.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2945_62x1271_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 . 4 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 935 patterns found. (out of a total of 1271 sites) . 411 sites without polymorphism (32.34%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 30Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 5 sec) [ -36495.9506] [GTR parameters ] . ( 5 sec) [ -36002.5932] [Alpha ][ 0.500960] . ( 5 sec) [ -36002.5932] [Topology ] . ( 7 sec) [ -35423.6231] [Topology ] . ( 10 sec) [ -35317.4470] [Topology ] . ( 12 sec) [ -35293.7583] [Topology ] . ( 14 sec) [ -35285.1407] [Topology ] . ( 16 sec) [ -35280.7055] [Topology ] . ( 19 sec) [ -35278.0935] [Topology ] . ( 21 sec) [ -35276.2739] [Topology ] . ( 23 sec) [ -35275.3266] [Topology ] . ( 25 sec) [ -35274.2363] [Topology ] . Checking for NNIs, optimizing five branches... . ( 50 sec) [ -35272.9942] [Topology ] . ( 54 sec) [ -35208.5581] [GTR parameters ] . ( 55 sec) [ -35204.6841] [Alpha ][ 0.464402] . ( 55 sec) [ -35204.6841] [Topology ] . ( 57 sec) [ -35193.4410] [Topology ] . ( 59 sec) [ -35186.4924] [Topology ] . ( 61 sec) [ -35181.2926] [Topology ] . ( 64 sec) [ -35177.0730] [Topology ] . ( 66 sec) [ -35173.4542] [Topology ] . ( 68 sec) [ -35170.3629] [Topology ] . ( 70 sec) [ -35167.7702] [Topology ] . ( 73 sec) [ -35165.6380] [Topology ] . Checking for NNIs, optimizing five branches... . ( 98 sec) [ -35155.5880] [GTR parameters ] . ( 99 sec) [ -35155.2055] [Alpha ][ 0.454189] . ( 99 sec) [ -35155.2055] [Topology ] . ( 101 sec) [ -35150.8159] [Topology ] . ( 103 sec) [ -35147.8747] [Topology ] . ( 106 sec) [ -35145.7696] [Topology ] . ( 108 sec) [ -35144.2357] [Topology ] . ( 110 sec) [ -35143.1072] [Topology ] . ( 112 sec) [ -35142.2702] [Topology ] . Checking for NNIs, optimizing five branches... . ( 137 sec) [ -35140.5502] [GTR parameters ] . ( 137 sec) [ -35140.0006] [Alpha ][ 0.442745] . ( 137 sec) [ -35140.0006] [Topology ] . ( 140 sec) [ -35138.4908] [Topology ] . ( 142 sec) [ -35137.4503] [Topology ] . ( 144 sec) [ -35136.6902] [Topology ] . ( 147 sec) [ -35136.1303] [Topology ] . ( 149 sec) [ -35135.7172] [Topology ] . ( 151 sec) [ -35135.4120] [Topology ] . Checking for NNIs, optimizing five branches... . ( 172 sec) [ -35135.3839] [Topology ] . ( 177 sec) [ -35134.7559] [GTR parameters ] . ( 177 sec) [ -35134.4189] [Alpha ][ 0.434211] . ( 177 sec) [ -35134.4189] [Topology ] . ( 179 sec) [ -35128.0537] [Topology ] . ( 182 sec) [ -35126.6368] [Topology ] . ( 184 sec) [ -35126.3037] [Topology ] . ( 186 sec) [ -35126.1149] [Topology ] . ( 188 sec) [ -35125.9887] [Topology ] . ( 191 sec) [ -35125.9007] [Topology ] . ( 193 sec) [ -35125.8389] [Topology ] . Checking for NNIs, optimizing five branches... . ( 217 sec) [ -35125.6522] [GTR parameters ] . ( 217 sec) [ -35125.4511] [Alpha ][ 0.427834] . ( 217 sec) [ -35125.4511] [Topology ] . ( 219 sec) [ -35125.2913] [Topology ] . ( 222 sec) [ -35125.1900] [Topology ] . ( 224 sec) [ -35125.1191] [Topology ] . ( 226 sec) [ -35125.0689] [Topology ] . ( 228 sec) [ -35125.0332] [Topology ] . ( 231 sec) [ -35125.0077] [Topology ] . Checking for NNIs, optimizing five branches... . ( 254 sec) [ -35124.9480] [GTR parameters ] . ( 254 sec) [ -35124.9013] [Alpha ][ 0.424805] . ( 254 sec) [ -35124.9013] [Topology ] . ( 257 sec) [ -35124.8461] [Topology ] . ( 259 sec) [ -35124.8103] [Topology ] . ( 261 sec) [ -35124.7850] [Topology ] . ( 264 sec) [ -35124.7670] [Topology ] . ( 266 sec) [ -35124.7541] [Topology ] . ( 268 sec) [ -35124.7449] [Topology ] . Checking for NNIs, optimizing five branches... . ( 291 sec) [ -35124.7299] [GTR parameters ] . ( 291 sec) [ -35124.7141] [Alpha ][ 0.423056] . ( 292 sec) [ -35124.7141] [Topology ] . ( 294 sec) [ -35124.6957] [Topology ] . ( 296 sec) [ -35124.6836] [Topology ] . ( 299 sec) [ -35124.6750] [Topology ] . ( 301 sec) [ -35124.6688] [Topology ] . ( 303 sec) [ -35124.6644] [Topology ] . ( 306 sec) [ -35124.6612] [Topology ] . Checking for NNIs, optimizing five branches... . ( 328 sec) [ -35124.6565] [GTR parameters ] . ( 328 sec) [ -35124.6511] [Alpha ][ 0.422039] . ( 329 sec) [ -35124.6511] [Topology ] . ( 331 sec) [ -35124.6451] [Topology ] . ( 333 sec) [ -35124.6411] [Topology ] . ( 335 sec) [ -35124.6382] [Topology ] . ( 338 sec) [ -35124.6362] [Topology ] . ( 340 sec) [ -35124.6348] [Topology ] . ( 342 sec) [ -35124.6337] [Topology ] . Checking for NNIs, optimizing five branches... . ( 365 sec) [ -35124.6310] [GTR parameters ] . ( 365 sec) [ -35124.6295] [Alpha ][ 0.421498] . ( 365 sec) [ -35124.6295] [Topology ] . ( 368 sec) [ -35124.6275] [Topology ] . ( 370 sec) [ -35124.6261] [Topology ] . ( 372 sec) [ -35124.6251] [Topology ] . Checking for NNIs, optimizing five branches... . ( 394 sec) [ -35124.6243] [GTR parameters ] . ( 394 sec) [ -35124.6243] [Alpha ][ 0.421077] . ( 394 sec) [ -35124.6243] [Topology ] . ( 396 sec) [ -35124.6228] [Topology ] . ( 399 sec) [ -35124.6219] [Topology ] . Checking for NNIs, optimizing five branches... . ( 420 sec) [ -35124.6216] [GTR parameters ] . ( 421 sec) [ -35124.6216] [Alpha ][ 0.421077] . ( 421 sec) [ -35124.6216] [Topology ] . ( 423 sec) [ -35124.6208] [Topology ] . Checking for NNIs, optimizing five branches... . ( 445 sec) [ -35124.6208] [GTR parameters ] . ( 445 sec) [ -35124.6208] [Alpha ][ 0.421077] . ( 445 sec) [ -35124.6208] [Topology ] . ( 448 sec) [ -35124.6201] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -35124.620116. . Printing the most likely tree in file 'nucleic_M2945_62x1271_2006.phy_phyml_tree.txt'... . Time used 0h8m12s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 490.47user 0.00system 8:12.24elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps