.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2662_60x1348_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 . 7 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 664 patterns found. (out of a total of 1348 sites) . 794 sites without polymorphism (58.90%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 21Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 3 sec) [ -12871.6129] [GTR parameters ] . ( 4 sec) [ -12665.7546] [Alpha ][ 0.500960] . ( 4 sec) [ -12665.7546] [Topology ] . ( 5 sec) [ -12467.2258] [Topology ] . ( 7 sec) [ -12431.6435] [Topology ] . ( 9 sec) [ -12420.9779] [Topology ] . ( 11 sec) [ -12417.1150] [Topology ] . ( 12 sec) [ -12415.5191] [Topology ] . ( 14 sec) [ -12414.8202] [Topology ] . ( 16 sec) [ -12414.5047] [Topology ] . ( 18 sec) [ -12414.3440] [Topology ] . Checking for NNIs, optimizing five branches... . ( 31 sec) [ -12413.0509] [Topology ] . ( 34 sec) [ -12409.7217] [GTR parameters ] . ( 34 sec) [ -12350.3670] [Alpha ][ 0.296953] . ( 34 sec) [ -12350.3670] [Topology ] . ( 36 sec) [ -12349.1010] [Topology ] . ( 38 sec) [ -12348.8323] [Topology ] . ( 40 sec) [ -12348.7770] [Topology ] . ( 41 sec) [ -12348.7575] [Topology ] . ( 43 sec) [ -12348.7485] [Topology ] . ( 45 sec) [ -12348.7439] [Topology ] . Checking for NNIs, optimizing five branches... . ( 58 sec) [ -12348.4350] [Topology ] . ( 61 sec) [ -12348.0258] [GTR parameters ] . ( 61 sec) [ -12347.9937] [Alpha ][ 0.293713] . ( 61 sec) [ -12347.9937] [Topology ] . ( 63 sec) [ -12347.9651] [Topology ] . ( 65 sec) [ -12347.9570] [Topology ] . ( 67 sec) [ -12347.9532] [Topology ] . ( 68 sec) [ -12347.9512] [Topology ] . ( 70 sec) [ -12347.9501] [Topology ] . ( 72 sec) [ -12347.9495] [Topology ] . Checking for NNIs, optimizing five branches... . ( 85 sec) [ -12347.8637] [Topology ] . ( 86 sec) [ -12347.8612] [GTR parameters ] . ( 86 sec) [ -12347.8612] [Alpha ][ 0.293713] . ( 86 sec) [ -12347.8612] [Topology ] . ( 88 sec) [ -12347.8510] [Topology ] . ( 90 sec) [ -12347.8483] [Topology ] . ( 92 sec) [ -12347.8471] [Topology ] . ( 94 sec) [ -12347.8465] [Topology ] . Checking for NNIs, optimizing five branches... . ( 108 sec) [ -12347.8461] [GTR parameters ] . ( 108 sec) [ -12347.8461] [Alpha ][ 0.293713] . ( 108 sec) [ -12347.8461] [Topology ] . ( 110 sec) [ -12347.8457] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12347.845692. . Printing the most likely tree in file 'nucleic_M2662_60x1348_2006.phy_phyml_tree.txt'... . Time used 0h2m17s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 136.85user 0.00system 2:18.31elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps