.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2933_99x1634_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 : NNIs . 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... . 578 patterns found. (out of a total of 1634 sites) . 1151 sites without polymorphism (70.44%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 30Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 6 sec) [ -7976.1365] [GTR parameters ] . ( 7 sec) [ -7938.7269] [Alpha ][ 0.500960] . ( 7 sec) [ -7938.7269] [Topology ] . ( 9 sec) [ -7771.5480] [Topology ] . ( 12 sec) [ -7728.7608] [Topology ] . ( 15 sec) [ -7700.1450] [Topology ] . ( 17 sec) [ -7680.7802] [Topology ] . ( 20 sec) [ -7678.2991] [Topology ] . ( 22 sec) [ -7676.5846] [Topology ] . ( 25 sec) [ -7674.6303] [Topology ] . ( 27 sec) [ -7667.7629] [Topology ] . ( 30 sec) [ -7667.4228] [Topology ] . ( 37 sec) [ -7664.6970] [GTR parameters ] . ( 37 sec) [ -7661.5225] [Alpha ][ 0.415125] . ( 37 sec) [ -7661.5225] [Topology ] . ( 40 sec) [ -7661.1540] [Topology ] . ( 42 sec) [ -7660.4607] [Topology ] . ( 45 sec) [ -7661.0734] [Topology ] . Moving backward . ( 45 sec) [ -7660.1118] [Topology ] . ( 47 sec) [ -7660.4785] [Topology ] . Moving backward . ( 47 sec) [ -7659.9803] [Topology ] . ( 50 sec) [ -7659.9438] [Topology ] . ( 53 sec) [ -7660.2313] [Topology ] . Moving backward . ( 53 sec) [ -7659.9080] [Topology ] . Checking for NNIs, optimizing five branches... . ( 73 sec) [ -7659.7717] [Topology ] . ( 75 sec) [ -7659.7392] [GTR parameters ] . ( 76 sec) [ -7659.5438] [Alpha ][ 0.396820] . ( 76 sec) [ -7659.5438] [Topology ] . ( 78 sec) [ -7659.7614] [Topology ] . Moving backward . ( 78 sec) [ -7659.4154] [Topology ] . ( 80 sec) [ -7659.3894] [Topology ] . ( 83 sec) [ -7659.7340] [Topology ] . Moving backward . ( 83 sec) [ -7659.3474] [Topology ] . ( 85 sec) [ -7659.3732] [Topology ] . Moving backward . ( 85 sec) [ -7659.3316] [Topology ] . ( 88 sec) [ -7659.3403] [Topology ] . Moving backward . ( 88 sec) [ -7659.3246] [Topology ] . Checking for NNIs, optimizing five branches... . ( 107 sec) [ -7659.2657] [Topology ] . ( 108 sec) [ -7659.2579] [GTR parameters ] . ( 109 sec) [ -7659.2400] [Alpha ][ 0.391325] . ( 109 sec) [ -7659.2400] [Topology ] . ( 111 sec) [ -7659.2530] [Topology ] . Moving backward . ( 111 sec) [ -7659.2325] [Topology ] . ( 113 sec) [ -7659.2332] [Topology ] . Checking for NNIs, optimizing five branches... . ( 131 sec) [ -7657.6420] [Topology ] . ( 132 sec) [ -7657.6412] [GTR parameters ] . ( 132 sec) [ -7657.6385] [Alpha ][ 0.393389] . ( 132 sec) [ -7657.6385] [Topology ] . ( 135 sec) [ -7657.6576] [Topology ] . Moving backward . ( 135 sec) [ -7657.6330] [Topology ] . ( 137 sec) [ -7657.6358] [Topology ] . Moving backward . ( 137 sec) [ -7657.6308] [Topology ] . ( 139 sec) [ -7657.6310] [Topology ] . Checking for NNIs, optimizing five branches... . ( 156 sec) [ -7657.6300] [Topology ] . ( 158 sec) [ -7657.6295] [GTR parameters ] . ( 158 sec) [ -7657.6294] [Alpha ][ 0.393782] . ( 158 sec) [ -7657.6294] [Topology ] . ( 160 sec) [ -7657.6331] [Topology ] . Moving backward . ( 161 sec) [ -7657.6281] [Topology ] . ( 163 sec) [ -7657.6289] [Topology ] . Checking for NNIs, optimizing five branches... . ( 179 sec) [ -7655.6257] [Topology ] . ( 181 sec) [ -7655.6247] [GTR parameters ] . ( 181 sec) [ -7655.6246] [Alpha ][ 0.394176] . ( 182 sec) [ -7655.6246] [Topology ] . ( 184 sec) [ -7655.6246] [Topology ] . Checking for NNIs, optimizing five branches... . ( 201 sec) [ -7655.6241] [Topology ] . ( 202 sec) [ -7655.6240] [GTR parameters ] . ( 202 sec) [ -7655.6240] [Alpha ][ 0.394176] . ( 202 sec) [ -7655.6240] [Topology ] . ( 204 sec) [ -7655.6365] [Topology ] . Moving backward . ( 204 sec) [ -7655.6196] [Topology ] . ( 207 sec) [ -7655.6137] [Topology ] . ( 209 sec) [ -7655.6234] [Topology ] . Moving backward . ( 209 sec) [ -7655.6064] [Topology ] . ( 211 sec) [ -7655.6022] [Topology ] . ( 214 sec) [ -7655.6164] [Topology ] . Moving backward . ( 214 sec) [ -7655.5950] [Topology ] . ( 216 sec) [ -7655.5924] [Topology ] . Checking for NNIs, optimizing five branches... . ( 233 sec) [ -7655.5921] [Topology ] . ( 233 sec) [ -7655.5921] [GTR parameters ] . ( 234 sec) [ -7655.5921] [Alpha ][ 0.394176] . ( 234 sec) [ -7655.5921] [Topology ] . ( 236 sec) [ -7655.6091] [Topology ] . Moving backward . ( 236 sec) [ -7655.5843] [Topology ] . ( 238 sec) [ -7655.5781] [Topology ] . ( 241 sec) [ -7655.6019] [Topology ] . Moving backward . ( 241 sec) [ -7655.5687] [Topology ] . ( 243 sec) [ -7655.5646] [Topology ] . ( 245 sec) [ -7655.0309] [Topology ] . ( 248 sec) [ -7653.2849] [Topology ] . ( 250 sec) [ -7652.7476] [Topology ] . Checking for NNIs, optimizing five branches... . ( 269 sec) [ -7652.7052] [Topology ] . ( 272 sec) [ -7652.6955] [GTR parameters ] . ( 273 sec) [ -7652.6930] [Alpha ][ 0.396188] . ( 273 sec) [ -7652.6930] [Topology ] . ( 275 sec) [ -7652.1134] [Topology ] . ( 277 sec) [ -7652.3556] [Topology ] . Moving backward . ( 278 sec) [ -7652.0414] [Topology ] . ( 280 sec) [ -7652.3909] [Topology ] . Moving backward . ( 280 sec) [ -7651.9902] [Topology ] . ( 282 sec) [ -7652.0309] [Topology ] . Moving backward . ( 282 sec) [ -7651.9729] [Topology ] . ( 285 sec) [ -7652.0462] [Topology ] . Moving backward . ( 285 sec) [ -7651.9610] [Topology ] . Checking for NNIs, optimizing five branches... . ( 304 sec) [ -7651.9756] [Topology ] . ( 304 sec) [ -7651.9756] [GTR parameters ] . ( 305 sec) [ -7651.9756] [Alpha ][ 0.396584] . ( 305 sec) [ -7651.9756] [Topology ] . ( 307 sec) [ -7652.3305] [Topology ] . Moving backward . ( 307 sec) [ -7651.9232] [Topology ] . ( 309 sec) [ -7651.9725] [Topology ] . Moving backward . ( 310 sec) [ -7651.9121] [Topology ] . ( 312 sec) [ -7651.9917] [Topology ] . Moving backward . ( 312 sec) [ -7651.9069] [Topology ] . ( 314 sec) [ -7651.9446] [Topology ] . Moving backward . ( 315 sec) [ -7651.9018] [Topology ] . ( 317 sec) [ -7651.9575] [Topology ] . Moving backward . Checking for NNIs, optimizing five branches... . ( 334 sec) [ -7651.8985] [Topology ] . ( 334 sec) [ -7651.8984] [GTR parameters ] . ( 335 sec) [ -7651.8984] [Alpha ][ 0.396584] . ( 335 sec) [ -7651.8984] [Topology ] . ( 337 sec) [ -7651.9250] [Topology ] . Moving backward . ( 337 sec) [ -7651.8946] [Topology ] . ( 339 sec) [ -7651.9260] [Topology ] . Moving backward . ( 340 sec) [ -7651.8920] [Topology ] . ( 342 sec) [ -7651.9111] [Topology ] . Moving backward . ( 342 sec) [ -7651.8902] [Topology ] . ( 344 sec) [ -7651.9102] [Topology ] . Moving backward . ( 345 sec) [ -7651.8880] [Topology ] . ( 347 sec) [ -7651.8988] [Topology ] . Moving backward . Checking for NNIs, optimizing five branches... . ( 363 sec) [ -7651.8863] [Topology ] . ( 364 sec) [ -7651.8863] [GTR parameters ] . ( 364 sec) [ -7651.8863] [Alpha ][ 0.396584] . ( 364 sec) [ -7651.8863] [Topology ] . ( 367 sec) [ -7651.8959] [Topology ] . Moving backward . ( 367 sec) [ -7651.8848] [Topology ] . ( 369 sec) [ -7651.8900] [Topology ] . Moving backward . ( 369 sec) [ -7651.8836] [Topology ] . ( 372 sec) [ -7651.8880] [Topology ] . Moving backward . ( 372 sec) [ -7651.8825] [Topology ] . ( 374 sec) [ -7651.8849] [Topology ] . Moving backward . ( 374 sec) [ -7651.8816] [Topology ] . Checking for NNIs, optimizing five branches... . ( 391 sec) [ -7650.2293] [Topology ] . ( 392 sec) [ -7650.2177] [GTR parameters ] . ( 392 sec) [ -7650.2175] [Alpha ][ 0.397081] . ( 392 sec) [ -7650.2175] [Topology ] . ( 395 sec) [ -7649.5030] [Topology ] . ( 397 sec) [ -7649.4525] [Topology ] . ( 399 sec) [ -7649.3903] [Topology ] . ( 402 sec) [ -7649.5926] [Topology ] . Moving backward . ( 402 sec) [ -7649.3115] [Topology ] . ( 404 sec) [ -7649.2912] [Topology ] . ( 407 sec) [ -7649.4242] [Topology ] . Checking for NNIs, optimizing five branches... . ( 423 sec) [ -7649.0423] [Topology ] . ( 426 sec) [ -7649.0379] [GTR parameters ] . ( 426 sec) [ -7649.0379] [Alpha ][ 0.397081] . ( 426 sec) [ -7649.0379] [Topology ] . ( 429 sec) [ -7648.9056] [Topology ] . ( 431 sec) [ -7648.8291] [Topology ] . ( 433 sec) [ -7648.7451] [Topology ] . ( 436 sec) [ -7648.6669] [Topology ] . ( 438 sec) [ -7648.6457] [Topology ] . ( 440 sec) [ -7648.6412] [Topology ] . Checking for NNIs, optimizing five branches... . ( 457 sec) [ -7648.6407] [Topology ] . ( 457 sec) [ -7648.6407] [GTR parameters ] . ( 458 sec) [ -7648.6407] [Alpha ][ 0.397081] . ( 458 sec) [ -7648.6407] [Topology ] . ( 460 sec) [ -7648.6396] [Topology ] . ( 462 sec) [ -7648.6389] [Topology ] . Checking for NNIs, optimizing five branches... . ( 479 sec) [ -7648.6296] [Topology ] . ( 480 sec) [ -7648.6295] [GTR parameters ] . ( 480 sec) [ -7648.6295] [Alpha ][ 0.397081] . ( 480 sec) [ -7648.6295] [Topology ] . ( 483 sec) [ -7648.6290] [Topology ] . Checking for NNIs, optimizing five branches... . ( 499 sec) [ -7648.6239] [Topology ] . ( 499 sec) [ -7648.6239] [GTR parameters ] . ( 500 sec) [ -7648.6239] [Alpha ][ 0.397081] . ( 500 sec) [ -7648.6239] [Topology ] . ( 502 sec) [ -7648.6235] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7648.623540. . Printing the most likely tree in file 'nucleic_M2933_99x1634_2006.phy_phyml_tree.txt'... . Time used 0h8m56s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 532.09user 0.00system 8:56.34elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps