.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2856_61x970_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 . 3 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 686 patterns found. (out of a total of 970 sites) . 322 sites without polymorphism (33.20%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 22Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 4 sec) [ -26079.2058] [GTR parameters ] . ( 4 sec) [ -25728.9409] [Alpha ][ 0.500960] . ( 4 sec) [ -25728.9409] [Topology ] . ( 6 sec) [ -25291.2425] [Topology ] . ( 8 sec) [ -25230.3848] [Topology ] . ( 10 sec) [ -25214.3514] [Topology ] . ( 11 sec) [ -25208.4878] [Topology ] . ( 13 sec) [ -25205.8920] [Topology ] . ( 15 sec) [ -25194.6256] [Topology ] . ( 16 sec) [ -25190.1344] [Topology ] . ( 18 sec) [ -25188.5150] [Topology ] . ( 20 sec) [ -25188.1330] [Topology ] . Checking for NNIs, optimizing five branches... . ( 41 sec) [ -25146.5950] [GTR parameters ] . ( 41 sec) [ -25136.1397] [Alpha ][ 0.428858] . ( 41 sec) [ -25136.1397] [Topology ] . ( 42 sec) [ -25131.9942] [Topology ] . ( 44 sec) [ -25130.7501] [Topology ] . ( 46 sec) [ -25130.0910] [Topology ] . ( 48 sec) [ -25129.6974] [Topology ] . ( 49 sec) [ -25129.4521] [Topology ] . ( 51 sec) [ -25129.2950] [Topology ] . Checking for NNIs, optimizing five branches... . ( 69 sec) [ -25126.2391] [GTR parameters ] . ( 69 sec) [ -25126.1947] [Alpha ][ 0.424452] . ( 69 sec) [ -25126.1947] [Topology ] . ( 71 sec) [ -25125.2580] [Topology ] . ( 73 sec) [ -25124.7461] [Topology ] . ( 74 sec) [ -25124.4178] [Topology ] . ( 76 sec) [ -25124.1998] [Topology ] . ( 78 sec) [ -25124.0522] [Topology ] . ( 80 sec) [ -25123.9521] [Topology ] . Checking for NNIs, optimizing five branches... . ( 97 sec) [ -25123.3318] [GTR parameters ] . ( 98 sec) [ -25123.3317] [Alpha ][ 0.424028] . ( 98 sec) [ -25123.3317] [Topology ] . ( 99 sec) [ -25123.0192] [Topology ] . ( 101 sec) [ -25122.8253] [Topology ] . ( 103 sec) [ -25122.6945] [Topology ] . ( 105 sec) [ -25122.6048] [Topology ] . ( 106 sec) [ -25122.5424] [Topology ] . ( 108 sec) [ -25122.4990] [Topology ] . Checking for NNIs, optimizing five branches... . ( 125 sec) [ -25122.3007] [GTR parameters ] . ( 126 sec) [ -25122.3006] [Alpha ][ 0.423604] . ( 126 sec) [ -25122.3006] [Topology ] . ( 127 sec) [ -25122.1866] [Topology ] . ( 129 sec) [ -25122.1127] [Topology ] . ( 131 sec) [ -25122.0612] [Topology ] . ( 133 sec) [ -25122.0251] [Topology ] . ( 134 sec) [ -25121.9995] [Topology ] . ( 136 sec) [ -25121.9812] [Topology ] . Checking for NNIs, optimizing five branches... . ( 153 sec) [ -25121.9076] [GTR parameters ] . ( 153 sec) [ -25121.9073] [Alpha ][ 0.423180] . ( 154 sec) [ -25121.9073] [Topology ] . ( 155 sec) [ -25121.8623] [Topology ] . ( 157 sec) [ -25121.8325] [Topology ] . ( 159 sec) [ -25121.8113] [Topology ] . ( 160 sec) [ -25121.7961] [Topology ] . ( 162 sec) [ -25121.7853] [Topology ] . ( 164 sec) [ -25121.7774] [Topology ] . Checking for NNIs, optimizing five branches... . ( 181 sec) [ -25121.7482] [GTR parameters ] . ( 182 sec) [ -25121.7480] [Alpha ][ 0.422757] . ( 182 sec) [ -25121.7480] [Topology ] . ( 183 sec) [ -25121.7303] [Topology ] . ( 185 sec) [ -25121.7185] [Topology ] . ( 187 sec) [ -25121.7100] [Topology ] . ( 189 sec) [ -25121.7039] [Topology ] . ( 190 sec) [ -25121.6994] [Topology ] . ( 192 sec) [ -25121.6962] [Topology ] . Checking for NNIs, optimizing five branches... . ( 209 sec) [ -25121.6832] [GTR parameters ] . ( 210 sec) [ -25121.6832] [Alpha ][ 0.422757] . ( 210 sec) [ -25121.6832] [Topology ] . ( 211 sec) [ -25121.6754] [Topology ] . ( 213 sec) [ -25121.6702] [Topology ] . ( 215 sec) [ -25121.6663] [Topology ] . ( 217 sec) [ -25121.6636] [Topology ] . ( 218 sec) [ -25121.6616] [Topology ] . ( 220 sec) [ -25121.6601] [Topology ] . Checking for NNIs, optimizing five branches... . ( 237 sec) [ -25121.6553] [GTR parameters ] . ( 237 sec) [ -25121.6549] [Alpha ][ 0.422334] . ( 237 sec) [ -25121.6549] [Topology ] . ( 239 sec) [ -25121.6518] [Topology ] . ( 241 sec) [ -25121.6497] [Topology ] . ( 243 sec) [ -25121.6482] [Topology ] . ( 244 sec) [ -25121.6471] [Topology ] . ( 246 sec) [ -25121.6463] [Topology ] . Checking for NNIs, optimizing five branches... . ( 263 sec) [ -25121.6442] [GTR parameters ] . ( 263 sec) [ -25121.6442] [Alpha ][ 0.422334] . ( 263 sec) [ -25121.6442] [Topology ] . ( 265 sec) [ -25121.6426] [Topology ] . ( 267 sec) [ -25121.6414] [Topology ] . ( 268 sec) [ -25121.6406] [Topology ] . Checking for NNIs, optimizing five branches... . ( 284 sec) [ -25121.6402] [GTR parameters ] . ( 285 sec) [ -25121.6402] [Alpha ][ 0.422334] . ( 285 sec) [ -25121.6402] [Topology ] . ( 286 sec) [ -25121.6393] [Topology ] . Checking for NNIs, optimizing five branches... . ( 303 sec) [ -25121.6393] [GTR parameters ] . ( 303 sec) [ -25121.6393] [Alpha ][ 0.422334] . ( 303 sec) [ -25121.6393] [Topology ] . ( 305 sec) [ -25121.6385] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 339 sec) [ -26079.2058] [GTR parameters ] . ( 340 sec) [ -25728.9409] [Alpha ][ 0.500960] . ( 341 sec) [ -25726.2013] [ 6340] [depth= 1] . ( 341 sec) [ -25715.3178] [ 6339] [depth= 1] . ( 341 sec) [ -25709.8673] [ 6334] [depth= 1] . ( 341 sec) [ -25700.1364] [ 6331] [depth= 1] . ( 342 sec) [ -25699.7942] [ 6333] [depth= 1] . ( 342 sec) [ -25695.6843] [ 6329] [depth= 1] . ( 342 sec) [ -25682.5744] [ 6317] [depth= 2] . ( 342 sec) [ -25682.3575] [ 6318] [depth= 1] . ( 342 sec) [ -25681.9471] [ 6322] [depth= 1] . ( 343 sec) [ -25667.9534] [ 6328] [depth= 1] . ( 343 sec) [ -25663.2486] [ 6322] [depth= 1] . ( 343 sec) [ -25645.8279] [ 6321] [depth= 1] . ( 344 sec) [ -25644.8841] [ 6325] [depth= 1] . ( 344 sec) [ -25613.7274] [ 6321] [depth= 1] . ( 344 sec) [ -25610.6254] [ 6315] [depth= 1] . ( 345 sec) [ -25610.2353] [ 6321] [depth= 1] . ( 345 sec) [ -25603.1721] [ 6325] [depth= 2] . ( 345 sec) [ -25601.1863] [ 6319] [depth= 1] . ( 345 sec) [ -25599.5298] [ 6318] [depth= 2] . ( 345 sec) [ -25589.3879] [ 6317] [depth= 1] . ( 346 sec) [ -25587.2064] [ 6323] [depth= 1] . ( 346 sec) [ -25581.9004] [ 6330] [depth= 1] . ( 346 sec) [ -25571.0055] [ 6330] [depth= 1] . ( 347 sec) [ -25568.1439] [ 6337] [depth= 1] . ( 347 sec) [ -25565.1961] [ 6342] [depth= 2] . ( 347 sec) [ -25558.3858] [ 6339] [depth= 1] . ( 347 sec) [ -25547.6821] [ 6342] [depth= 1] . ( 347 sec) [ -25533.3166] [ 6337] [depth= 1] . ( 347 sec) [ -25528.1986] [ 6338] [depth= 2] . ( 348 sec) [ -25519.9391] [ 6345] [depth= 5] . ( 348 sec) [ -25519.3026] [ 6347] [depth= 1] . ( 348 sec) [ -25492.9153] [ 6356] [depth= 1] . ( 348 sec) [ -25480.8205] [ 6347] [depth= 1] . ( 348 sec) [ -25463.5785] [ 6357] [depth= 1] . ( 348 sec) [ -25453.7727] [ 6346] [depth= 3] . ( 348 sec) [ -25444.9652] [ 6355] [depth= 3] . ( 348 sec) [ -25444.2532] [ 6349] [depth= 3] . ( 349 sec) [ -25436.1849] [ 6353] [depth= 1] . ( 349 sec) [ -25428.1178] [ 6348] [depth= 1] . ( 349 sec) [ -25421.3539] [ 6339] [depth= 4] . ( 349 sec) [ -25420.6965] [ 6342] [depth= 1] . ( 349 sec) [ -25419.0576] [ 6343] [depth= 1] . ( 350 sec) [ -25412.3345] [ 6346] [depth= 1] . ( 350 sec) [ -25403.9203] [ 6342] [depth= 1] . ( 350 sec) [ -25403.2716] [ 6346] [depth= 1] . ( 350 sec) [ -25401.0608] [ 6351] [depth= 3] . ( 351 sec) [ -25399.8385] [ 6351] [depth= 1] . ( 351 sec) [ -25398.4449] [ 6345] [depth= 4] . ( 351 sec) [ -25259.6230] [Branch lengths ] . ( 354 sec) [ -25228.8373] [GTR parameters ] . ( 354 sec) [ -25215.1313] [Alpha ][ 0.418957] . ( 357 sec) [ -25213.1995] [ 6341] [depth= 1] . ( 358 sec) [ -25193.9020] [ 6334] [depth= 1] . ( 359 sec) [ -25188.9409] [ 6334] [depth= 1] . ( 359 sec) [ -25186.0249] [ 6333] [depth= 2] . ( 360 sec) [ -25184.5957] [ 6331] [depth= 1] . ( 360 sec) [ -25184.0624] [ 6333] [depth= 1] . ( 360 sec) [ -25177.1292] [ 6332] [depth= 1] . ( 362 sec) [ -25175.9585] [ 6331] [depth= 1] . ( 363 sec) [ -25172.5163] [ 6327] [depth= 1] . ( 364 sec) [ -25172.2133] [ 6329] [depth= 1] . ( 364 sec) [ -25171.0182] [ 6329] [depth= 1] . ( 365 sec) [ -25137.1760] [Branch lengths ] . ( 368 sec) [ -25133.5479] [GTR parameters ] . ( 368 sec) [ -25133.5472] [Alpha ][ 0.419473] . ( 373 sec) [ -25132.8941] [ 6325] [depth= 1] . ( 379 sec) [ -25126.4129] [Branch lengths ] . ( 381 sec) [ -25125.9114] [GTR parameters ] . ( 382 sec) [ -25125.9114] [Alpha ][ 0.419473] . ( 392 sec) [ -25123.7702] [Branch lengths ] . ( 452 sec) [ -25123.1291] [Branch lengths ] . ( 452 sec) [ -25123.1291] [Topology ] . ( 453 sec) [ -25123.0298] [Topology ] . ( 455 sec) [ -25122.9895] [Topology ] . ( 457 sec) [ -25122.9672] [Topology ] . ( 459 sec) [ -25122.9539] [Topology ] . ( 460 sec) [ -25122.9459] [Topology ] . ( 462 sec) [ -25122.9410] [Topology ] . ( 464 sec) [ -25122.2835] [GTR parameters ] . ( 464 sec) [ -25122.2829] [Alpha ][ 0.418928] . ( 464 sec) [ -25122.2829] [Topology ] . ( 466 sec) [ -25122.1370] [Topology ] . ( 468 sec) [ -25122.0636] [Topology ] . ( 470 sec) [ -25122.0194] [Topology ] . ( 471 sec) [ -25121.9923] [Topology ] . ( 473 sec) [ -25121.9755] [Topology ] . ( 475 sec) [ -25121.9650] [Topology ] . ( 477 sec) [ -25121.8839] [GTR parameters ] . ( 477 sec) [ -25121.8834] [Alpha ][ 0.418431] . ( 477 sec) [ -25121.8834] [Topology ] . ( 479 sec) [ -25121.8475] [Topology ] . ( 480 sec) [ -25121.8273] [Topology ] . ( 482 sec) [ -25121.8147] [Topology ] . ( 484 sec) [ -25121.8068] [Topology ] . ( 486 sec) [ -25121.8019] [Topology ] . ( 487 sec) [ -25121.7988] [Topology ] . ( 489 sec) [ -25121.7745] [GTR parameters ] . ( 489 sec) [ -25121.7744] [Alpha ][ 0.418013] . ( 489 sec) [ -25121.7744] [Topology ] . ( 491 sec) [ -25121.7635] [Topology ] . ( 492 sec) [ -25121.7572] [Topology ] . ( 494 sec) [ -25121.7533] [Topology ] . ( 496 sec) [ -25121.7509] [Topology ] . ( 498 sec) [ -25121.7493] [Topology ] . ( 499 sec) [ -25121.7484] [Topology ] . ( 501 sec) [ -25121.7411] [GTR parameters ] . ( 501 sec) [ -25121.7411] [Alpha ][ 0.418013] . ( 501 sec) [ -25121.7411] [Topology ] . ( 503 sec) [ -25121.7376] [Topology ] . ( 505 sec) [ -25121.7356] [Topology ] . ( 506 sec) [ -25121.7343] [Topology ] . ( 508 sec) [ -25121.7335] [Topology ] . ( 509 sec) [ -25121.7324] [GTR parameters ] . ( 509 sec) [ -25121.7324] [Alpha ][ 0.418013] . ( 509 sec) [ -25121.7324] [Topology ] . ( 511 sec) [ -25121.7313] [Topology ] . ( 513 sec) [ -25121.7306] [Topology ] . ( 514 sec) [ -25121.7302] [GTR parameters ] . ( 514 sec) [ -25121.7302] [Alpha ][ 0.418013] . ( 514 sec) [ -25121.7302] [Topology ] . ( 516 sec) [ -25121.7293] [Topology ] . ( 517 sec) [ -25121.7292] [GTR parameters ] . ( 517 sec) [ -25121.7292] [Alpha ][ 0.418013] . ( 517 sec) [ -25121.7292] [Topology ] . ( 518 sec) [ -25121.7287] [Topology ] . ( 519 sec) [ -25121.7287] [GTR parameters ] . ( 519 sec) [ -25121.7287] [Alpha ][ 0.418013] . Checking for NNIs, optimizing five branches... . ( 535 sec) [ -25121.6886] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -25121.638540 . Log likelihood obtained after SPR moves : -25121.688640 . Log likelihood of the current tree: -25121.638540. . Printing the most likely tree in file 'nucleic_M2856_61x970_2006.phy_phyml_tree.txt'... . Time used 0h9m12s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 547.50user 0.00system 9:11.86elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps