.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data89.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... . 394 patterns found. (out of a total of 500 sites) . 98 sites without polymorphism (19.60%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 8Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-7626.759928 . ( 1 sec) [ -7623.0405] [GTR parameters ] . ( 1 sec) [ -7623.0403] [Alpha ][ 0.998309] . ( 1 sec) [ -7623.0403] [Topology ] . ( 2 sec) [ -7584.2163] [Topology ] . ( 3 sec) [ -7580.8218] [Topology ] . ( 4 sec) [ -7580.1370] [Topology ] . ( 4 sec) [ -7579.9092] [Topology ] . ( 5 sec) [ -7579.8162] [Topology ] . ( 6 sec) [ -7579.7754] [Topology ] . ( 7 sec) [ -7579.7569] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7579.756885 . ( 12 sec) [ -7579.6895] [GTR parameters ] . ( 12 sec) [ -7579.5945] [Alpha ][ 1.035635] . ( 12 sec) [ -7579.5945] [Topology ] . ( 13 sec) [ -7579.5739] [Topology ] . ( 14 sec) [ -7579.5652] [Topology ] . ( 14 sec) [ -7579.5613] [Topology ] . ( 15 sec) [ -7579.5595] [Topology ] . ( 16 sec) [ -7579.5587] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7579.558706 . ( 21 sec) [ -7579.5585] [GTR parameters ] . ( 21 sec) [ -7579.5576] [Alpha ][ 1.039455] . ( 21 sec) [ -7579.5576] [Topology ] . ( 22 sec) [ -7579.5571] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7579.557055 . ( 27 sec) [ -7579.5570] [GTR parameters ] . ( 27 sec) [ -7579.5570] [Alpha ][ 1.039455] . ( 27 sec) [ -7579.5570] [Topology ] . ( 28 sec) [ -7579.5568] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7579.556808. . Printing the most likely tree in file 'data89.phy_phyml_tree.txt'... . Time used 0h0m39s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo