.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2792_166x812_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 : 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... . 616 patterns found. (out of a total of 812 sites) . 322 sites without polymorphism (39.66%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 54Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 11 sec) [ -10920.5693] [GTR parameters ] . ( 11 sec) [ -10843.4467] [Alpha ][ 0.500960] . ( 12 sec) [ -10843.4467] [Topology ] . ( 17 sec) [ -10644.8145] [Topology ] . ( 22 sec) [ -10607.9159] [Topology ] . ( 28 sec) [ -10595.7401] [Topology ] . ( 33 sec) [ -10590.1961] [Topology ] . ( 38 sec) [ -10588.4493] [Topology ] . ( 43 sec) [ -10586.5619] [Topology ] . ( 48 sec) [ -10584.3708] [Topology ] . ( 52 sec) [ -10578.6510] [Topology ] . ( 57 sec) [ -10572.0697] [Topology ] . Checking for NNIs, optimizing five branches... . ( 101 sec) [ -10568.0199] [GTR parameters ] . ( 101 sec) [ -10568.0199] [Alpha ][ 0.500459] . ( 102 sec) [ -10568.0199] [Topology ] . ( 106 sec) [ -10567.7915] [Topology ] . ( 111 sec) [ -10567.6878] [Topology ] . ( 116 sec) [ -10567.5951] [Topology ] . ( 121 sec) [ -10567.4896] [Topology ] . ( 125 sec) [ -10567.3527] [Topology ] . ( 130 sec) [ -10567.2307] [Topology ] . Checking for NNIs, optimizing five branches... . ( 161 sec) [ -10567.2306] [Topology ] . ( 168 sec) [ -10567.2263] [GTR parameters ] . ( 168 sec) [ -10567.2263] [Alpha ][ 0.500959] . ( 168 sec) [ -10567.2263] [Topology ] . ( 173 sec) [ -10567.1805] [Topology ] . ( 178 sec) [ -10567.1684] [Topology ] . ( 182 sec) [ -10567.1638] [Topology ] . ( 187 sec) [ -10567.1616] [Topology ] . ( 192 sec) [ -10567.1602] [Topology ] . ( 196 sec) [ -10567.1594] [Topology ] . Checking for NNIs, optimizing five branches... . ( 228 sec) [ -10567.1593] [Topology ] . ( 232 sec) [ -10567.1588] [GTR parameters ] . ( 232 sec) [ -10567.1588] [Alpha ][ 0.500959] . ( 232 sec) [ -10567.1588] [Topology ] . ( 237 sec) [ -10567.1582] [Topology ] . Checking for NNIs, optimizing five branches... . ( 269 sec) [ -10567.1582] [GTR parameters ] . ( 269 sec) [ -10567.1582] [Alpha ][ 0.500959] . ( 269 sec) [ -10567.1582] [Topology ] . ( 274 sec) [ -10567.1578] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 346 sec) [ -10920.5693] [GTR parameters ] . ( 347 sec) [ -10843.4467] [Alpha ][ 0.500960] . ( 347 sec) [ -10833.0450] [ 1899] [depth= 1] . ( 348 sec) [ -10824.3371] [ 1899] [depth= 1] . ( 348 sec) [ -10822.9897] [ 1899] [depth= 1] . ( 348 sec) [ -10791.3332] [ 1894] [depth= 4] . ( 350 sec) [ -10790.3800] [ 1899] [depth= 2] . ( 350 sec) [ -10788.1402] [ 1899] [depth= 2] . ( 350 sec) [ -10784.3954] [ 1893] [depth= 3] . ( 351 sec) [ -10783.4863] [ 1892] [depth= 1] . ( 351 sec) [ -10782.3911] [ 1895] [depth= 2] . ( 352 sec) [ -10778.1389] [ 1894] [depth= 1] . ( 352 sec) [ -10778.1003] [ 1895] [depth= 1] . ( 353 sec) [ -10776.4412] [ 1894] [depth= 1] . ( 354 sec) [ -10773.3184] [ 1897] [depth= 3] . ( 354 sec) [ -10773.2906] [ 1897] [depth= 1] . ( 355 sec) [ -10772.3624] [ 1895] [depth= 1] . ( 355 sec) [ -10771.8613] [ 1892] [depth= 2] . ( 356 sec) [ -10768.9173] [ 1895] [depth= 6] . ( 357 sec) [ -10768.5778] [ 1895] [depth= 1] . ( 358 sec) [ -10768.2604] [ 1895] [depth= 1] . ( 358 sec) [ -10768.2172] [ 1895] [depth= 1] . ( 358 sec) [ -10768.2020] [ 1895] [depth= 2] . ( 360 sec) [ -10758.7448] [ 1894] [depth= 1] . ( 360 sec) [ -10757.4991] [ 1894] [depth= 1] . ( 362 sec) [ -10754.6029] [ 1893] [depth= 1] . ( 364 sec) [ -10754.4603] [ 1893] [depth= 1] . ( 364 sec) [ -10754.1764] [ 1893] [depth= 1] . ( 365 sec) [ -10752.9864] [ 1893] [depth= 2] . ( 367 sec) [ -10752.9725] [ 1894] [depth= 1] . ( 367 sec) [ -10752.2728] [ 1893] [depth= 2] . ( 367 sec) [ -10751.7533] [ 1893] [depth= 1] . ( 368 sec) [ -10750.0196] [ 1893] [depth= 2] . ( 368 sec) [ -10749.9878] [ 1893] [depth= 1] . ( 369 sec) [ -10749.5398] [ 1893] [depth= 4] . ( 369 sec) [ -10743.0036] [ 1892] [depth= 2] . ( 369 sec) [ -10742.9142] [ 1892] [depth= 2] . ( 369 sec) [ -10742.6185] [ 1892] [depth= 1] . ( 370 sec) [ -10742.4708] [ 1892] [depth= 1] . ( 371 sec) [ -10742.4274] [ 1892] [depth= 2] . ( 373 sec) [ -10740.3783] [ 1891] [depth= 3] . ( 374 sec) [ -10739.1523] [ 1893] [depth= 1] . ( 374 sec) [ -10735.1946] [ 1893] [depth= 1] . ( 375 sec) [ -10735.1794] [ 1893] [depth= 3] . ( 376 sec) [ -10735.1476] [ 1893] [depth= 2] . ( 377 sec) [ -10733.0325] [ 1895] [depth= 1] . ( 377 sec) [ -10730.1520] [ 1897] [depth= 2] . ( 378 sec) [ -10725.0269] [ 1895] [depth= 1] . ( 379 sec) [ -10722.0972] [ 1897] [depth= 1] . ( 381 sec) [ -10720.9980] [ 1897] [depth= 1] . ( 381 sec) [ -10720.5131] [ 1897] [depth= 1] . ( 381 sec) [ -10718.0460] [ 1896] [depth= 1] . ( 384 sec) [ -10717.9519] [ 1896] [depth= 1] . ( 384 sec) [ -10717.3589] [ 1896] [depth= 1] . ( 385 sec) [ -10716.5362] [ 1896] [depth= 1] . ( 385 sec) [ -10716.1311] [ 1896] [depth= 1] . ( 385 sec) [ -10716.0787] [ 1896] [depth= 1] . ( 386 sec) [ -10715.7447] [ 1897] [depth= 1] . ( 388 sec) [ -10714.9558] [ 1897] [depth= 1] . ( 388 sec) [ -10714.4401] [ 1897] [depth= 1] . ( 391 sec) [ -10714.4055] [ 1897] [depth= 1] . ( 391 sec) [ -10714.3768] [ 1897] [depth= 1] . ( 392 sec) [ -10714.2861] [ 1897] [depth= 1] . ( 393 sec) [ -10714.2612] [ 1897] [depth= 1] . ( 393 sec) [ -10713.7522] [ 1897] [depth= 1] . ( 394 sec) [ -10713.4028] [ 1897] [depth= 1] . ( 399 sec) [ -10713.3893] [ 1897] [depth= 1] . ( 400 sec) [ -10713.2754] [ 1897] [depth= 1] . ( 400 sec) [ -10713.2400] [ 1897] [depth= 1] . ( 400 sec) [ -10713.2299] [ 1897] [depth= 1] . ( 403 sec) [ -10711.6663] [ 1897] [depth= 1] . ( 407 sec) [ -10710.7936] [ 1897] [depth= 1] . ( 407 sec) [ -10710.3317] [ 1897] [depth= 1] . ( 408 sec) [ -10710.2656] [ 1897] [depth= 1] . ( 409 sec) [ -10710.1041] [ 1897] [depth= 2] . ( 409 sec) [ -10708.7989] [ 1897] [depth= 1] . ( 409 sec) [ -10708.2067] [ 1896] [depth= 2] . ( 410 sec) [ -10708.0095] [ 1896] [depth= 1] . ( 410 sec) [ -10707.9901] [ 1897] [depth= 2] . ( 410 sec) [ -10707.9443] [ 1897] [depth= 1] . ( 411 sec) [ -10707.6909] [ 1897] [depth= 1] . ( 411 sec) [ -10707.5701] [ 1897] [depth= 2] . ( 411 sec) [ -10707.3794] [ 1897] [depth= 2] . ( 411 sec) [ -10707.0799] [ 1897] [depth= 2] . ( 412 sec) [ -10707.0545] [ 1897] [depth= 2] . ( 413 sec) [ -10706.6013] [ 1896] [depth= 2] . ( 413 sec) [ -10706.4671] [ 1896] [depth= 2] . ( 414 sec) [ -10706.4310] [ 1896] [depth= 3] . ( 414 sec) [ -10706.2125] [ 1896] [depth= 4] . ( 416 sec) [ -10705.2071] [ 1899] [depth= 1] . ( 417 sec) [ -10704.7333] [ 1901] [depth= 1] . ( 418 sec) [ -10691.1342] [ 1899] [depth= 1] . ( 419 sec) [ -10690.0068] [ 1902] [depth= 1] . ( 420 sec) [ -10689.0919] [ 1899] [depth= 2] . ( 420 sec) [ -10687.4277] [ 1898] [depth= 1] . ( 421 sec) [ -10684.6848] [ 1901] [depth= 1] . ( 422 sec) [ -10683.0017] [ 1903] [depth= 1] . ( 422 sec) [ -10679.0227] [ 1898] [depth= 1] . ( 422 sec) [ -10678.2585] [ 1897] [depth= 1] . ( 423 sec) [ -10676.2270] [ 1892] [depth= 1] . ( 424 sec) [ -10675.6161] [ 1893] [depth= 3] . ( 424 sec) [ -10669.6765] [ 1891] [depth= 1] . ( 424 sec) [ -10668.7923] [ 1892] [depth= 3] . ( 424 sec) [ -10668.5766] [ 1893] [depth= 1] . ( 425 sec) [ -10664.1686] [ 1892] [depth= 1] . ( 426 sec) [ -10663.8366] [ 1892] [depth= 1] . ( 426 sec) [ -10663.7551] [ 1892] [depth= 1] . ( 426 sec) [ -10663.5123] [ 1892] [depth= 1] . ( 427 sec) [ -10663.0611] [ 1892] [depth= 1] . ( 427 sec) [ -10663.0440] [ 1892] [depth= 2] . ( 428 sec) [ -10662.7257] [ 1892] [depth= 1] . ( 428 sec) [ -10662.6157] [ 1892] [depth= 1] . ( 428 sec) [ -10662.5804] [ 1892] [depth= 2] . ( 429 sec) [ -10662.5610] [ 1892] [depth= 1] . ( 431 sec) [ -10661.5397] [ 1892] [depth= 1] . ( 432 sec) [ -10661.2123] [ 1892] [depth= 2] . ( 432 sec) [ -10660.5062] [ 1892] [depth= 1] . ( 434 sec) [ -10660.4801] [ 1893] [depth= 1] . ( 434 sec) [ -10659.4863] [ 1892] [depth= 1] . ( 436 sec) [ -10659.4481] [ 1893] [depth= 1] . ( 436 sec) [ -10659.3935] [ 1896] [depth= 1] . ( 436 sec) [ -10657.3791] [ 1897] [depth= 4] . ( 436 sec) [ -10656.3488] [ 1898] [depth= 2] . ( 437 sec) [ -10655.1263] [ 1898] [depth= 1] . ( 437 sec) [ -10655.1072] [ 1898] [depth= 1] . ( 439 sec) [ -10654.7958] [ 1895] [depth= 3] . ( 439 sec) [ -10653.8546] [ 1899] [depth= 2] . ( 442 sec) [ -10653.4158] [ 1899] [depth= 2] . ( 443 sec) [ -10652.9693] [ 1899] [depth= 3] . ( 444 sec) [ -10652.9586] [ 1899] [depth= 1] . ( 445 sec) [ -10651.4701] [ 1899] [depth= 2] . ( 446 sec) [ -10651.0350] [ 1899] [depth= 1] . ( 446 sec) [ -10649.3589] [ 1898] [depth= 1] . ( 448 sec) [ -10649.2358] [ 1900] [depth= 2] . ( 449 sec) [ -10645.9657] [ 1895] [depth= 1] . ( 449 sec) [ -10645.7787] [ 1895] [depth= 1] . ( 452 sec) [ -10643.5554] [ 1894] [depth= 3] . ( 455 sec) [ -10643.1528] [ 1895] [depth= 2] . ( 455 sec) [ -10642.9132] [ 1895] [depth= 1] . ( 455 sec) [ -10641.2229] [ 1894] [depth= 1] . ( 458 sec) [ -10637.8641] [ 1893] [depth= 2] . ( 463 sec) [ -10637.6462] [ 1893] [depth= 1] . ( 463 sec) [ -10637.1486] [ 1893] [depth= 1] . ( 464 sec) [ -10637.0793] [ 1893] [depth= 1] . ( 464 sec) [ -10637.0417] [ 1893] [depth= 1] . ( 465 sec) [ -10636.9939] [ 1893] [depth= 2] . ( 466 sec) [ -10636.9506] [ 1893] [depth= 3] . ( 467 sec) [ -10636.9347] [ 1893] [depth= 1] . ( 474 sec) [ -10583.3989] [Branch lengths ] . ( 481 sec) [ -10581.2627] [GTR parameters ] . ( 482 sec) [ -10581.2383] [Alpha ][ 0.494606] . ( 483 sec) [ -10581.0634] [ 1896] [depth= 1] . ( 486 sec) [ -10580.7755] [ 1897] [depth= 1] . ( 487 sec) [ -10580.6856] [ 1896] [depth= 1] . ( 491 sec) [ -10577.9614] [ 1893] [depth= 3] . ( 512 sec) [ -10576.7480] [ 1893] [depth= 5] . ( 513 sec) [ -10576.6615] [ 1893] [depth= 1] . ( 513 sec) [ -10576.6351] [ 1893] [depth= 4] . ( 518 sec) [ -10576.6245] [ 1893] [depth= 3] . ( 522 sec) [ -10576.5552] [ 1892] [depth= 1] . ( 567 sec) [ -10574.7486] [ 1893] [depth= 1] . ( 568 sec) [ -10574.5257] [ 1887] [depth= 1] . ( 578 sec) [ -10574.5117] [ 1887] [depth= 1] . ( 579 sec) [ -10574.2353] [ 1887] [depth= 2] . ( 582 sec) [ -10574.1925] [ 1887] [depth= 1] . ( 617 sec) [ -10574.1799] [ 1887] [depth= 5] . ( 630 sec) [ -10565.4246] [Branch lengths ] . ( 638 sec) [ -10565.3566] [GTR parameters ] . ( 639 sec) [ -10565.3564] [Alpha ][ 0.495100] . ( 640 sec) [ -10565.2954] [ 1891] [depth= 1] . ( 642 sec) [ -10565.2020] [ 1890] [depth= 1] . ( 643 sec) [ -10565.0797] [ 1891] [depth= 1] . ( 664 sec) [ -10565.0263] [ 1891] [depth= 2] . ( 788 sec) [ -10560.6709] [Branch lengths ] . ( 795 sec) [ -10560.6545] [GTR parameters ] . ( 795 sec) [ -10560.6545] [Alpha ][ 0.494605] . ( 944 sec) [ -10559.3123] [Branch lengths ] . ( 1197 sec) [ -10559.1643] [Branch lengths ] . ( 1198 sec) [ -10559.1643] [Topology ] . ( 1202 sec) [ -10558.7606] [Topology ] . ( 1207 sec) [ -10557.2268] [Topology ] . ( 1212 sec) [ -10555.2186] [Topology ] . ( 1216 sec) [ -10554.8440] [Topology ] . ( 1221 sec) [ -10554.8062] [Topology ] . ( 1226 sec) [ -10554.7986] [Topology ] . ( 1230 sec) [ -10554.7859] [GTR parameters ] . ( 1231 sec) [ -10554.7858] [Alpha ][ 0.495100] . ( 1231 sec) [ -10554.7858] [Topology ] . ( 1236 sec) [ -10554.7833] [Topology ] . ( 1240 sec) [ -10554.7824] [Topology ] . ( 1242 sec) [ -10554.7824] [GTR parameters ] . ( 1242 sec) [ -10554.7824] [Alpha ][ 0.495100] . ( 1243 sec) [ -10554.7824] [Topology ] . ( 1247 sec) [ -10554.7819] [Topology ] . ( 1249 sec) [ -10554.7818] [GTR parameters ] . ( 1249 sec) [ -10554.7818] [Alpha ][ 0.495100] . Checking for NNIs, optimizing five branches... . ( 1282 sec) [ -10554.7813] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1314 sec) [ -10554.7812] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10567.157839 . Log likelihood obtained after SPR moves : -10554.781167 . Log likelihood of the current tree: -10554.781167. . Printing the most likely tree in file 'nucleic_M2792_166x812_2006.phy_phyml_tree.txt'... . Time used 0h22m27s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1346.85user 0.00system 22:29.10elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps