.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data29.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... . 457 patterns found. (out of a total of 500 sites) . 34 sites without polymorphism (6.80%). . 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=-10897.223759 . ( 1 sec) [ -10895.0531] [GTR parameters ] . ( 1 sec) [ -10892.5292] [Alpha ][ 1.177564] . ( 1 sec) [ -10892.5292] [Topology ] . ( 2 sec) [ -10821.8961] [Topology ] . ( 3 sec) [ -10809.2564] [Topology ] . ( 4 sec) [ -10804.6495] [Topology ] . ( 5 sec) [ -10802.5218] [Topology ] . ( 7 sec) [ -10801.6487] [Topology ] . ( 8 sec) [ -10801.2787] [Topology ] . ( 10 sec) [ -10801.0902] [Topology ] . ( 11 sec) [ -10800.9891] [Topology ] . ( 12 sec) [ -10800.9333] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10800.902207 . ( 24 sec) [ -10800.8556] [GTR parameters ] . ( 24 sec) [ -10800.7768] [Alpha ][ 1.146085] . ( 24 sec) [ -10800.7768] [Topology ] . ( 25 sec) [ -10800.7500] [Topology ] . ( 26 sec) [ -10800.7373] [Topology ] . ( 27 sec) [ -10800.7301] [Topology ] . ( 29 sec) [ -10800.7259] [Topology ] . ( 30 sec) [ -10800.7235] [Topology ] . ( 31 sec) [ -10800.7221] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10800.722117 . ( 40 sec) [ -10800.7220] [GTR parameters ] . ( 41 sec) [ -10800.7210] [Alpha ][ 1.142439] . ( 41 sec) [ -10800.7210] [Topology ] . ( 42 sec) [ -10800.7200] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10800.720028 . ( 52 sec) [ -10800.7200] [GTR parameters ] . ( 52 sec) [ -10800.7200] [Alpha ][ 1.142439] . ( 52 sec) [ -10800.7200] [Topology ] . ( 54 sec) [ -10800.7195] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10800.719503. . Printing the most likely tree in file 'data29.phy_phyml_tree.txt'... . Time used 0h1m14s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo