.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2711_123x1181_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 . 18 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 617 patterns found. (out of a total of 1181 sites) . 633 sites without polymorphism (53.60%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 40Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 7 sec) [ -11331.0777] [GTR parameters ] . ( 8 sec) [ -11137.6083] [Alpha ][ 0.500960] . ( 8 sec) [ -11137.6083] [Topology ] . ( 11 sec) [ -10846.7133] [Topology ] . ( 15 sec) [ -10788.2050] [Topology ] . ( 18 sec) [ -10770.4417] [Topology ] . ( 22 sec) [ -10764.1705] [Topology ] . ( 25 sec) [ -10761.8527] [Topology ] . ( 28 sec) [ -10760.1538] [Topology ] . ( 31 sec) [ -10756.2242] [Topology ] . ( 34 sec) [ -10751.2212] [Topology ] . ( 37 sec) [ -10746.7046] [Topology ] . Checking for NNIs, optimizing five branches... . ( 61 sec) [ -10745.2234] [Topology ] . ( 67 sec) [ -10738.9458] [GTR parameters ] . ( 68 sec) [ -10676.9327] [Alpha ][ 0.283794] . ( 68 sec) [ -10676.9327] [Topology ] . ( 71 sec) [ -10673.0638] [Topology ] . ( 74 sec) [ -10672.5895] [Topology ] . ( 77 sec) [ -10672.4366] [Topology ] . ( 80 sec) [ -10672.3670] [Topology ] . ( 83 sec) [ -10672.3314] [Topology ] . ( 86 sec) [ -10672.3125] [Topology ] . Checking for NNIs, optimizing five branches... . ( 107 sec) [ -10672.1784] [Topology ] . ( 113 sec) [ -10671.1857] [GTR parameters ] . ( 113 sec) [ -10670.9081] [Alpha ][ 0.273953] . ( 114 sec) [ -10670.9081] [Topology ] . ( 117 sec) [ -10670.8062] [Topology ] . ( 120 sec) [ -10670.7758] [Topology ] . ( 123 sec) [ -10670.7613] [Topology ] . ( 126 sec) [ -10670.7537] [Topology ] . ( 129 sec) [ -10670.7496] [Topology ] . ( 132 sec) [ -10670.7474] [Topology ] . Checking for NNIs, optimizing five branches... . ( 153 sec) [ -10670.6067] [Topology ] . ( 158 sec) [ -10670.5596] [GTR parameters ] . ( 158 sec) [ -10670.5518] [Alpha ][ 0.272238] . ( 158 sec) [ -10670.5518] [Topology ] . ( 161 sec) [ -10670.4424] [Topology ] . ( 165 sec) [ -10670.4221] [Topology ] . ( 168 sec) [ -10670.4162] [Topology ] . ( 171 sec) [ -10670.4142] [Topology ] . ( 174 sec) [ -10670.4134] [Topology ] . Checking for NNIs, optimizing five branches... . ( 196 sec) [ -10670.4133] [GTR parameters ] . ( 196 sec) [ -10670.4130] [Alpha ][ 0.272549] . ( 196 sec) [ -10670.4130] [Topology ] . ( 199 sec) [ -10670.4126] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10670.412606. . Printing the most likely tree in file 'nucleic_M2711_123x1181_2006.phy_phyml_tree.txt'... . Time used 0h4m2s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 242.19user 0.00system 4:03.53elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps