.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2752_106x1292_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 . 11 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 427 patterns found. (out of a total of 1292 sites) . 807 sites without polymorphism (62.46%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 24Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 2 sec) [ -7952.3607] [GTR parameters ] . ( 2 sec) [ -7922.0045] [Alpha ][ 0.500960] . ( 3 sec) [ -7922.0045] [Topology ] . ( 5 sec) [ -7888.2427] [Topology ] . ( 7 sec) [ -7882.0784] [Topology ] . ( 9 sec) [ -7877.5421] [Topology ] . ( 12 sec) [ -7874.9338] [Topology ] . ( 14 sec) [ -7873.6053] [Topology ] . ( 16 sec) [ -7873.2530] [Topology ] . ( 18 sec) [ -7873.0995] [Topology ] . ( 20 sec) [ -7872.9835] [Topology ] . ( 22 sec) [ -7872.9341] [Topology ] . Checking for NNIs, optimizing five branches... . ( 38 sec) [ -7872.6117] [GTR parameters ] . ( 38 sec) [ -7872.4034] [Alpha ][ 0.474317] . ( 38 sec) [ -7872.4034] [Topology ] . ( 40 sec) [ -7872.3979] [Topology ] . ( 42 sec) [ -7872.3966] [Topology ] . ( 44 sec) [ -7872.3961] [Topology ] . Checking for NNIs, optimizing five branches... . ( 57 sec) [ -7872.3933] [GTR parameters ] . ( 58 sec) [ -7872.3933] [Alpha ][ 0.473843] . ( 58 sec) [ -7872.3933] [Topology ] . ( 60 sec) [ -7872.3931] [Topology ] . Checking for NNIs, optimizing five branches... . ( 72 sec) [ -7872.3931] [GTR parameters ] . ( 72 sec) [ -7872.3931] [Alpha ][ 0.473843] . ( 72 sec) [ -7872.3931] [Topology ] . ( 74 sec) [ -7872.3930] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7872.392970. . Printing the most likely tree in file 'nucleic_M2752_106x1292_2006.phy_phyml_tree.txt'... . Time used 0h1m39s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 98.71user 0.00system 1:39.36elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps