] [ 8466] [depth= 4] . ( 37 sec) [ -35767.1359] [ 8463] [depth= 1] . ( 38 sec) [ -35750.5319] [ 8457] [depth= 2] . ( 38 sec) [ -35734.5894] [ 8438] [depth= 1] . ( 38 sec) [ -35730.3498] [ 8450] [depth= 1] . ( 39 sec) [ -35723.0899] [ 8439] [depth= 1] . ( 39 sec) [ -35719.3109] [ 8439] [depth= 3] . ( 39 sec) [ -35711.2291] [ 8442] [depth= 1] . ( 39 sec) [ -35632.3099] [ 8391] [depth= 3] . ( 40 sec) [ -35531.2252] [ 8325] [depth= 2] . ( 41 sec) [ -35525.2450] [ 8322] [depth= 1] . ( 41 sec) [ -35506.4804] [ 8303] [depth= 1] . ( 42 sec) [ -35482.3930] [ 8298] [depth= 1] . ( 42 sec) [ -35474.9408] [ 8296] [depth= 3] . ( 43 sec) [ -35473.8886] [ 8292] [depth= 1] . ( 43 sec) [ -35473.5790] [ 8290] [depth= 1] . ( 43 sec) [ -35452.7804] [ 8268] [depth= 1] . ( 44 sec) [ -35445.6615] [ 8260] [depth= 1] . ( 45 sec) [ -35445.1933] [ 8259] [depth= 1] . ( 45 sec) [ -35402.4316] [ 8246] [depth= 1] . ( 46 sec) [ -35401.8303] [ 8253] [depth= 1] . ( 46 sec) [ -35397.1368] [ 8250] [depth= 1] . ( 47 sec) [ -35395.6014] [ 8243] [depth= 1] . ( 47 sec) [ -35368.8269] [ 8241] [depth= 1] . ( 48 sec) [ -35363.3652] [ 8236] [depth= 1] . ( 51 sec) [ -35357.4752] [ 8234] [depth= 1] . ( 52 sec) [ -35289.2026] [Branch lengths ] . ( 56 sec) [ -35286.4530] [GTR parameters ] . ( 57 sec) [ -35284.6963] [Alpha ][ 0.485786] . ( 57 sec) [ -35283.8398] [ 8233] [depth= 1] . ( 58 sec) [ -35280.9549] [ 8235] [depth= 1] . ( 61 sec) [ -35278.5260] [ 8231] [depth= 1] . ( 68 sec) [ -35277.6943] [ 8235] [depth= 1] . ( 71 sec) [ -35265.8877] [Branch lengths ] . ( 76 sec) [ -35265.7277] [GTR parameters ] . ( 76 sec) [ -35265.5096] [Alpha ][ 0.495995] . ( 86 sec) [ -35263.2777] [ 8231] [depth= 1] . ( 91 sec) [ -35257.6893] [Branch lengths ] . ( 95 sec) [ -35257.5338] [GTR parameters ] . ( 96 sec) [ -35257.5225] [Alpha ][ 0.498287] . ( 112 sec) [ -35255.6010] [Branch lengths ] . ( 199 sec) [ -35254.8182] [Branch lengths ] . ( 199 sec) [ -35254.8182] [Topology ] . ( 202 sec) [ -35254.6322] [Topology ] . ( 204 sec) [ -35254.5347] [Topology ] . ( 207 sec) [ -35254.4652] [Topology ] . ( 210 sec) [ -35254.4144] [Topology ] . ( 213 sec) [ -35254.3769] [Topology ] . ( 216 sec) [ -35254.3491] [Topology ] . ( 221 sec) [ -35253.8028] [GTR parameters ] . ( 221 sec) [ -35253.7962] [Alpha ][ 0.500011] . ( 221 sec) [ -35253.7962] [Topology ] . ( 224 sec) [ -35253.6608] [Topology ] . ( 227 sec) [ -35253.5722] [Topology ] . ( 230 sec) [ -35253.5074] [Topology ] . ( 233 sec) [ -35253.4594] [Topology ] . ( 236 sec) [ -35253.4237] [Topology ] . ( 239 sec) [ -35253.3969] [Topology ] . ( 240 sec) [ -35253.3517] [GTR parameters ] . ( 240 sec) [ -35253.3516] [Alpha ][ 0.499511] . ( 240 sec) [ -35253.3516] [Topology ] . ( 243 sec) [ -35253.3114] [Topology ] . ( 246 sec) [ -35253.2827] [Topology ] . ( 249 sec) [ -35253.2611] [Topology ] . ( 252 sec) [ -35253.2450] [Topology ] . ( 254 sec) [ -35253.2328] [Topology ] . ( 257 sec) [ -35253.2237] [Topology ] . ( 258 sec) [ -35253.2060] [GTR parameters ] . ( 258 sec) [ -35253.2060] [Alpha ][ 0.499511] . ( 259 sec) [ -35253.2060] [Topology ] . ( 261 sec) [ -35253.1914] [Topology ] . ( 264 sec) [ -35253.1809] [Topology ] . ( 267 sec) [ -35253.1731] [Topology ] . ( 270 sec) [ -35253.1671] [Topology ] . ( 273 sec) [ -35253.1626] [Topology ] . ( 276 sec) [ -35253.1592] [Topology ] . ( 277 sec) [ -35253.1535] [GTR parameters ] . ( 277 sec) [ -35253.1535] [Alpha ][ 0.499511] . ( 277 sec) [ -35253.1535] [Topology ] . ( 280 sec) [ -35253.1484] [Topology ] . ( 283 sec) [ -35253.1446] [Topology ] . ( 286 sec) [ -35253.1418] [Topology ] . ( 289 sec) [ -35253.1396] [Topology ] . ( 291 sec) [ -35253.1380] [Topology ] . ( 294 sec) [ -35253.1368] [Topology ] . ( 295 sec) [ -35253.1348] [GTR parameters ] . ( 295 sec) [ -35253.1345] [Alpha ][ 0.499011] . ( 296 sec) [ -35253.1345] [Topology ] . ( 298 sec) [ -35253.1327] [Topology ] . ( 301 sec) [ -35253.1314] [Topology ] . ( 304 sec) [ -35253.1304] [Topology ] . ( 306 sec) [ -35253.1298] [GTR parameters ] . ( 306 sec) [ -35253.1298] [Alpha ][ 0.499011] . ( 306 sec) [ -35253.1298] [Topology ] . ( 309 sec) [ -35253.1287] [Topology ] . ( 312 sec) [ -35253.1278] [Topology ] . ( 313 sec) [ -35253.1278] [GTR parameters ] . ( 313 sec) [ -35253.1278] [Alpha ][ 0.499011] . ( 313 sec) [ -35253.1278] [Topology ] . ( 316 sec) [ -35253.1270] [Topology ] . ( 317 sec) [ -35253.1270] [GTR parameters ] . ( 317 sec) [ -35253.1270] [Alpha ][ 0.499011] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -35253.126978. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 4 sec) [ -72845.5236] [GTR parameters ] . ( 4 sec) [ -71441.2527] [Alpha ][ 0.500960] . ( 4 sec) [ -71210.1984] [13983] [depth= 5] . ( 5 sec) [ -60053.1395] [13982] [depth= 10] . ( 5 sec) [ -59915.0073] [13975] [depth= 3] . ( 5 sec) [ -59771.2097] [13960] [depth= 1] . ( 5 sec) [ -58792.6399] [13879] [depth= 5] . ( 5 sec) [ -58561.8112] [13847] [depth= 4] . ( 5 sec) [ -58398.4356] [13809] [depth= 3] . ( 6 sec) [ -58344.8124] [13801] [depth= 4] . ( 6 sec) [ -58121.5147] [13676] [depth= 14] . ( 6 sec) [ -57881.7856] [13669] [depth= 4] . ( 6 sec) [ -57507.1245] [13622] [depth= 1] . ( 6 sec) [ -57276.9296] [13616] [depth= 7] . ( 6 sec) [ -57220.7191] [13609] [depth= 3] . ( 7 sec) [ -57118.3879] [13491] [depth= 15] . ( 7 sec) [ -56260.1044] [13428] [depth= 2] . ( 7 sec) [ -55367.0067] [13239] [depth= 6] . ( 7 sec) [ -54777.2712] [13075] [depth= 3] . ( 7 sec) [ -54728.4911] [13065] [depth= 5] . ( 7 sec) [ -54680.3592] [13015] [depth= 13] . ( 7 sec) [ -54586.8068] [12989] [depth= 2] . ( 8 sec) [ -54084.3981] [12911] [depth= 22] . ( 8 sec) [ -53558.7045] [12837] [depth= 1] . ( 8 sec) [ -53342.5580] [12777] [depth= 11] . ( 8 sec) [ -53050.6399] [12613] [depth= 1] . ( 8 sec) [ -52854.4052] [12576] [depth= 1] . ( 8 sec) [ -52030.2264] [12484] [depth= 10] . ( 9 sec) [ -51743.8846] [12481] [depth= 16] . ( 9 sec) [ -51589.0537] [12474] [depth= 4] . ( 9 sec) [ -51199.6077] [12377] [depth= 9] . ( 9 sec) [ -50769.2522] [12123] [depth= 20] . ( 9 sec) [ -50531.9128] [12085] [depth= 5] . ( 10 sec) [ -50352.3512] [12067] [depth= 9] . ( 10 sec) [ -49605.5623] [12009] [depth= 4] . ( 10 sec) [ -49347.2462] [11926] [depth= 1] . ( 10 sec) [ -48985.9659] [11781] [depth= 12] . ( 10 sec) [ -48578.7903] [11742] [depth= 15] . ( 10 sec) [ -48204.4408] [11601] [depth= 15] . ( 11 sec) [ -48038.3214] [11559] [depth= 19] . ( 11 sec) [ -47920.1851] [11549] [depth= 5] . ( 11 sec) [ -47702.1713] [11489] [depth= 4] . ( 11 sec) [ -46643.2249] [11234] [depth= 9] . ( 12 sec) [ -46229.2236] [11048] [depth= 12] . ( 12 sec) [ -45625.3123] [10959] [depth= 5] . ( 12 sec) [ -45171.7073] [10914] [depth= 1] . ( 12 sec) [ -45136.2325] [10916] [depth= 1] . ( 12 sec) [ -44912.3454] [10859] [depth= 17] . ( 12 sec) [ -44526.1759] [10828] [depth= 6] . ( 13 sec) [ -44362.6359] [10780] [depth= 3] . ( 13 sec) [ -44118.7893] [10771] [depth= 1] . ( 13 sec) [ -43800.6662] [10703] [depth= 4] . ( 13 sec) [ -43765.4288] [10670] [depth= 1] . ( 13 sec) [ -43484.2072] [10628] [depth= 1] . ( 13 sec) [ -43411.0063] [10637] [depth= 1] . ( 14 sec) [ -43127.7438] [10384] [depth= 1] . ( 14 sec) [ -43027.8185] [10370] [depth= 3] . ( 14 sec) [ -42813.4982] [10202] [depth= 23] . ( 14 sec) [ -42274.8457] [10019] [depth= 13] . ( 14 sec) [ -42156.7311] [10018] [depth= 1] . ( 15 sec) [ -42079.8179] [ 9964] [depth= 2] . ( 15 sec) [ -41907.6521] [ 9923] [depth= 8] . ( 15 sec) [ -41693.5680] [ 9913] [depth= 3] . ( 15 sec) [ -41407.1334] [ 9815] [depth= 3] . ( 15 sec) [ -41175.0838] [ 9769] [depth= 1] . ( 15 sec) [ -41049.2626] [ 9737] [depth= 5] . ( 15 sec) [ -40765.2093] [ 9644] [depth= 6] . ( 16 sec) [ -40698.5019] [ 9612] [depth= 1] . ( 16 sec) [ -40660.0263] [ 9606] [depth= 1] . ( 16 sec) [ -40461.6622] [ 9536] [depth= 5] . ( 16 sec) [ -40365.0219] [ 9508] [depth= 3] . ( 17 sec) [ -40329.3286] [ 9476] [depth= 1] . ( 17 sec) [ -40171.0332] [ 9410] [depth= 2] . ( 17 sec) [ -40046.6007] [ 9391] [depth= 1] . ( 17 sec) [ -40025.8381] [ 9389] [depth= 1] . ( 17 sec) [ -40014.2847] [ 9383] [depth= 1] . ( 17 sec) [ -39813.3024] [ 9360] [depth= 1] . ( 18 sec) [ -39796.8136] [ 9254] [depth= 2] . ( 18 sec) [ -39058.4771] [ 9182] [depth= 2] . ( 18 sec) [ -38822.2018] [ 9168] [depth= 12] . ( 18 sec) [ -38819.0102] [ 9181] [depth= 1] . ( 18 sec) [ -38798.6984] [ 9168] [depth= 1] . ( 19 sec) [ -38775.9654] [ 9127] [depth= 1] . ( 19 sec) [ -38640.1507] [ 9110] [depth= 11] . ( 19 sec) [ -38625.0432] [ 8975] [depth= 1] . ( 19 sec) [ -38605.6426] [ 8957] [depth= 11] . ( 20 sec) [ -38503.8783] [ 8951] [depth= 1] . ( 20 sec) [ -38398.8396] [ 8900] [depth= 4] . ( 20 sec) [ -38349.9129] [ 8815] [depth= 3] . ( 20 sec) [ -38345.1778] [ 8813] [depth= 1] . ( 20 sec) [ -38234.0505] [ 8814] [depth= 8] . ( 21 sec) [ -38180.6208] [ 8807] [depth= 1] . ( 21 sec) [ -38175.4652] [ 8834] [depth= 1] . ( 21 sec) [ -37669.9300] [ 8807] [depth= 1] . ( 21 sec) [ -37539.0228] [ 8779] [depth= 7] . ( 21 sec) [ -37495.6428] [ 8778] [depth= 5] . ( 22 sec) [ -37256.1235] [ 8695] [depth= 2] . ( 22 sec) [ -37230.2672] [ 8681] [depth= 1] . ( 22 sec) [ -37180.0510] [ 8647] [depth= 1] . ( 22 sec) [ -37170.8766] [ 8647] [depth= 1] . ( 23 sec) [ -37155.3343] [ 8643] [depth= 2] . ( 23 sec) [ -37049.3564] [ 8613] [depth= 1] . ( 24 sec) [ -37028.6230] [ 8612] [depth= 1] . ( 24 sec) [ -36990.6522] [ 8618] [depth= 1] . ( 24 sec) [ -36845.6651] [ 8588] [depth= 17] . ( 24 sec) [ -36845.0082] [ 8590] [depth= 1] . ( 26 sec) [ -36387.7746] [Branch lengths ] . ( 30 sec) [ -35827.4121] [GTR parameters ] . ( 30 sec) [ -35825.5712] [Alpha ][ 0.472388] . ( 30 sec) [ -35809.2582] [ 8576] [depth= 2] . ( 32 sec) [ -35808.1432] [ 8576] [depth= 1] . ( 33 sec) [ -35765.2273] [ 8536] [depth= 1] . ( 33 sec) [ -35737.6460] [ 8526] [depth= 1] . ( 34 sec) [ -35737.2907] [ 8523] [depth= 1] . ( 35 sec) [ -35586.0561] [ 8317] [depth= 14] . ( 35 sec) [ -35541.3640] [ 8323] [depth= 1] . ( 37 sec) [ -35503.8279] [ 8257] [depth= 1] . ( 38 sec) [ -35486.7707] [ 8259] [depth= 1] . ( 38 sec) [ -35485.0650] [ 8262] [depth= 1] . ( 39 sec) [ -35468.4080] [ 8279] [depth= 3] . ( 40 sec) [ -35462.2405] [ 8281] [depth= 1] . ( 40 sec) [ -35454.3278] [ 8284] [depth= 2] . ( 40 sec) [ -35423.8294] [ 8285] [depth= 1] . ( 41 sec) [ -35417.0638] [ 8286] [depth= 1] . ( 42 sec) [ -35353.8998] [ 8247] [depth= 3] . ( 42 sec) [ -35345.1913] [ 8239] [depth= 1] . ( 46 sec) [ -35332.4028] [ 8246] [depth= 1] . ( 47 sec) [ -35327.3301] [ 8235] [depth= 1] . ( 49 sec) [ -35271.6657] [Branch lengths ] . ( 51 sec) [ -35270.7429] [GTR parameters ] . ( 51 sec) [ -35270.1971] [Alpha ][ 0.487814] . ( 60 sec) [ -35268.2570] [ 8231] [depth= 1] . ( 66 sec) [ -35260.1725] [Branch lengths ] . ( 68 sec) [ -35260.0470] [GTR parameters ] . ( 68 sec) [ -35259.9629] [Alpha ][ 0.494116] . ( 81 sec) [ -35256.6619] [Branch lengths ] . ( 162 sec) [ -35255.4334] [Branch lengths ] . ( 162 sec) [ -35255.4334] [Topology ] . ( 165 sec) [ -35255.1580] [Topology ] . ( 168 sec) [ -35255.0141] [Topology ] . ( 171 sec) [ -35254.9122] [Topology ] . ( 174 sec) [ -35254.8381] [Topology ] . ( 177 sec) [ -35254.7837] [Topology ] . ( 180 sec) [ -35254.7435] [Topology ] . ( 182 sec) [ -35254.0741] [GTR parameters ] . ( 182 sec) [ -35254.0058] [Alpha ][ 0.499734] . ( 182 sec) [ -35254.0058] [Topology ] . ( 185 sec) [ -35253.8236] [Topology ] . ( 188 sec) [ -35253.7002] [Topology ] . ( 191 sec) [ -35253.6097] [Topology ] . ( 194 sec) [ -35253.5430] [Topology ] . ( 197 sec) [ -35253.4936] [Topology ] . ( 199 sec) [ -35253.4568] [Topology ] . ( 200 sec) [ -35253.4099] [GTR parameters ] . ( 201 sec) [ -35253.4099] [Alpha ][ 0.499734] . ( 201 sec) [ -35253.4099] [Topology ] . ( 203 sec) [ -35253.3587] [Topology ] . ( 206 sec) [ -35253.3216] [Topology ] . ( 209 sec) [ -35253.2939] [Topology ] . ( 212 sec) [ -35253.2732] [Topology ] . ( 215 sec) [ -35253.2576] [Topology ] . ( 218 sec) [ -35253.2459] [Topology ] . ( 220 sec) [ -35253.2255] [GTR parameters ] . ( 220 sec) [ -35253.2255] [Alpha ][ 0.499734] . ( 220 sec) [ -35253.2255] [Topology ] . ( 223 sec) [ -35253.2076] [Topology ] . ( 226 sec) [ -35253.1946] [Topology ] . ( 229 sec) [ -35253.1849] [Topology ] . ( 232 sec) [ -35253.1776] [Topology ] . ( 235 sec) [ -35253.1721] [Topology ] . ( 237 sec) [ -35253.1679] [Topology ] . ( 238 sec) [ -35253.1608] [GTR parameters ] . ( 239 sec) [ -35253.1605] [Alpha ][ 0.499234] . ( 239 sec) [ -35253.1605] [Topology ] . ( 242 sec) [ -35253.1542] [Topology ] . ( 244 sec) [ -35253.1496] [Topology ] . ( 247 sec) [ -35253.1462] [Topology ] . ( 250 sec) [ -35253.1437] [Topology ] . ( 253 sec) [ -35253.1417] [Topology ] . ( 256 sec) [ -35253.1402] [Topology ] . ( 256 sec) [ -35253.1372] [GTR parameters ] . ( 257 sec) [ -35253.1372] [Alpha ][ 0.499234] . ( 257 sec) [ -35253.1372] [Topology ] . ( 260 sec) [ -35253.1348] [Topology ] . ( 263 sec) [ -35253.1331] [Topology ] . ( 265 sec) [ -35253.1318] [Topology ] . ( 268 sec) [ -35253.1308] [Topology ] . ( 269 sec) [ -35253.1302] [GTR parameters ] . ( 269 sec) [ -35253.1302] [Alpha ][ 0.499234] . ( 269 sec) [ -35253.1302] [Topology ] . ( 272 sec) [ -35253.1291] [Topology ] . ( 275 sec) [ -35253.1282] [Topology ] . ( 276 sec) [ -35253.1281] [GTR parameters ] . ( 276 sec) [ -35253.1281] [Alpha ][ 0.499234] . ( 276 sec) [ -35253.1281] [Topology ] . ( 279 sec) [ -35253.1273] [Topology ] . ( 279 sec) [ -35253.1273] [GTR parameters ] . ( 280 sec) [ -35253.1273] [Alpha ][ 0.499234] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -35253.127291. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -72111.9948] [GTR parameters ] . ( 4 sec) [ -70681.9017] [Alpha ][ 0.500960] . ( 4 sec) [ -70382.7963] [13972] [depth= 12] . ( 4 sec) [ -69365.3031] [13907] [depth= 6] . ( 4 sec) [ -68950.4180] [13884] [depth= 12] . ( 4 sec) [ -68877.1056] [13731] [depth= 1] . ( 5 sec) [ -68255.3083] [13703] [depth= 9] . ( 5 sec) [ -67964.4526] [13679] [depth= 1] . ( 5 sec) [ -67660.4187] [13586] [depth= 5] . ( 5 sec) [ -67313.6287] [13492] [depth= 1] . ( 5 sec) [ -67018.4047] [13407] [depth= 6] . ( 5 sec) [ -66815.8798] [13389] [depth= 9] . ( 5 sec) [ -66759.9621] [13374] [depth= 1] . ( 6 sec) [ -66639.4996] [13357] [depth= 9] . ( 6 sec) [ -66181.2557] [13322] [depth= 4] . ( 6 sec) [ -66153.8169] [13359] [depth= 1] . ( 6 sec) [ -65575.9756] [13240] [depth= 2] . ( 6 sec) [ -65221.5645] [13120] [depth= 6] . ( 6 sec) [ -65106.0516] [13121] [depth= 1] . ( 7 sec) [ -65095.8134] [13111] [depth= 2] . ( 7 sec) [ -64914.7320] [13005] [depth= 4] . ( 7 sec) [ -64820.8187] [12889] [depth= 8] . ( 7 sec) [ -63932.3997] [12815] [depth= 4] . ( 7 sec) [ -63908.8118] [12831] [depth= 1] . ( 7 sec) [ -63145.3221] [12667] [depth= 14] . ( 8 sec) [ -62301.5693] [12557] [depth= 12] . ( 8 sec) [ -62137.0991] [12536] [depth= 11] . ( 8 sec) [ -61952.2180] [12528] [depth= 1] . ( 8 sec) [ -61894.4230] [12496] [depth= 13] . ( 8 sec) [ -61332.9871] [12279] [depth= 9] . ( 8 sec) [ -60801.1335] [12156] [depth= 1] . ( 9 sec) [ -60430.9661] [12090] [depth= 10] . ( 9 sec) [ -59668.5017] [11930] [depth= 7] . ( 9 sec) [ -59632.1674] [11935] [depth= 2] . ( 9 sec) [ -59525.0324] [11944] [depth= 12] . ( 9 sec) [ -59491.5629] [11933] [depth= 1] . ( 9 sec) [ -48873.8784] [11645] [depth= 7] . ( 10 sec) [ -48686.1488] [11613] [depth= 2] . ( 10 sec) [ -48281.0075] [11472] [depth= 7] . ( 10 sec) [ -48268.9447] [11463] [depth= 3] . ( 10 sec) [ -47841.9867] [11460] [depth= 1] . ( 10 sec) [ -47527.8600] [11362] [depth= 3] . ( 10 sec) [ -47499.5238] [11359] [depth= 1] . ( 11 sec) [ -47393.6506] [11361] [depth= 1] . ( 11 sec) [ -47236.8416] [11287] [depth= 1] . ( 11 sec) [ -46575.9891] [11247] [depth= 3] . ( 11 sec) [ -46386.9419] [11070] [depth= 11] . ( 11 sec) [ -46297.1186] [11065] [depth= 3] . ( 11 sec) [ -46262.9674] [10991] [depth= 12] . ( 11 sec) [ -45173.9217] [10961] [depth= 1] . ( 12 sec) [ -44661.9614] [10793] [depth= 11] . ( 12 sec) [ -44036.7283] [10786] [depth= 3] . ( 12 sec) [ -43928.9741] [10802] [depth= 8] . ( 12 sec) [ -43925.0155] [10806] [depth= 1] . ( 12 sec) [ -43324.1007] [10560] [depth= 7] . ( 13 sec) [ -42551.3298] [10233] [depth= 7] . ( 13 sec) [ -42179.3215] [10165] [depth= 20] . ( 13 sec) [ -41953.2966] [10048] [depth= 18] . ( 13 sec) [ -41880.7843] [10006] [depth= 1] . ( 13 sec) [ -41820.0486] [ 9988] [depth= 1] . ( 14 sec) [ -41594.0703] [ 9966] [depth= 4] . ( 14 sec) [ -41296.7545] [ 9860] [depth= 3] . ( 14 sec) [ -41278.8297] [ 9852] [depth= 4] . ( 14 sec) [ -41167.8920] [ 9847] [depth= 5] . ( 14 sec) [ -40863.9798] [ 9737] [depth= 1] . ( 14 sec) [ -40803.1584] [ 9726] [depth= 1] . ( 14 sec) [ -40760.4904] [ 9737] [depth= 2] . ( 15 sec) [ -40641.7791] [ 9759] [depth= 1] . ( 15 sec) [ -40397.9465] [ 9671] [depth= 10] . ( 15 sec) [ -40326.8896] [ 9646] [depth= 1] . ( 15 sec) [ -40187.3997] [ 9623] [depth= 7] . ( 16 sec) [ -39977.8450] [ 9620] [depth= 3] . ( 16 sec) [ -39969.1210] [ 9634] [depth= 1] . ( 16 sec) [ -39965.2383] [ 9637] [depth= 1] . ( 16 sec) [ -39784.9785] [ 9501] [depth= 9] . ( 16 sec) [ -39701.0846] [ 9465] [depth= 1] . ( 17 sec) [ -39667.6351] [ 9416] [depth= 5] . ( 17 sec) [ -39506.2139] [ 9339] [depth= 1] . ( 17 sec) [ -39404.3072] [ 9310] [depth= 2] . ( 17 sec) [ -39276.9192] [ 9290] [depth= 7] . ( 17 sec) [ -39073.8501] [ 9286] [depth= 1] . ( 17 sec) [ -38671.4353] [ 9067] [depth= 9] . ( 18 sec) [ -38619.5970] [ 9055] [depth= 3] . ( 18 sec) [ -38609.5582] [ 9056] [depth= 2] . ( 18 sec) [ -38608.4280] [ 9061] [depth= 1] . ( 18 sec) [ -38532.2700] [ 8984] [depth= 1] . ( 18 sec) [ -38455.6327] [ 8970] [depth= 5] . ( 19 sec) [ -38412.0955] [ 8961] [depth= 2] . ( 19 sec) [ -38412.0482] [ 8960] [depth= 1] . ( 19 sec) [ -38374.4116] [ 9029] [depth= 1] . ( 19 sec) [ -38280.8268] [ 9007] [depth= 1] . ( 19 sec) [ -38103.0812] [ 8964] [depth= 3] . ( 19 sec) [ -38101.9450] [ 8962] [depth= 1] . ( 20 sec) [ -38091.2906] [ 8953] [depth= 1] . ( 20 sec) [ -38044.9453] [ 8941] [depth= 4] . ( 20 sec) [ -38017.5999] [ 8927] [depth= 1] . ( 20 sec) [ -37785.8586] [ 8841] [depth= 4] . ( 21 sec) [ -37666.9341] [ 8831] [depth= 1] . ( 21 sec) [ -37666.1736] [ 8831] [depth= 1] . ( 21 sec) [ -37648.6205] [ 8827] [depth= 1] . ( 21 sec) [ -37630.4265] [ 8824] [depth= 1] . ( 22 sec) [ -37629.4260] [ 8824] [depth= 1] . ( 22 sec) [ -37498.2076] [ 8766] [depth= 1] . ( 22 sec) [ -37418.8587] [ 8740] [depth= 3] . ( 22 sec) [ -37413.4467] [ 8755] [depth= 1] . ( 23 sec) [ -37348.2249] [ 8680] [depth= 4] . ( 23 sec) [ -37238.3841] [ 8607] [depth= 7] . ( 24 sec) [ -37194.3640] [ 8577] [depth= 3] . ( 24 sec) [ -37158.6959] [ 8562] [depth= 2] . ( 24 sec) [ -37151.7144] [ 8557] [depth= 2] . ( 24 sec) [ -37133.9686] [ 8554] [depth= 4] . ( 26 sec) [ -36445.3095] [Branch lengths ] . ( 29 sec) [ -36044.8931] [GTR parameters ] . ( 30 sec) [ -36043.0745] [Alpha ][ 0.472632] . ( 30 sec) [ -35961.4551] [ 8542] [depth= 6] . ( 30 sec) [ -35817.5317] [ 8461] [depth= 4] . ( 30 sec) [ -35790.3636] [ 8457] [depth= 1] . ( 31 sec) [ -35767.5659] [ 8450] [depth= 2] . ( 31 sec) [ -35639.2846] [ 8381] [depth= 5] . ( 32 sec) [ -35581.0298] [ 8346] [depth= 1] . ( 32 sec) [ -35576.8394] [ 8346] [depth= 1] . ( 33 sec) [ -35552.0654] [ 8328] [depth= 1] . ( 33 sec) [ -35536.3196] [ 8316] [depth= 1] . ( 34 sec) [ -35518.1384] [ 8301] [depth= 1] . ( 34 sec) [ -35517.8839] [ 8298] [depth= 1] . ( 35 sec) [ -35506.5902] [ 8289] [depth= 2] . ( 35 sec) [ -35465.5843] [ 8258] [depth= 1] . ( 35 sec) [ -35463.6843] [ 8263] [depth= 1] . ( 36 sec) [ -35459.8642] [ 8261] [depth= 2] . ( 38 sec) [ -35444.6087] [ 8246] [depth= 1] . ( 38 sec) [ -35437.6681] [ 8249] [depth= 3] . ( 39 sec) [ -35430.4568] [ 8245] [depth= 1] . ( 39 sec) [ -35424.6590] [ 8244] [depth= 1] . ( 40 sec) [ -35423.5577] [ 8241] [depth= 1] . ( 41 sec) [ -35410.2709] [ 8236] [depth= 1] . ( 43 sec) [ -35394.4440] [ 8235] [depth= 1] . ( 45 sec) [ -35341.3098] [Branch lengths ] . ( 47 sec) [ -35337.6651] [GTR parameters ] . ( 48 sec) [ -35337.0492] [Alpha ][ 0.488763] . ( 48 sec) [ -35333.3927] [ 8233] [depth= 1] . ( 48 sec) [ -35331.6670] [ 8231] [depth= 1] . ( 62 sec) [ -35323.7823] [Branch lengths ] . ( 64 sec) [ -35323.6646] [GTR parameters ] . ( 64 sec) [ -35323.5781] [Alpha ][ 0.495090] . ( 79 sec) [ -35320.0139] [Branch lengths ] . ( 160 sec) [ -35316.9090] [Branch lengths ] . ( 160 sec) [ -35316.9090] [Topology ] . ( 163 sec) [ -35307.1822] [Topology ] . ( 166 sec) [ -35277.7205] [Topology ] . ( 169 sec) [ -35261.4347] [Topology ] . ( 172 sec) [ -35256.1839] [Topology ] . ( 175 sec) [ -35254.7350] [Topology ] . ( 177 sec) [ -35254.3799] [Topology ] . ( 180 sec) [ -35253.5122] [GTR parameters ] . ( 180 sec) [ -35253.4632] [Alpha ][ 0.499809] . ( 180 sec) [ -35253.4632] [Topology ] . ( 183 sec) [ -35253.3205] [Topology ] . ( 186 sec) [ -35253.2699] [Topology ] . ( 189 sec) [ -35253.2431] [Topology ] . ( 192 sec) [ -35253.2253] [Topology ] . ( 195 sec) [ -35253.2125] [Topology ] . ( 197 sec) [ -35253.2029] [Topology ] . ( 199 sec) [ -35253.1943] [GTR parameters ] . ( 199 sec) [ -35253.1939] [Alpha ][ 0.499310] . ( 199 sec) [ -35253.1939] [Topology ] . ( 202 sec) [ -35253.1814] [Topology ] . ( 205 sec) [ -35253.1723] [Topology ] . ( 208 sec) [ -35253.1655] [Topology ] . ( 210 sec) [ -35253.1604] [Topology ] . ( 213 sec) [ -35253.1565] [Topology ] . ( 216 sec) [ -35253.1535] [Topology ] . ( 217 sec) [ -35253.1489] [GTR parameters ] . ( 217 sec) [ -35253.1489] [Alpha ][ 0.499310] . ( 217 sec) [ -35253.1489] [Topology ] . ( 220 sec) [ -35253.1443] [Topology ] . ( 223 sec) [ -35253.1410] [Topology ] . ( 226 sec) [ -35253.1384] [Topology ] . ( 229 sec) [ -35253.1365] [Topology ] . ( 231 sec) [ -35253.1351] [Topology ] . ( 234 sec) [ -35253.1340] [Topology ] . ( 235 sec) [ -35253.1325] [GTR parameters ] . ( 235 sec) [ -35253.1325] [Alpha ][ 0.499310] . ( 235 sec) [ -35253.1325] [Topology ] . ( 238 sec) [ -35253.1310] [Topology ] . ( 241 sec) [ -35253.1298] [Topology ] . ( 244 sec) [ -35253.1289] [Topology ] . ( 244 sec) [ -35253.1287] [GTR parameters ] . ( 245 sec) [ -35253.1287] [Alpha ][ 0.499310] . ( 245 sec) [ -35253.1287] [Topology ] . ( 248 sec) [ -35253.1278] [Topology ] . ( 248 sec) [ -35253.1278] [GTR parameters ] . ( 248 sec) [ -35253.1278] [Alpha ][ 0.498810] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -35253.127753. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -36710.7724] [GTR parameters ] . ( 2 sec) [ -36466.0989] [Alpha ][ 0.500960] . ( 2 sec) [ -36466.0989] [Topology ] . ( 5 sec) [ -36209.2967] [Topology ] . ( 7 sec) [ -36187.4972] [Topology ] . ( 10 sec) [ -36183.6050] [Topology ] . ( 13 sec) [ -36182.2546] [Topology ] . ( 16 sec) [ -36181.6395] [Topology ] . ( 19 sec) [ -36181.3321] [Topology ] . ( 21 sec) [ -36181.1727] [Topology ] . ( 24 sec) [ -36181.0882] [Topology ] . Checking for NNIs, optimizing five branches... . ( 47 sec) [ -36180.6868] [Topology ] . ( 54 sec) [ -35322.5824] [GTR parameters ] . ( 55 sec) [ -35320.2697] [Alpha ][ 0.467463] . ( 55 sec) [ -35320.2697] [Topology ] . ( 58 sec) [ -35294.8290] [Topology ] . ( 60 sec) [ -35286.3497] [Topology ] . ( 63 sec) [ -35282.3406] [Topology ] . ( 66 sec) [ -35280.0868] [Topology ] . ( 69 sec) [ -35278.7376] [Topology ] . ( 72 sec) [ -35277.8949] [Topology ] . ( 75 sec) [ -35277.3529] [Topology ] . Checking for NNIs, optimizing five branches... . ( 103 sec) [ -35269.7035] [GTR parameters ] . ( 103 sec) [ -35268.4270] [Alpha ][ 0.491109] . ( 103 sec) [ -35268.4270] [Topology ] . ( 106 sec) [ -35265.7908] [Topology ] . ( 109 sec) [ -35264.1797] [Topology ] . ( 112 sec) [ -35263.1137] [Topology ] . ( 115 sec) [ -35262.3863] [Topology ] . ( 118 sec) [ -35261.8806] [Topology ] . ( 120 sec) [ -35261.5229] [Topology ] . Checking for NNIs, optimizing five branches... . ( 148 sec) [ -35260.9682] [GTR parameters ] . ( 148 sec) [ -35260.8456] [Alpha ][ 0.498712] . ( 149 sec) [ -35260.8456] [Topology ] . ( 151 sec) [ -35260.2677] [Topology ] . ( 154 sec) [ -35259.8627] [Topology ] . ( 157 sec) [ -35259.5713] [Topology ] . ( 160 sec) [ -35259.3594] [Topology ] . ( 163 sec) [ -35259.2041] [Topology ] . ( 166 sec) [ -35259.0888] [Topology ] . Checking for NNIs, optimizing five branches... . ( 193 sec) [ -35258.9334] [GTR parameters ] . ( 193 sec) [ -35258.9280] [Alpha ][ 0.500271] . ( 193 sec) [ -35258.9280] [Topology ] . ( 196 sec) [ -35258.7614] [Topology ] . ( 199 sec) [ -35258.6406] [Topology ] . ( 202 sec) [ -35258.5508] [Topology ] . ( 205 sec) [ -35258.4836] [Topology ] . ( 208 sec) [ -35258.4333] [Topology ] . ( 211 sec) [ -35258.3953] [Topology ] . Checking for NNIs, optimizing five branches... . ( 236 sec) [ -35258.3366] [GTR parameters ] . ( 236 sec) [ -35258.3366] [Alpha ][ 0.500271] . ( 236 sec) [ -35258.3366] [Topology ] . ( 239 sec) [ -35258.2807] [Topology ] . ( 242 sec) [ -35258.2399] [Topology ] . ( 245 sec) [ -35258.2092] [Topology ] . ( 248 sec) [ -35258.1859] [Topology ] . ( 251 sec) [ -35258.1682] [Topology ] . ( 253 sec) [ -35258.1547] [Topology ] . Checking for NNIs, optimizing five branches... . ( 278 sec) [ -35258.1319] [GTR parameters ] . ( 278 sec) [ -35258.1319] [Alpha ][ 0.500271] . ( 278 sec) [ -35258.1319] [Topology ] . ( 281 sec) [ -35258.1114] [Topology ] . ( 284 sec) [ -35258.0963] [Topology ] . ( 287 sec) [ -35258.0849] [Topology ] . ( 290 sec) [ -35258.0762] [Topology ] . ( 292 sec) [ -35258.0695] [Topology ] . ( 295 sec) [ -35258.0644] [Topology ] . Checking for NNIs, optimizing five branches... . ( 319 sec) [ -35258.0563] [GTR parameters ] . ( 320 sec) [ -35258.0563] [Alpha ][ 0.500271] . ( 320 sec) [ -35258.0563] [Topology ] . ( 323 sec) [ -35258.0487] [Topology ] . ( 326 sec) [ -35258.0431] [Topology ] . ( 328 sec) [ -35258.0389] [Topology ] . ( 331 sec) [ -35258.0356] [Topology ] . ( 334 sec) [ -35258.0331] [Topology ] . ( 337 sec) [ -35258.0312] [Topology ] . Checking for NNIs, optimizing five branches... . ( 361 sec) [ -35258.0280] [GTR parameters ] . ( 362 sec) [ -35258.0277] [Alpha ][ 0.499771] . ( 362 sec) [ -35258.0277] [Topology ] . ( 365 sec) [ -35258.0248] [Topology ] . ( 367 sec) [ -35258.0228] [Topology ] . ( 370 sec) [ -35258.0212] [Topology ] . ( 373 sec) [ -35258.0200] [Topology ] . ( 376 sec) [ -35258.0190] [Topology ] . Checking for NNIs, optimizing five branches... . ( 401 sec) [ -35258.0177] [GTR parameters ] . ( 402 sec) [ -35258.0177] [Alpha ][ 0.499771] . ( 402 sec) [ -35258.0177] [Topology ] . ( 405 sec) [ -35258.0164] [Topology ] . ( 407 sec) [ -35258.0154] [Topology ] . Checking for NNIs, optimizing five branches... . ( 432 sec) [ -35258.0153] [GTR parameters ] . ( 432 sec) [ -35258.0153] [Alpha ][ 0.499771] . ( 432 sec) [ -35258.0153] [Topology ] . ( 435 sec) [ -35258.0145] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 483 sec) [ -36710.7724] [GTR parameters ] . ( 483 sec) [ -36466.0989] [Alpha ][ 0.500960] . ( 488 sec) [ -36464.9677] [ 8258] [depth= 1] . ( 488 sec) [ -36460.8603] [ 8291] [depth= 2] . ( 488 sec) [ -36413.8896] [ 8255] [depth= 2] . ( 489 sec) [ -36411.3454] [ 8249] [depth= 1] . ( 489 sec) [ -36397.3331] [ 8254] [depth= 1] . ( 489 sec) [ -36396.4495] [ 8264] [depth= 1] . ( 490 sec) [ -36396.4283] [ 8268] [depth= 1] . ( 490 sec) [ -36393.2290] [ 8263] [depth= 2] . ( 490 sec) [ -36391.5326] [ 8259] [depth= 1] . ( 491 sec) [ -36388.9751] [ 8260] [depth= 1] . ( 491 sec) [ -36362.6353] [ 8249] [depth= 5] . ( 491 sec) [ -36359.1347] [ 8255] [depth= 1] . ( 492 sec) [ -36350.2260] [ 8249] [depth= 1] . ( 493 sec) [ -36349.7371] [ 8242] [depth= 1] . ( 493 sec) [ -36349.4200] [ 8246] [depth= 1] . ( 494 sec) [ -36343.2807] [ 8241] [depth= 1] . ( 494 sec) [ -36329.9012] [ 8240] [depth= 1] . ( 498 sec) [ -36327.9565] [ 8239] [depth= 1] . ( 500 sec) [ -36197.4375] [Branch lengths ] . ( 507 sec) [ -35337.0661] [GTR parameters ] . ( 507 sec) [ -35334.1525] [Alpha ][ 0.463557] . ( 510 sec) [ -35331.7797] [ 8231] [depth= 1] . ( 512 sec) [ -35326.9401] [ 8235] [depth= 1] . ( 512 sec) [ -35323.2659] [ 8231] [depth= 1] . ( 521 sec) [ -35284.2968] [Branch lengths ] . ( 525 sec) [ -35280.5360] [GTR parameters ] . ( 525 sec) [ -35279.7293] [Alpha ][ 0.482446] . ( 539 sec) [ -35265.7588] [Branch lengths ] . ( 620 sec) [ -35261.5709] [Branch lengths ] . ( 620 sec) [ -35261.5709] [Topology ] . ( 623 sec) [ -35260.7430] [Topology ] . ( 626 sec) [ -35260.3509] [Topology ] . ( 629 sec) [ -35260.0876] [Topology ] . ( 632 sec) [ -35259.9043] [Topology ] . ( 635 sec) [ -35259.7739] [Topology ] . ( 637 sec) [ -35259.6805] [Topology ] . ( 641 sec) [ -35256.7278] [GTR parameters ] . ( 641 sec) [ -35256.1861] [Alpha ][ 0.497802] . ( 641 sec) [ -35256.1861] [Topology ] . ( 644 sec) [ -35255.4758] [Topology ] . ( 647 sec) [ -35255.0131] [Topology ] . ( 650 sec) [ -35254.6866] [Topology ] . ( 652 sec) [ -35254.4527] [Topology ] . ( 655 sec) [ -35254.2838] [Topology ] . ( 658 sec) [ -35254.1601] [Topology ] . ( 660 sec) [ -35254.0202] [GTR parameters ] . ( 660 sec) [ -35254.0124] [Alpha ][ 0.499682] . ( 660 sec) [ -35254.0124] [Topology ] . ( 663 sec) [ -35253.8451] [Topology ] . ( 666 sec) [ -35253.7249] [Topology ] . ( 669 sec) [ -35253.6364] [Topology ] . ( 672 sec) [ -35253.5712] [Topology ] . ( 674 sec) [ -35253.5228] [Topology ] . ( 677 sec) [ -35253.4868] [Topology ] . ( 679 sec) [ -35253.4261] [GTR parameters ] . ( 679 sec) [ -35253.4261] [Alpha ][ 0.499682] . ( 679 sec) [ -35253.4261] [Topology ] . ( 682 sec) [ -35253.3725] [Topology ] . ( 685 sec) [ -35253.3340] [Topology ] . ( 688 sec) [ -35253.3053] [Topology ] . ( 690 sec) [ -35253.2838] [Topology ] . ( 693 sec) [ -35253.2676] [Topology ] . ( 696 sec) [ -35253.2554] [Topology ] . ( 697 sec) [ -35253.2326] [GTR parameters ] . ( 697 sec) [ -35253.2326] [Alpha ][ 0.499682] . ( 697 sec) [ -35253.2326] [Topology ] . ( 700 sec) [ -35253.2134] [Topology ] . ( 703 sec) [ -35253.1996] [Topology ] . ( 706 sec) [ -35253.1893] [Topology ] . ( 709 sec) [ -35253.1815] [Topology ] . ( 712 sec) [ -35253.1756] [Topology ] . ( 715 sec) [ -35253.1711] [Topology ] . ( 716 sec) [ -35253.1631] [GTR parameters ] . ( 717 sec) [ -35253.1629] [Alpha ][ 0.499183] . ( 717 sec) [ -35253.1629] [Topology ] . ( 720 sec) [ -35253.1561] [Topology ] . ( 722 sec) [ -35253.1513] [Topology ] . ( 725 sec) [ -35253.1476] [Topology ] . ( 728 sec) [ -35253.1448] [Topology ] . ( 731 sec) [ -35253.1427] [Topology ] . ( 734 sec) [ -35253.1412] [Topology ] . ( 736 sec) [ -35253.1379] [GTR parameters ] . ( 736 sec) [ -35253.1379] [Alpha ][ 0.499183] . ( 736 sec) [ -35253.1379] [Topology ] . ( 739 sec) [ -35253.1354] [Topology ] . ( 742 sec) [ -35253.1335] [Topology ] . ( 745 sec) [ -35253.1321] [Topology ] . ( 747 sec) [ -35253.1311] [Topology ] . ( 750 sec) [ -35253.1302] [Topology ] . ( 752 sec) [ -35253.1295] [GTR parameters ] . ( 752 sec) [ -35253.1295] [Alpha ][ 0.499183] . ( 752 sec) [ -35253.1295] [Topology ] . ( 755 sec) [ -35253.1285] [Topology ] . ( 756 sec) [ -35253.1284] [GTR parameters ] . ( 756 sec) [ -35253.1284] [Alpha ][ 0.499183] . ( 756 sec) [ -35253.1284] [Topology ] . ( 759 sec) [ -35253.1275] [Topology ] . ( 760 sec) [ -35253.1274] [GTR parameters ] . ( 760 sec) [ -35253.1274] [Alpha ][ 0.499183] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -35258.014465 . Log likelihood obtained after SPR moves : -35253.127376 . Log likelihood of the current tree: -35253.127376. . Printing the most likely tree in file 'nucleic_M2627_54x1915_2006.phy_phyml_tree.txt'... . Best log likelihood : -35253.126978 . Time used 0h13m5s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 2309.90user 0.00system 38:47.21elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps