.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data68.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... . 417 patterns found. (out of a total of 500 sites) . 78 sites without polymorphism (15.60%). . 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=-9047.095058 . ( 1 sec) [ -9041.3256] [GTR parameters ] . ( 1 sec) [ -9041.2523] [Alpha ][ 0.970005] . ( 1 sec) [ -9041.2523] [Topology ] . ( 2 sec) [ -8996.4322] [Topology ] . ( 3 sec) [ -8988.7327] [Topology ] . ( 4 sec) [ -8970.9581] [Topology ] . ( 4 sec) [ -8965.6059] [Topology ] . ( 5 sec) [ -8964.7395] [Topology ] . ( 6 sec) [ -8964.4999] [Topology ] . ( 7 sec) [ -8964.4081] [Topology ] . ( 8 sec) [ -8964.3656] [Topology ] . ( 9 sec) [ -8964.3441] [Topology ] . Checking for NNIs, optimizing five branches... . ( 16 sec) [ -8964.0843] [Topology ] . Before opt ts/t=1.000000 LK=-8964.084298 . ( 17 sec) [ -8964.0076] [GTR parameters ] . ( 17 sec) [ -8963.7412] [Alpha ][ 1.026015] . ( 17 sec) [ -8963.7412] [Topology ] . ( 18 sec) [ -8963.7104] [Topology ] . ( 18 sec) [ -8963.7021] [Topology ] . ( 19 sec) [ -8963.6987] [Topology ] . ( 20 sec) [ -8963.6971] [Topology ] . ( 21 sec) [ -8963.6963] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8963.696322 . ( 28 sec) [ -8963.6956] [GTR parameters ] . ( 28 sec) [ -8963.6952] [Alpha ][ 1.028310] . ( 28 sec) [ -8963.6952] [Topology ] . ( 29 sec) [ -8963.6948] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8963.694758 . ( 38 sec) [ -8963.6948] [GTR parameters ] . ( 38 sec) [ -8963.6948] [Alpha ][ 1.028310] . ( 38 sec) [ -8963.6948] [Topology ] . ( 39 sec) [ -8963.6945] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8963.694528. . Printing the most likely tree in file 'data68.phy_phyml_tree.txt'... . Time used 0h0m56s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo