.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2661_66x1027_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 . 9 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 596 patterns found. (out of a total of 1027 sites) . 417 sites without polymorphism (40.60%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 21Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 3 sec) [ -9359.5522] [GTR parameters ] . ( 3 sec) [ -9317.1831] [Alpha ][ 0.504181] . ( 3 sec) [ -9317.1831] [Topology ] . ( 5 sec) [ -9164.4237] [Topology ] . ( 7 sec) [ -9148.3480] [Topology ] . ( 9 sec) [ -9145.2237] [Topology ] . ( 11 sec) [ -9144.2204] [Topology ] . ( 12 sec) [ -9143.8194] [Topology ] . ( 14 sec) [ -9143.4921] [Topology ] . ( 16 sec) [ -9142.5506] [Topology ] . ( 17 sec) [ -9140.3922] [Topology ] . Checking for NNIs, optimizing five branches... . ( 29 sec) [ -9139.8066] [Topology ] . ( 32 sec) [ -9133.7956] [GTR parameters ] . ( 33 sec) [ -9133.7578] [Alpha ][ 0.496003] . ( 33 sec) [ -9133.7578] [Topology ] . ( 34 sec) [ -9132.4617] [Topology ] . ( 36 sec) [ -9132.3132] [Topology ] . ( 38 sec) [ -9132.2662] [Topology ] . ( 40 sec) [ -9132.2468] [Topology ] . ( 41 sec) [ -9132.2379] [Topology ] . ( 43 sec) [ -9132.2334] [Topology ] . Checking for NNIs, optimizing five branches... . ( 55 sec) [ -9131.6484] [Topology ] . ( 57 sec) [ -9131.6026] [GTR parameters ] . ( 57 sec) [ -9131.5779] [Alpha ][ 0.489167] . ( 57 sec) [ -9131.5779] [Topology ] . ( 58 sec) [ -9131.5633] [Topology ] . ( 60 sec) [ -9131.5605] [Topology ] . ( 62 sec) [ -9131.5593] [Topology ] . ( 63 sec) [ -9131.5585] [Topology ] . Checking for NNIs, optimizing five branches... . ( 75 sec) [ -9131.5572] [GTR parameters ] . ( 76 sec) [ -9131.5554] [Alpha ][ 0.487312] . ( 76 sec) [ -9131.5554] [Topology ] . ( 77 sec) [ -9131.5542] [Topology ] . ( 79 sec) [ -9131.5538] [Topology ] . Checking for NNIs, optimizing five branches... . ( 91 sec) [ -9131.5537] [GTR parameters ] . ( 91 sec) [ -9131.5536] [Alpha ][ 0.486824] . ( 91 sec) [ -9131.5536] [Topology ] . ( 93 sec) [ -9131.5533] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9131.553329. . Printing the most likely tree in file 'nucleic_M2661_66x1027_2006.phy_phyml_tree.txt'... . Time used 0h1m57s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 116.04user 0.00system 1:57.55elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps