.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M3862_362x1207_2008.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 : SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 1 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 1028 patterns found. (out of a total of 1207 sites) . 273 sites without polymorphism (22.62%). . Computing pairwise distances... . Building BioNJ tree... . WARNING: this analysis will use at least 199Mo of memory space... . Maximizing likelihood (using SPR moves)... . ( 32 sec) [ -99137.4102] [GTR parameters ] . ( 35 sec) [ -97876.2894] [Alpha ][ 0.500960] . ( 39 sec) [ -97871.2572] [22800] [depth= 4] . ( 39 sec) [ -97865.6299] [22795] [depth= 2] . ( 40 sec) [ -97853.6553] [22797] [depth= 1] . ( 41 sec) [ -97851.0512] [22797] [depth= 1] . ( 45 sec) [ -97848.2107] [22804] [depth= 1] . ( 45 sec) [ -97836.0887] [22797] [depth= 1] . ( 51 sec) [ -97833.8292] [22798] [depth= 1] . ( 52 sec) [ -97832.7915] [22797] [depth= 1] . ( 54 sec) [ -97831.3691] [22794] [depth= 1] . ( 56 sec) [ -97827.2937] [22798] [depth= 1] . ( 58 sec) [ -97826.9794] [22798] [depth= 1] . ( 63 sec) [ -97822.0830] [22803] [depth= 2] . ( 64 sec) [ -97812.0483] [22793] [depth= 2] . ( 69 sec) [ -97810.1106] [22793] [depth= 1] . ( 74 sec) [ -97805.7644] [22794] [depth= 2] . ( 76 sec) [ -97803.4618] [22796] [depth= 1] . ( 77 sec) [ -97802.2188] [22800] [depth= 2] . ( 77 sec) [ -97794.2900] [22797] [depth= 2] . ( 88 sec) [ -97784.9335] [22791] [depth= 1] . ( 95 sec) [ -97781.9152] [22793] [depth= 1] . ( 96 sec) [ -97780.8375] [22792] [depth= 1] . ( 97 sec) [ -97780.2051] [22793] [depth= 1] . ( 99 sec) [ -97779.1998] [22791] [depth= 1] . ( 100 sec) [ -97777.6865] [22793] [depth= 1] . ( 103 sec) [ -97775.0827] [22791] [depth= 2] . ( 104 sec) [ -97774.5913] [22792] [depth= 1] . ( 107 sec) [ -97774.1002] [22792] [depth= 1] . ( 108 sec) [ -97771.8121] [22792] [depth= 1] . ( 109 sec) [ -97771.1982] [22792] [depth= 1] . ( 113 sec) [ -97756.6905] [22790] [depth= 5] . ( 114 sec) [ -97756.2977] [22787] [depth= 1] . ( 115 sec) [ -97746.6080] [22780] [depth= 1] . ( 117 sec) [ -97736.6673] [22776] [depth= 2] . ( 121 sec) [ -97734.9719] [22774] [depth= 1] . ( 122 sec) [ -97707.6208] [22760] [depth= 5] . ( 123 sec) [ -97702.0429] [22762] [depth= 1] . ( 124 sec) [ -97700.1513] [22760] [depth= 2] . ( 124 sec) [ -97693.2902] [22759] [depth= 1] . ( 128 sec) [ -97693.2128] [22761] [depth= 1] . ( 131 sec) [ -97691.7787] [22759] [depth= 1] . ( 138 sec) [ -97677.5372] [22759] [depth= 1] . ( 139 sec) [ -97671.5815] [22764] [depth= 1] . ( 145 sec) [ -97670.4458] [22766] [depth= 2] . ( 146 sec) [ -97664.3737] [22763] [depth= 1] . ( 151 sec) [ -97651.3961] [22758] [depth= 2] . ( 155 sec) [ -97650.5316] [22758] [depth= 1] . ( 156 sec) [ -97647.1604] [22758] [depth= 1] . ( 159 sec) [ -97644.3010] [22757] [depth= 1] . ( 161 sec) [ -97642.9095] [22760] [depth= 1] . ( 162 sec) [ -97636.0775] [22757] [depth= 1] . ( 163 sec) [ -97621.4481] [22754] [depth= 2] . ( 164 sec) [ -97613.9404] [22751] [depth= 1] . ( 165 sec) [ -97612.4827] [22752] [depth= 1] . ( 166 sec) [ -97604.9557] [22750] [depth= 1] . ( 168 sec) [ -97603.5583] [22753] [depth= 1] . ( 169 sec) [ -97600.2640] [22750] [depth= 1] . ( 170 sec) [ -97593.7506] [22748] [depth= 2] . ( 171 sec) [ -97592.7586] [22745] [depth= 2] . ( 175 sec) [ -97592.0733] [22745] [depth= 1] . ( 175 sec) [ -97588.1288] [22745] [depth= 3] . ( 176 sec) [ -97587.9832] [22749] [depth= 1] . ( 177 sec) [ -97560.2791] [22741] [depth= 3] . ( 178 sec) [ -97559.0270] [22739] [depth= 1] . ( 179 sec) [ -97555.9393] [22742] [depth= 1] . ( 179 sec) [ -97554.5932] [22739] [depth= 1] . ( 180 sec) [ -97548.3502] [22737] [depth= 1] . ( 183 sec) [ -97547.4386] [22738] [depth= 1] . ( 184 sec) [ -97543.7250] [22745] [depth= 3] . ( 189 sec) [ -97539.1018] [22744] [depth= 2] . ( 190 sec) [ -97536.5650] [22741] [depth= 1] . ( 192 sec) [ -97534.9999] [22741] [depth= 1] . ( 196 sec) [ -97529.4021] [22746] [depth= 3] . ( 198 sec) [ -97525.9175] [22745] [depth= 2] . ( 203 sec) [ -97520.0650] [22744] [depth= 1] . ( 204 sec) [ -97519.4358] [22744] [depth= 1] . ( 206 sec) [ -97519.0203] [22745] [depth= 1] . ( 208 sec) [ -97518.8334] [22748] [depth= 1] . ( 208 sec) [ -97515.1850] [22748] [depth= 1] . ( 209 sec) [ -97513.7748] [22746] [depth= 1] . ( 212 sec) [ -97513.5024] [22747] [depth= 1] . ( 213 sec) [ -97513.3930] [22748] [depth= 1] . ( 214 sec) [ -97504.6865] [22744] [depth= 2] . ( 215 sec) [ -97503.6109] [22746] [depth= 1] . ( 217 sec) [ -97503.3262] [22745] [depth= 1] . ( 218 sec) [ -97501.8227] [22744] [depth= 3] . ( 220 sec) [ -97500.1594] [22743] [depth= 2] . ( 222 sec) [ -97497.3203] [22737] [depth= 2] . ( 224 sec) [ -97496.4643] [22737] [depth= 1] . ( 224 sec) [ -97490.9253] [22739] [depth= 2] . ( 225 sec) [ -97486.2106] [22736] [depth= 2] . ( 226 sec) [ -97485.4195] [22738] [depth= 1] . ( 227 sec) [ -97480.2477] [22749] [depth= 2] . ( 228 sec) [ -97476.9410] [22747] [depth= 1] . ( 229 sec) [ -97476.4921] [22749] [depth= 2] . ( 230 sec) [ -97476.0964] [22749] [depth= 1] . ( 232 sec) [ -97471.3478] [22744] [depth= 1] . ( 234 sec) [ -97463.9708] [22740] [depth= 1] . ( 235 sec) [ -97462.6073] [22741] [depth= 1] . ( 236 sec) [ -97454.7129] [22742] [depth= 1] . ( 237 sec) [ -97453.7078] [22740] [depth= 1] . ( 237 sec) [ -97453.0015] [22742] [depth= 1] . ( 238 sec) [ -97442.6301] [22735] [depth= 3] . ( 241 sec) [ -97439.2031] [22735] [depth= 3] . ( 242 sec) [ -97433.0117] [22731] [depth= 1] . ( 242 sec) [ -97431.5706] [22735] [depth= 1] . ( 245 sec) [ -97427.0754] [22739] [depth= 2] . ( 246 sec) [ -97418.0600] [22733] [depth= 2] . ( 247 sec) [ -97417.9967] [22732] [depth= 1] . ( 248 sec) [ -97401.6373] [22733] [depth= 4] . ( 249 sec) [ -97394.1491] [22728] [depth= 1] . ( 250 sec) [ -97389.1573] [22725] [depth= 1] . ( 251 sec) [ -97387.8087] [22726] [depth= 1] . ( 253 sec) [ -97378.3077] [22727] [depth= 1] . ( 254 sec) [ -97376.8646] [22730] [depth= 1] . ( 255 sec) [ -97370.7806] [22729] [depth= 2] . ( 255 sec) [ -97365.2666] [22726] [depth= 1] . ( 256 sec) [ -97351.2131] [22723] [depth= 1] . ( 258 sec) [ -97331.1426] [22717] [depth= 1] . ( 259 sec) [ -97329.1567] [22716] [depth= 1] . ( 262 sec) [ -97327.7644] [22719] [depth= 1] . ( 263 sec) [ -97315.8278] [22724] [depth= 3] . ( 263 sec) [ -97313.8393] [22723] [depth= 1] . ( 264 sec) [ -97312.0058] [22720] [depth= 1] . ( 265 sec) [ -97311.9272] [22718] [depth= 1] . ( 266 sec) [ -97298.8354] [22710] [depth= 3] . ( 267 sec) [ -97297.8639] [22715] [depth= 1] . ( 269 sec) [ -97296.5004] [22720] [depth= 3] . ( 271 sec) [ -97279.0726] [22703] [depth= 4] . ( 273 sec) [ -97264.3941] [22693] [depth= 3] . ( 274 sec) [ -97260.1887] [22688] [depth= 1] . ( 275 sec) [ -97259.7568] [22687] [depth= 1] . ( 276 sec) [ -97257.3064] [22689] [depth= 1] . ( 276 sec) [ -97256.1982] [22693] [depth= 2] . ( 277 sec) [ -97245.7015] [22689] [depth= 2] . ( 278 sec) [ -97236.2164] [22687] [depth= 1] . ( 279 sec) [ -97225.9441] [22692] [depth= 1] . ( 280 sec) [ -97215.7519] [22685] [depth= 1] . ( 281 sec) [ -97198.9028] [22677] [depth= 1] . ( 281 sec) [ -97198.4551] [22679] [depth= 1] . ( 283 sec) [ -97191.4245] [22685] [depth= 1] . ( 284 sec) [ -97183.9212] [22682] [depth= 2] . ( 285 sec) [ -97178.3289] [22684] [depth= 1] . ( 287 sec) [ -97175.9048] [22682] [depth= 1] . ( 288 sec) [ -97167.1207] [22678] [depth= 1] . ( 290 sec) [ -97161.7883] [22674] [depth= 1] . ( 291 sec) [ -97153.4295] [22678] [depth= 1] . ( 292 sec) [ -97151.2515] [22676] [depth= 1] . ( 293 sec) [ -97150.0372] [22675] [depth= 1] . ( 296 sec) [ -97149.7896] [22676] [depth= 1] . ( 297 sec) [ -97147.1255] [22678] [depth= 1] . ( 298 sec) [ -97142.0518] [22670] [depth= 3] . ( 299 sec) [ -97115.3391] [22672] [depth= 3] . ( 300 sec) [ -97115.2876] [22672] [depth= 1] . ( 301 sec) [ -97113.8502] [22672] [depth= 1] . ( 302 sec) [ -97100.6959] [22674] [depth= 2] . ( 303 sec) [ -97065.9881] [22665] [depth= 2] . ( 303 sec) [ -97056.0129] [22663] [depth= 1] . ( 304 sec) [ -96998.9847] [22649] [depth= 1] . ( 306 sec) [ -96989.6870] [22649] [depth= 1] . ( 307 sec) [ -96987.5145] [22654] [depth= 1] . ( 308 sec) [ -96983.6442] [22649] [depth= 1] . ( 309 sec) [ -96981.1238] [22649] [depth= 1] . ( 310 sec) [ -96974.8798] [22649] [depth= 1] . ( 312 sec) [ -96943.4473] [22644] [depth= 5] . ( 313 sec) [ -96939.5373] [22654] [depth= 1] . ( 313 sec) [ -96922.1524] [22644] [depth= 1] . ( 314 sec) [ -96904.3012] [22644] [depth= 1] . ( 317 sec) [ -96899.4771] [22645] [depth= 1] . ( 318 sec) [ -96897.1115] [22644] [depth= 1] . ( 320 sec) [ -96896.1535] [22642] [depth= 1] . ( 321 sec) [ -96885.0601] [22636] [depth= 1] . ( 322 sec) [ -96874.7505] [22650] [depth= 1] . ( 323 sec) [ -96856.4559] [22636] [depth= 1] . ( 324 sec) [ -96853.3278] [22637] [depth= 1] . ( 325 sec) [ -96846.2676] [22636] [depth= 1] . ( 325 sec) [ -96838.5376] [22632] [depth= 1] . ( 326 sec) [ -96837.3912] [22632] [depth= 1] . ( 327 sec) [ -96835.4221] [22629] [depth= 1] . ( 328 sec) [ -96834.3970] [22632] [depth= 1] . ( 330 sec) [ -96824.0780] [22633] [depth= 1] . ( 331 sec) [ -96818.4331] [22639] [depth= 1] . ( 331 sec) [ -96795.1951] [22637] [depth= 1] . ( 332 sec) [ -96794.2327] [22637] [depth= 1] . ( 335 sec) [ -96793.6932] [22638] [depth= 1] . ( 336 sec) [ -96792.0064] [22638] [depth= 1] . ( 337 sec) [ -96788.9525] [22638] [depth= 1] . ( 338 sec) [ -96788.4367] [22637] [depth= 2] . ( 339 sec) [ -96782.2593] [22637] [depth= 1] . ( 340 sec) [ -96781.9858] [22642] [depth= 1] . ( 342 sec) [ -96778.3155] [22639] [depth= 1] . ( 342 sec) [ -96763.9687] [22632] [depth= 3] . ( 343 sec) [ -96763.3808] [22636] [depth= 3] . ( 345 sec) [ -96752.5994] [22637] [depth= 1] . ( 346 sec) [ -96734.2708] [22631] [depth= 4] . ( 347 sec) [ -96709.6259] [22629] [depth= 1] . ( 350 sec) [ -96683.4260] [22628] [depth= 8] . ( 350 sec) [ -96678.4907] [22626] [depth= 1] . ( 353 sec) [ -96675.8982] [22628] [depth= 2] . ( 354 sec) [ -96674.4597] [22628] [depth= 1] . ( 357 sec) [ -96673.9528] [22628] [depth= 1] . ( 359 sec) [ -96673.2261] [22628] [depth= 1] . ( 360 sec) [ -96661.2620] [22623] [depth= 1] . ( 361 sec) [ -96660.8687] [22623] [depth= 1] . ( 361 sec) [ -96653.3515] [22618] [depth= 1] . ( 364 sec) [ -96647.1849] [22615] [depth= 1] . ( 365 sec) [ -96646.9217] [22614] [depth= 2] . ( 366 sec) [ -96642.8103] [22613] [depth= 1] . ( 366 sec) [ -96639.9277] [22609] [depth= 2] . ( 367 sec) [ -96639.0289] [22615] [depth= 1] . ( 369 sec) [ -96637.7868] [22616] [depth= 1] . ( 370 sec) [ -96637.4180] [22615] [depth= 1] . ( 371 sec) [ -96637.3767] [22620] [depth= 3] . ( 374 sec) [ -96636.9080] [22619] [depth= 1] . ( 375 sec) [ -96630.4638] [22622] [depth= 7] . ( 376 sec) [ -96627.6010] [22621] [depth= 7] . ( 377 sec) [ -96623.8560] [22621] [depth= 2] . ( 378 sec) [ -96616.3922] [22622] [depth= 1] . ( 379 sec) [ -96608.1009] [22626] [depth= 1] . ( 380 sec) [ -96605.2482] [22626] [depth= 1] . ( 381 sec) [ -96604.7729] [22628] [depth= 3] . ( 382 sec) [ -96593.3466] [22624] [depth= 2] . ( 383 sec) [ -96591.6304] [22622] [depth= 3] . ( 384 sec) [ -96588.3559] [22621] [depth= 4] . ( 385 sec) [ -96586.8232] [22624] [depth= 1] . ( 387 sec) [ -96579.3317] [22620] [depth= 2] . ( 387 sec) [ -96577.9989] [22619] [depth= 1] . ( 388 sec) [ -96576.2260] [22619] [depth= 1] . ( 389 sec) [ -96573.1558] [22623] [depth= 1] . ( 391 sec) [ -96571.1232] [22619] [depth= 1] . ( 392 sec) [ -96561.8244] [22623] [depth= 3] . ( 395 sec) [ -96555.9724] [22627] [depth= 1] . ( 396 sec) [ -96552.7463] [22625] [depth= 2] . ( 397 sec) [ -96552.6450] [22630] [depth= 3] . ( 399 sec) [ -96547.6268] [22620] [depth= 2] . ( 401 sec) [ -96529.5935] [22614] [depth= 4] . ( 402 sec) [ -96528.6232] [22613] [depth= 1] . ( 403 sec) [ -96518.8401] [22606] [depth= 3] . ( 404 sec) [ -96507.2151] [22609] [depth= 6] . ( 405 sec) [ -96506.7063] [22612] [depth= 1] . ( 405 sec) [ -96501.5134] [22614] [depth= 3] . ( 406 sec) [ -96500.4633] [22612] [depth= 1] . ( 408 sec) [ -96499.6828] [22614] [depth= 5] . ( 408 sec) [ -96468.9883] [22618] [depth= 4] . ( 409 sec) [ -96467.5713] [22611] [depth= 3] . ( 412 sec) [ -96454.8307] [22617] [depth= 4] . ( 413 sec) [ -96448.8489] [22607] [depth= 1] . ( 414 sec) [ -96448.1292] [22610] [depth= 2] . ( 416 sec) [ -96441.6972] [22612] [depth= 1] . ( 417 sec) [ -96438.6651] [22613] [depth= 1] . ( 418 sec) [ -96427.0489] [22609] [depth= 1] . ( 418 sec) [ -96426.0360] [22606] [depth= 2] . ( 419 sec) [ -96414.2208] [22614] [depth= 2] . ( 420 sec) [ -96406.6288] [22608] [depth= 1] . ( 421 sec) [ -96403.1868] [22606] [depth= 1] . ( 422 sec) [ -96397.5062] [22608] [depth= 1] . ( 423 sec) [ -96383.8483] [22613] [depth= 1] . ( 424 sec) [ -96381.9082] [22616] [depth= 1] . ( 425 sec) [ -96381.7749] [22620] [depth= 1] . ( 426 sec) [ -96379.9799] [22624] [depth= 2] . ( 427 sec) [ -96372.0221] [22624] [depth= 1] . ( 429 sec) [ -96365.5161] [22630] [depth= 1] . ( 429 sec) [ -96351.2232] [22637] [depth= 1] . ( 430 sec) [ -96330.1811] [22630] [depth= 1] . ( 432 sec) [ -96323.3267] [22630] [depth= 2] . ( 433 sec) [ -96320.6887] [22628] [depth= 1] . ( 435 sec) [ -96312.4079] [22631] [depth= 1] . ( 436 sec) [ -96310.8988] [22620] [depth= 1] . ( 437 sec) [ -96310.7428] [22621] [depth= 1] . ( 438 sec) [ -96299.4661] [22619] [depth= 2] . ( 439 sec) [ -96292.5881] [22619] [depth= 1] . ( 440 sec) [ -96287.5475] [22624] [depth= 1] . ( 440 sec) [ -96282.3108] [22627] [depth= 2] . ( 441 sec) [ -96267.0180] [22622] [depth= 2] . ( 442 sec) [ -96254.0736] [22618] [depth= 1] . ( 444 sec) [ -96251.8291] [22613] [depth= 3] . ( 445 sec) [ -96241.6121] [22619] [depth= 1] . ( 445 sec) [ -96238.8635] [22624] [depth= 1] . ( 447 sec) [ -96235.4439] [22619] [depth= 1] . ( 448 sec) [ -96226.2390] [22628] [depth= 1] . ( 449 sec) [ -96223.1944] [22632] [depth= 2] . ( 450 sec) [ -96222.8648] [22628] [depth= 2] . ( 451 sec) [ -96214.0799] [22629] [depth= 1] . ( 452 sec) [ -96213.9467] [22633] [depth= 2] . ( 453 sec) [ -96208.3552] [22629] [depth= 2] . ( 454 sec) [ -96195.9889] [22620] [depth= 1] . ( 455 sec) [ -96193.3144] [22615] [depth= 2] . ( 456 sec) [ -96187.8038] [22617] [depth= 1] . ( 457 sec) [ -96184.9866] [22615] [depth= 1] . ( 459 sec) [ -96181.6840] [22613] [depth= 1] . ( 460 sec) [ -96181.2893] [22616] [depth= 1] . ( 463 sec) [ -96175.4720] [22614] [depth= 4] . ( 464 sec) [ -96172.7658] [22611] [depth= 1] . ( 464 sec) [ -96170.6721] [22613] [depth= 1] . ( 466 sec) [ -96167.8272] [22616] [depth= 1] . ( 467 sec) [ -96160.1911] [22619] [depth= 3] . ( 469 sec) [ -96157.7950] [22621] [depth= 3] . ( 470 sec) [ -96140.6011] [22622] [depth= 1] . ( 470 sec) [ -96133.1545] [22625] [depth= 4] . ( 471 sec) [ -96122.3043] [22623] [depth= 1] . ( 472 sec) [ -96116.4828] [22621] [depth= 1] . ( 473 sec) [ -96106.7609] [22623] [depth= 1] . ( 474 sec) [ -96106.1803] [22621] [depth= 1] . ( 474 sec) [ -96105.7350] [22624] [depth= 1] . ( 476 sec) [ -96103.1109] [22621] [depth= 2] . ( 477 sec) [ -96101.9180] [22628] [depth= 1] . ( 478 sec) [ -96101.1142] [22625] [depth= 1] . ( 478 sec) [ -96096.1556] [22627] [depth= 1] . ( 479 sec) [ -96086.5556] [22616] [depth= 2] . ( 480 sec) [ -96070.6105] [22612] [depth= 2] . ( 482 sec) [ -96061.7950] [22611] [depth= 1] . ( 483 sec) [ -96058.3898] [22615] [depth= 1] . ( 484 sec) [ -96056.8909] [22617] [depth= 1] . ( 486 sec) [ -96044.8336] [22617] [depth= 2] . ( 487 sec) [ -96044.4558] [22612] [depth= 3] . ( 488 sec) [ -96032.7232] [22612] [depth= 1] . ( 489 sec) [ -96030.5690] [22612] [depth= 1] . ( 492 sec) [ -96027.0350] [22612] [depth= 2] . ( 495 sec) [ -96024.1255] [22611] [depth= 1] . ( 496 sec) [ -96011.3777] [22609] [depth= 1] . ( 496 sec) [ -96008.9953] [22611] [depth= 1] . ( 497 sec) [ -96002.2176] [22611] [depth= 3] . ( 498 sec) [ -96002.1849] [22612] [depth= 2] . ( 499 sec) [ -95997.6057] [22610] [depth= 1] . ( 500 sec) [ -95988.2223] [22611] [depth= 1] . ( 502 sec) [ -95987.5305] [22610] [depth= 1] . ( 504 sec) [ -95983.5469] [22607] [depth= 5] . ( 505 sec) [ -95978.0340] [22594] [depth= 4] . ( 506 sec) [ -95976.2447] [22594] [depth= 1] . ( 507 sec) [ -95973.2805] [22594] [depth= 2] . ( 508 sec) [ -95971.9528] [22596] [depth= 1] . ( 508 sec) [ -95969.3859] [22599] [depth= 1] . ( 510 sec) [ -95968.9656] [22599] [depth= 3] . ( 511 sec) [ -95968.5784] [22598] [depth= 1] . ( 513 sec) [ -95965.6087] [22595] [depth= 2] . ( 515 sec) [ -95964.6683] [22594] [depth= 1] . ( 521 sec) [ -95287.9938] [Branch lengths ] . ( 533 sec) [ -95247.7247] [GTR parameters ] . ( 534 sec) [ -95246.6182] [Alpha ][ 0.488208] . ( 549 sec) [ -95246.5206] [22593] [depth= 1] . ( 551 sec) [ -95246.4912] [22597] [depth= 1] . ( 552 sec) [ -95246.1090] [22594] [depth= 1] . ( 554 sec) [ -95245.5362] [22597] [depth= 1] . ( 560 sec) [ -95244.4021] [22595] [depth= 1] . ( 573 sec) [ -95239.1220] [22588] [depth= 1] . ( 596 sec) [ -95238.9589] [22589] [depth= 1] . ( 597 sec) [ -95238.6973] [22588] [depth= 1] . ( 607 sec) [ -95238.6705] [22588] [depth= 1] . ( 609 sec) [ -95238.5679] [22589] [depth= 1] . ( 617 sec) [ -95238.4228] [22590] [depth= 1] . ( 655 sec) [ -95237.9318] [22591] [depth= 1] . ( 676 sec) [ -95235.1358] [22591] [depth= 1] . ( 677 sec) [ -95232.6299] [22588] [depth= 1] . ( 680 sec) [ -95232.1670] [22588] [depth= 1] . ( 691 sec) [ -95231.9764] [22588] [depth= 1] . ( 696 sec) [ -95231.6167] [22592] [depth= 1] . ( 719 sec) [ -95231.2979] [22593] [depth= 1] . ( 729 sec) [ -95229.5961] [22591] [depth= 2] . ( 730 sec) [ -95229.2801] [22594] [depth= 1] . ( 748 sec) [ -95229.2284] [22594] [depth= 1] . ( 749 sec) [ -95227.1684] [22596] [depth= 2] . ( 759 sec) [ -95225.3416] [22596] [depth= 1] . ( 762 sec) [ -95225.2590] [22594] [depth= 1] . ( 763 sec) [ -95225.1572] [22596] [depth= 1] . ( 765 sec) [ -95220.8214] [22600] [depth= 1] . ( 779 sec) [ -95216.7521] [22601] [depth= 3] . ( 780 sec) [ -95216.2168] [22600] [depth= 1] . ( 781 sec) [ -95215.0754] [22598] [depth= 1] . ( 782 sec) [ -95213.9851] [22597] [depth= 1] . ( 785 sec) [ -95213.5940] [22597] [depth= 1] . ( 787 sec) [ -95208.1648] [22596] [depth= 1] . ( 790 sec) [ -95206.2102] [22595] [depth= 7] . ( 792 sec) [ -95204.0390] [22592] [depth= 3] . ( 803 sec) [ -95201.9211] [22590] [depth= 2] . ( 804 sec) [ -95201.7183] [22588] [depth= 1] . ( 805 sec) [ -95198.9124] [22587] [depth= 2] . ( 806 sec) [ -95197.4248] [22586] [depth= 1] . ( 814 sec) [ -95196.4697] [22585] [depth= 1] . ( 816 sec) [ -95196.0673] [22585] [depth= 1] . ( 817 sec) [ -95195.4501] [22581] [depth= 2] . ( 819 sec) [ -95195.4281] [22576] [depth= 1] . ( 821 sec) [ -95195.3382] [22577] [depth= 1] . ( 828 sec) [ -95193.1938] [22581] [depth= 1] . ( 829 sec) [ -95193.0935] [22574] [depth= 1] . ( 835 sec) [ -95192.4594] [22570] [depth= 6] . ( 837 sec) [ -95189.5400] [22575] [depth= 2] . ( 840 sec) [ -95186.9543] [22574] [depth= 1] . ( 845 sec) [ -95184.2173] [22577] [depth= 1] . ( 846 sec) [ -95183.8051] [22575] [depth= 1] . ( 854 sec) [ -95179.8062] [22580] [depth= 2] . ( 856 sec) [ -95178.8215] [22578] [depth= 1] . ( 861 sec) [ -95177.8094] [22582] [depth= 2] . ( 863 sec) [ -95177.4148] [22582] [depth= 1] . ( 867 sec) [ -95177.2969] [22580] [depth= 1] . ( 870 sec) [ -95174.5791] [22578] [depth= 2] . ( 871 sec) [ -95174.0757] [22577] [depth= 1] . ( 883 sec) [ -95173.0485] [22582] [depth= 1] . ( 885 sec) [ -95170.0791] [22583] [depth= 6] . ( 896 sec) [ -95169.4501] [22585] [depth= 1] . ( 910 sec) [ -95168.0414] [22582] [depth= 1] . ( 913 sec) [ -95168.0313] [22581] [depth= 1] . ( 921 sec) [ -95167.5157] [22582] [depth= 1] . ( 927 sec) [ -95023.3081] [Branch lengths ] . ( 939 sec) [ -95018.5060] [GTR parameters ] . ( 940 sec) [ -95012.3477] [Alpha ][ 0.518960] . ( 957 sec) [ -95012.1924] [22578] [depth= 1] . ( 999 sec) [ -95012.1487] [22577] [depth= 1] . ( 1010 sec) [ -95011.8077] [22577] [depth= 1] . ( 1011 sec) [ -95011.6927] [22578] [depth= 1] . ( 1020 sec) [ -95011.6153] [22578] [depth= 1] . ( 1091 sec) [ -95010.3694] [22579] [depth= 1] . ( 1162 sec) [ -95009.5973] [22580] [depth= 2] . ( 1213 sec) [ -95008.6470] [22582] [depth= 2] . ( 1228 sec) [ -95006.6761] [22582] [depth= 1] . ( 1229 sec) [ -95005.7128] [22581] [depth= 1] . ( 1231 sec) [ -95000.0579] [22579] [depth= 7] . ( 1268 sec) [ -94999.2693] [22577] [depth= 1] . ( 1298 sec) [ -94998.2848] [22579] [depth= 4] . ( 1299 sec) [ -94997.1687] [22577] [depth= 1] . ( 1313 sec) [ -94933.6034] [Branch lengths ] . ( 1323 sec) [ -94932.4001] [GTR parameters ] . ( 1324 sec) [ -94931.8070] [Alpha ][ 0.527771] . ( 1339 sec) [ -94931.3680] [22581] [depth= 1] . ( 1385 sec) [ -94931.3135] [22581] [depth= 1] . ( 1405 sec) [ -94931.2577] [22581] [depth= 1] . ( 1575 sec) [ -94931.0139] [22585] [depth= 1] . ( 1618 sec) [ -94930.9799] [22583] [depth= 1] . ( 1638 sec) [ -94930.5168] [22587] [depth= 1] . ( 1704 sec) [ -94893.1955] [Branch lengths ] . ( 1714 sec) [ -94891.8905] [GTR parameters ] . ( 1715 sec) [ -94891.8828] [Alpha ][ 0.526738] . ( 1775 sec) [ -94891.8494] [22587] [depth= 1] . ( 1795 sec) [ -94891.8273] [22587] [depth= 1] . ( 1916 sec) [ -94891.1892] [22591] [depth= 2] . ( 1991 sec) [ -94890.9826] [22593] [depth= 1] . ( 2006 sec) [ -94890.9170] [22595] [depth= 1] . ( 2015 sec) [ -94890.4142] [22597] [depth= 1] . ( 2101 sec) [ -94874.9631] [Branch lengths ] . ( 2113 sec) [ -94874.4586] [GTR parameters ] . ( 2114 sec) [ -94874.4124] [Alpha ][ 0.524258] . ( 2424 sec) [ -94874.3739] [22595] [depth= 1] . ( 2463 sec) [ -94874.1409] [22594] [depth= 1] . ( 2499 sec) [ -94869.6501] [Branch lengths ] . ( 2509 sec) [ -94869.5568] [GTR parameters ] . ( 2511 sec) [ -94869.5514] [Alpha ][ 0.523368] . ( 2695 sec) [ -94869.5037] [22593] [depth= 1] . ( 2894 sec) [ -94868.0070] [Branch lengths ] . ( 2903 sec) [ -94867.9868] [GTR parameters ] . ( 2904 sec) [ -94867.9868] [Alpha ][ 0.523368] . ( 3291 sec) [ -94867.7038] [Branch lengths ] . ( 3665 sec) [ -94867.6932] [22592] [depth= 1] . ( 3817 sec) [ -94866.6550] [22594] [depth= 1] . ( 4137 sec) [ -94865.7923] [22590] [depth= 2] . ( 4398 sec) [ -94864.4228] [Branch lengths ] . ( 4402 sec) [ -94864.4156] [GTR parameters ] . ( 4403 sec) [ -94864.4103] [Alpha ][ 0.522488] . ( 5487 sec) [ -94864.3436] [Branch lengths ] . ( 5487 sec) [ -94864.3436] [Topology ] . ( 5512 sec) [ -94864.1750] [Topology ] . ( 5536 sec) [ -94863.3591] [Topology ] . ( 5561 sec) [ -94863.2674] [Topology ] . ( 5586 sec) [ -94863.2580] [Topology ] . ( 5610 sec) [ -94863.2564] [Topology ] . ( 5635 sec) [ -94863.2561] [Topology ] . ( 5643 sec) [ -94863.2537] [GTR parameters ] . ( 5644 sec) [ -94863.2537] [Alpha ][ 0.522488] . ( 5644 sec) [ -94863.2537] [Topology ] . ( 5669 sec) [ -94863.2535] [Topology ] . ( 5672 sec) [ -94863.2535] [GTR parameters ] . ( 5673 sec) [ -94863.2535] [Alpha ][ 0.522488] . Checking for NNIs, optimizing five branches... . ( 5796 sec) [ -94863.1436] [Topology ] . Checking for NNIs, optimizing five branches... . ( 5920 sec) [ -94863.1276] [Topology ] . Checking for NNIs, optimizing five branches... . ( 6043 sec) [ -94863.1255] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -94863.125459. . Printing the most likely tree in file 'nucleic_M3862_362x1207_2008.phy_phyml_tree.txt'... . Time used 1h42m48s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 6179.48user 0.00system 1:43:02elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps