.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2564_142x1130_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 . Compressing sequences... . 780 patterns found. (out of a total of 1130 sites) . 486 sites without polymorphism (43.01%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 59Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 7 sec) [ -21575.3354] [GTR parameters ] . ( 8 sec) [ -21206.7214] [Alpha ][ 0.500960] . ( 8 sec) [ -21206.7214] [Topology ] . ( 13 sec) [ -20737.3169] [Topology ] . ( 18 sec) [ -20622.9577] [Topology ] . ( 23 sec) [ -20586.6538] [Topology ] . ( 28 sec) [ -20570.9427] [Topology ] . ( 34 sec) [ -20566.3417] [Topology ] . ( 39 sec) [ -20561.9455] [Topology ] . ( 44 sec) [ -20559.4520] [Topology ] . ( 49 sec) [ -20551.4915] [Topology ] . ( 54 sec) [ -20546.5863] [Topology ] . Checking for NNIs, optimizing five branches... . ( 103 sec) [ -20541.1422] [Topology ] . ( 108 sec) [ -20529.9550] [GTR parameters ] . ( 108 sec) [ -20478.5225] [Alpha ][ 0.348656] . ( 109 sec) [ -20478.5225] [Topology ] . ( 114 sec) [ -20471.3446] [Topology ] . ( 119 sec) [ -20470.4270] [Topology ] . ( 125 sec) [ -20469.8076] [Topology ] . ( 130 sec) [ -20469.2380] [Topology ] . ( 135 sec) [ -20469.1369] [Topology ] . ( 140 sec) [ -20469.1145] [Topology ] . ( 145 sec) [ -20469.1090] [Topology ] . ( 150 sec) [ -20469.1075] [Topology ] . ( 156 sec) [ -20469.1071] [Topology ] . Checking for NNIs, optimizing five branches... . ( 192 sec) [ -20468.5217] [Topology ] . ( 196 sec) [ -20468.0511] [GTR parameters ] . ( 196 sec) [ -20467.8627] [Alpha ][ 0.341568] . ( 197 sec) [ -20467.8627] [Topology ] . ( 202 sec) [ -20467.5304] [Topology ] . ( 207 sec) [ -20467.1917] [Topology ] . ( 212 sec) [ -20465.9457] [Topology ] . ( 217 sec) [ -20465.8018] [Topology ] . ( 222 sec) [ -20465.7725] [Topology ] . ( 227 sec) [ -20465.7638] [Topology ] . ( 233 sec) [ -20465.7610] [Topology ] . ( 238 sec) [ -20465.7599] [Topology ] . Checking for NNIs, optimizing five branches... . ( 275 sec) [ -20465.2554] [Topology ] . ( 277 sec) [ -20465.2491] [GTR parameters ] . ( 277 sec) [ -20465.2471] [Alpha ][ 0.340728] . ( 277 sec) [ -20465.2471] [Topology ] . ( 282 sec) [ -20465.2386] [Topology ] . ( 288 sec) [ -20465.2368] [Topology ] . ( 293 sec) [ -20465.2364] [Topology ] . Checking for NNIs, optimizing five branches... . ( 330 sec) [ -20464.7322] [Topology ] . ( 332 sec) [ -20464.7257] [GTR parameters ] . ( 332 sec) [ -20464.7251] [Alpha ][ 0.341069] . ( 332 sec) [ -20464.7251] [Topology ] . ( 338 sec) [ -20464.6624] [Topology ] . ( 343 sec) [ -20464.6484] [Topology ] . ( 348 sec) [ -20464.6430] [Topology ] . ( 353 sec) [ -20464.6405] [Topology ] . ( 358 sec) [ -20464.6392] [Topology ] . ( 363 sec) [ -20464.6386] [Topology ] . Checking for NNIs, optimizing five branches... . ( 400 sec) [ -20464.6349] [Topology ] . ( 401 sec) [ -20464.6341] [GTR parameters ] . ( 402 sec) [ -20464.6335] [Alpha ][ 0.341410] . ( 402 sec) [ -20464.6335] [Topology ] . ( 407 sec) [ -20464.6329] [Topology ] . Checking for NNIs, optimizing five branches... . ( 444 sec) [ -20464.6329] [GTR parameters ] . ( 445 sec) [ -20464.6329] [Alpha ][ 0.341410] . ( 445 sec) [ -20464.6329] [Topology ] . ( 450 sec) [ -20464.6326] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -20464.632592. . Printing the most likely tree in file 'nucleic_M2564_142x1130_2006.phy_phyml_tree.txt'... . Time used 0h8m44s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 519.16user 0.00system 8:46.43elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps