.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2845_68x1715_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... . 649 patterns found. (out of a total of 1715 sites) . 1119 sites without polymorphism (65.25%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 23Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 5 sec) [ -11816.7722] [GTR parameters ] . ( 5 sec) [ -11662.0849] [Alpha ][ 0.500960] . ( 6 sec) [ -11662.0849] [Topology ] . ( 7 sec) [ -11513.5370] [Topology ] . ( 9 sec) [ -11479.6099] [Topology ] . ( 11 sec) [ -11468.4331] [Topology ] . ( 13 sec) [ -11460.4879] [Topology ] . ( 15 sec) [ -11454.4989] [Topology ] . ( 17 sec) [ -11448.0247] [Topology ] . ( 19 sec) [ -11444.6531] [Topology ] . ( 21 sec) [ -11443.4847] [Topology ] . ( 23 sec) [ -11443.3898] [Topology ] . Checking for NNIs, optimizing five branches... . ( 40 sec) [ -11443.1080] [Topology ] . ( 42 sec) [ -11441.9514] [GTR parameters ] . ( 42 sec) [ -11364.0125] [Alpha ][ 0.254613] . ( 42 sec) [ -11364.0125] [Topology ] . ( 44 sec) [ -11362.8246] [Topology ] . ( 46 sec) [ -11362.2598] [Topology ] . ( 48 sec) [ -11361.9487] [Topology ] . ( 50 sec) [ -11361.7736] [Topology ] . ( 52 sec) [ -11361.6743] [Topology ] . ( 54 sec) [ -11361.6180] [Topology ] . Checking for NNIs, optimizing five branches... . ( 70 sec) [ -11361.4064] [GTR parameters ] . ( 70 sec) [ -11361.4060] [Alpha ][ 0.254194] . ( 70 sec) [ -11361.4060] [Topology ] . ( 72 sec) [ -11361.3635] [Topology ] . ( 74 sec) [ -11361.3397] [Topology ] . ( 76 sec) [ -11361.3261] [Topology ] . ( 78 sec) [ -11361.3184] [Topology ] . ( 80 sec) [ -11361.3140] [Topology ] . ( 82 sec) [ -11361.3114] [Topology ] . Checking for NNIs, optimizing five branches... . ( 97 sec) [ -11361.3108] [GTR parameters ] . ( 97 sec) [ -11361.3108] [Alpha ][ 0.254194] . ( 97 sec) [ -11361.3108] [Topology ] . ( 99 sec) [ -11361.3092] [Topology ] . ( 101 sec) [ -11361.3083] [Topology ] . Checking for NNIs, optimizing five branches... . ( 115 sec) [ -11361.3083] [GTR parameters ] . ( 116 sec) [ -11361.3083] [Alpha ][ 0.254194] . ( 116 sec) [ -11361.3083] [Topology ] . ( 118 sec) [ -11361.3078] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11361.307799. . Printing the most likely tree in file 'nucleic_M2845_68x1715_2006.phy_phyml_tree.txt'... . Time used 0h2m27s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 144.92user 0.00system 2:26.99elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps