.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2600_69x814_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 : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 5 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 78 patterns found. (out of a total of 814 sites) . 733 sites without polymorphism (90.05%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 3Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -1760.0324] [GTR parameters ] . ( 1 sec) [ -1758.8364] [Alpha ][ 0.500960] . ( 1 sec) [ -1758.8364] [Topology ] . ( 1 sec) [ -1757.9994] [Topology ] . ( 1 sec) [ -1757.7988] [Topology ] . ( 1 sec) [ -1757.6159] [Topology ] . ( 1 sec) [ -1757.1661] [Topology ] . ( 2 sec) [ -1756.5983] [Topology ] . ( 2 sec) [ -1756.4486] [Topology ] . Checking for NNIs, optimizing five branches... . ( 3 sec) [ -1756.4477] [GTR parameters ] . ( 3 sec) [ -1756.0064] [Alpha ][ 0.263992] . ( 3 sec) [ -1756.0064] [Topology ] . ( 3 sec) [ -1755.9699] [Topology ] . ( 3 sec) [ -1755.9612] [Topology ] . ( 4 sec) [ -1755.9590] [Topology ] . ( 4 sec) [ -1755.9585] [Topology ] . Checking for NNIs, optimizing five branches... . ( 6 sec) [ -1755.9574] [GTR parameters ] . ( 6 sec) [ -1755.9574] [Alpha ][ 0.263266] . ( 6 sec) [ -1755.9574] [Topology ] . ( 6 sec) [ -1755.9572] [Topology ] . Checking for NNIs, optimizing five branches... . ( 7 sec) [ -1755.9572] [GTR parameters ] . ( 7 sec) [ -1755.9572] [Alpha ][ 0.263266] . ( 7 sec) [ -1755.9572] [Topology ] . ( 7 sec) [ -1755.9572] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 10 sec) [ -1760.0324] [GTR parameters ] . ( 10 sec) [ -1758.8364] [Alpha ][ 0.500960] . ( 12 sec) [ -1758.7889] [ 88] [depth= 2] . ( 12 sec) [ -1758.5381] [ 88] [depth= 1] . ( 18 sec) [ -1758.5276] [ 88] [depth= 3] . ( 20 sec) [ -1758.5154] [ 88] [depth= 1] . ( 23 sec) [ -1755.8668] [ 88] [depth= 3] . ( 23 sec) [ -1755.8502] [ 88] [depth= 1] . ( 26 sec) [ -1755.8342] [ 88] [depth= 5] . ( 30 sec) [ -1755.8239] [ 88] [depth= 2] . ( 30 sec) [ -1755.6700] [ 88] [depth= 2] . ( 30 sec) [ -1755.6352] [ 88] [depth= 2] . ( 34 sec) [ -1753.7134] [Branch lengths ] . ( 34 sec) [ -1753.6296] [GTR parameters ] . ( 34 sec) [ -1753.1857] [Alpha ][ 0.263760] . ( 55 sec) [ -1753.0375] [ 88] [depth= 9] . ( 55 sec) [ -1753.0205] [ 88] [depth= 8] . ( 60 sec) [ -1752.9378] [Branch lengths ] . ( 60 sec) [ -1752.9365] [GTR parameters ] . ( 60 sec) [ -1752.9365] [Alpha ][ 0.262989] . ( 72 sec) [ -1752.9364] [Branch lengths ] . ( 72 sec) [ -1752.9364] [Topology ] . ( 72 sec) [ -1752.9364] [Topology ] . ( 72 sec) [ -1752.9364] [GTR parameters ] . ( 72 sec) [ -1752.9364] [Alpha ][ 0.262989] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -1755.957162 . Log likelihood obtained after SPR moves : -1752.936430 . Log likelihood of the current tree: -1752.936430. . Printing the most likely tree in file 'nucleic_M2600_69x814_2006.phy_phyml_tree.txt'... . Time used 0h1m14s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 72.94user 0.00system 1:13.66elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps