.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2565_51x1951_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 . 6 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 763 patterns found. (out of a total of 1951 sites) . 1244 sites without polymorphism (63.76%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 20Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 3 sec) [ -15365.1345] [GTR parameters ] . ( 3 sec) [ -15101.1310] [Alpha ][ 0.500960] . ( 3 sec) [ -15101.1310] [Topology ] . ( 5 sec) [ -14867.9767] [Topology ] . ( 6 sec) [ -14827.6590] [Topology ] . ( 8 sec) [ -14813.5467] [Topology ] . ( 10 sec) [ -14806.6086] [Topology ] . ( 11 sec) [ -14803.6705] [Topology ] . ( 13 sec) [ -14802.4499] [Topology ] . ( 15 sec) [ -14801.9650] [Topology ] . ( 16 sec) [ -14801.0546] [Topology ] . ( 18 sec) [ -14798.5980] [Topology ] . Checking for NNIs, optimizing five branches... . ( 33 sec) [ -14797.1571] [Topology ] . ( 35 sec) [ -14794.9999] [GTR parameters ] . ( 35 sec) [ -14662.2856] [Alpha ][ 0.250961] . ( 35 sec) [ -14662.2856] [Topology ] . ( 36 sec) [ -14660.9408] [Topology ] . ( 38 sec) [ -14660.5526] [Topology ] . ( 40 sec) [ -14660.3874] [Topology ] . ( 41 sec) [ -14660.3135] [Topology ] . ( 43 sec) [ -14660.2777] [Topology ] . ( 44 sec) [ -14660.2591] [Topology ] . Checking for NNIs, optimizing five branches... . ( 60 sec) [ -14659.7059] [GTR parameters ] . ( 60 sec) [ -14659.4964] [Alpha ][ 0.244536] . ( 60 sec) [ -14659.4964] [Topology ] . ( 61 sec) [ -14659.4851] [Topology ] . ( 63 sec) [ -14659.4811] [Topology ] . ( 65 sec) [ -14659.4791] [Topology ] . ( 66 sec) [ -14659.4781] [Topology ] . ( 68 sec) [ -14659.4775] [Topology ] . Checking for NNIs, optimizing five branches... . ( 82 sec) [ -14659.4757] [GTR parameters ] . ( 82 sec) [ -14659.4757] [Alpha ][ 0.244536] . ( 82 sec) [ -14659.4757] [Topology ] . ( 84 sec) [ -14659.4753] [Topology ] . Checking for NNIs, optimizing five branches... . ( 97 sec) [ -14659.4752] [GTR parameters ] . ( 98 sec) [ -14659.4752] [Alpha ][ 0.244536] . ( 98 sec) [ -14659.4752] [Topology ] . ( 99 sec) [ -14659.4750] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -14659.474973. . Printing the most likely tree in file 'nucleic_M2565_51x1951_2006.phy_phyml_tree.txt'... . Time used 0h2m7s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 125.70user 0.00system 2:07.76elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps