.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data78.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 . Compressing sequences... . 418 patterns found. (out of a total of 500 sites) . 72 sites without polymorphism (14.40%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-8419.296833 . ( 1 sec) [ -8412.2618] [GTR parameters ] . ( 1 sec) [ -8409.5051] [Alpha ][ 1.225301] . ( 1 sec) [ -8409.5051] [Topology ] . ( 2 sec) [ -8391.5520] [Topology ] . ( 3 sec) [ -8388.7643] [Topology ] . ( 4 sec) [ -8387.8745] [Topology ] . ( 5 sec) [ -8387.5222] [Topology ] . ( 7 sec) [ -8387.3734] [Topology ] . ( 8 sec) [ -8387.3068] [Topology ] . ( 9 sec) [ -8387.2763] [Topology ] . Checking for NNIs, optimizing five branches... . ( 17 sec) [ -8387.1901] [Topology ] . Before opt ts/t=1.000000 LK=-8387.190119 . ( 17 sec) [ -8387.1746] [GTR parameters ] . ( 17 sec) [ -8387.1528] [Alpha ][ 1.248016] . ( 17 sec) [ -8387.1528] [Topology ] . ( 18 sec) [ -8387.1313] [Topology ] . ( 19 sec) [ -8387.1219] [Topology ] . ( 20 sec) [ -8387.1175] [Topology ] . ( 21 sec) [ -8387.1155] [Topology ] . ( 22 sec) [ -8387.1145] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8387.114542 . ( 29 sec) [ -8387.1145] [GTR parameters ] . ( 29 sec) [ -8387.1145] [Alpha ][ 1.249264] . ( 29 sec) [ -8387.1145] [Topology ] . ( 30 sec) [ -8387.1140] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8387.114006. . Printing the most likely tree in file 'data78.phy_phyml_tree.txt'... . Time used 0h0m46s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo