.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2587_117x1910_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... . 1192 patterns found. (out of a total of 1910 sites) . 932 sites without polymorphism (48.80%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 74Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 7 sec) [ -17118.5858] [GTR parameters ] . ( 8 sec) [ -17061.9139] [Alpha ][ 0.510962] . ( 8 sec) [ -17061.9139] [Topology ] . ( 14 sec) [ -16566.4637] [Topology ] . ( 21 sec) [ -16395.7592] [Topology ] . ( 27 sec) [ -16329.6622] [Topology ] . ( 34 sec) [ -16301.5525] [Topology ] . ( 41 sec) [ -16281.5882] [Topology ] . ( 47 sec) [ -16253.3293] [Topology ] . ( 54 sec) [ -16225.5514] [Topology ] . ( 61 sec) [ -16192.4716] [Topology ] . ( 68 sec) [ -16169.6603] [Topology ] . Checking for NNIs, optimizing five branches... . ( 122 sec) [ -16162.8883] [Topology ] . ( 128 sec) [ -16161.1635] [GTR parameters ] . ( 128 sec) [ -16152.8076] [Alpha ][ 0.421205] . ( 129 sec) [ -16152.8076] [Topology ] . ( 135 sec) [ -16146.8031] [Topology ] . ( 142 sec) [ -16143.9114] [Topology ] . ( 149 sec) [ -16142.3110] [Topology ] . ( 155 sec) [ -16141.4056] [Topology ] . ( 162 sec) [ -16140.8910] [Topology ] . ( 168 sec) [ -16140.5715] [Topology ] . ( 175 sec) [ -16140.3591] [Topology ] . Checking for NNIs, optimizing five branches... . ( 222 sec) [ -16140.3560] [Topology ] . ( 225 sec) [ -16140.3138] [GTR parameters ] . ( 226 sec) [ -16138.7899] [Alpha ][ 0.389395] . ( 226 sec) [ -16138.7899] [Topology ] . ( 233 sec) [ -16138.1767] [Topology ] . ( 239 sec) [ -16137.7959] [Topology ] . ( 246 sec) [ -16137.5477] [Topology ] . ( 252 sec) [ -16137.3834] [Topology ] . ( 259 sec) [ -16137.2736] [Topology ] . ( 266 sec) [ -16137.1999] [Topology ] . Checking for NNIs, optimizing five branches... . ( 316 sec) [ -16137.1919] [GTR parameters ] . ( 317 sec) [ -16136.9231] [Alpha ][ 0.377080] . ( 317 sec) [ -16136.9231] [Topology ] . ( 324 sec) [ -16136.7700] [Topology ] . ( 330 sec) [ -16136.6701] [Topology ] . ( 337 sec) [ -16136.6028] [Topology ] . ( 343 sec) [ -16136.5574] [Topology ] . ( 350 sec) [ -16136.5266] [Topology ] . ( 356 sec) [ -16136.5058] [Topology ] . Checking for NNIs, optimizing five branches... . ( 407 sec) [ -16136.5034] [GTR parameters ] . ( 408 sec) [ -16136.4332] [Alpha ][ 0.370790] . ( 408 sec) [ -16136.4332] [Topology ] . ( 414 sec) [ -16136.3904] [Topology ] . ( 421 sec) [ -16136.3622] [Topology ] . ( 428 sec) [ -16136.3432] [Topology ] . ( 434 sec) [ -16136.3303] [Topology ] . ( 441 sec) [ -16136.3216] [Topology ] . ( 447 sec) [ -16136.3156] [Topology ] . Checking for NNIs, optimizing five branches... . ( 498 sec) [ -16136.3147] [GTR parameters ] . ( 498 sec) [ -16136.2980] [Alpha ][ 0.367753] . ( 499 sec) [ -16136.2980] [Topology ] . ( 505 sec) [ -16136.2865] [Topology ] . ( 512 sec) [ -16136.2790] [Topology ] . ( 518 sec) [ -16136.2739] [Topology ] . ( 525 sec) [ -16136.2704] [Topology ] . ( 531 sec) [ -16136.2681] [Topology ] . ( 538 sec) [ -16136.2665] [Topology ] . Checking for NNIs, optimizing five branches... . ( 588 sec) [ -16136.2663] [GTR parameters ] . ( 588 sec) [ -16136.2619] [Alpha ][ 0.366216] . ( 589 sec) [ -16136.2619] [Topology ] . ( 595 sec) [ -16136.2589] [Topology ] . ( 602 sec) [ -16136.2569] [Topology ] . ( 608 sec) [ -16136.2556] [Topology ] . ( 615 sec) [ -16136.2546] [Topology ] . Checking for NNIs, optimizing five branches... . ( 665 sec) [ -16136.2545] [GTR parameters ] . ( 665 sec) [ -16136.2538] [Alpha ][ 0.365592] . ( 666 sec) [ -16136.2538] [Topology ] . ( 672 sec) [ -16136.2527] [Topology ] . ( 679 sec) [ -16136.2519] [Topology ] . Checking for NNIs, optimizing five branches... . ( 728 sec) [ -16136.2519] [GTR parameters ] . ( 728 sec) [ -16136.2518] [Alpha ][ 0.365227] . ( 729 sec) [ -16136.2518] [Topology ] . ( 735 sec) [ -16136.2510] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -16136.251048. . Printing the most likely tree in file 'nucleic_M2587_117x1910_2006.phy_phyml_tree.txt'... . Time used 0h13m53s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 831.81user 0.00system 13:55.95elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps