.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data80.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... . 409 patterns found. (out of a total of 500 sites) . 90 sites without polymorphism (18.00%). . 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=-9414.383223 . ( 1 sec) [ -9401.9651] [GTR parameters ] . ( 1 sec) [ -9400.9169] [Alpha ][ 0.893448] . ( 1 sec) [ -9400.9169] [Topology ] . ( 2 sec) [ -9356.1912] [Topology ] . ( 3 sec) [ -9350.5757] [Topology ] . ( 4 sec) [ -9349.4320] [Topology ] . ( 4 sec) [ -9348.9751] [Topology ] . ( 5 sec) [ -9348.7678] [Topology ] . ( 6 sec) [ -9348.6682] [Topology ] . ( 7 sec) [ -9348.6185] [Topology ] . ( 7 sec) [ -9348.5933] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9348.593346 . ( 14 sec) [ -9348.5517] [GTR parameters ] . ( 14 sec) [ -9348.5034] [Alpha ][ 0.914037] . ( 14 sec) [ -9348.5034] [Topology ] . ( 15 sec) [ -9348.4836] [Topology ] . ( 15 sec) [ -9348.4746] [Topology ] . ( 16 sec) [ -9348.4701] [Topology ] . ( 17 sec) [ -9348.4678] [Topology ] . ( 18 sec) [ -9348.4666] [Topology ] . ( 18 sec) [ -9348.4660] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9348.466014 . ( 24 sec) [ -9348.4660] [GTR parameters ] . ( 24 sec) [ -9348.4650] [Alpha ][ 0.917096] . ( 24 sec) [ -9348.4650] [Topology ] . ( 25 sec) [ -9348.4645] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9348.464522 . ( 31 sec) [ -9348.4645] [GTR parameters ] . ( 31 sec) [ -9348.4645] [Alpha ][ 0.917096] . ( 31 sec) [ -9348.4645] [Topology ] . ( 32 sec) [ -9348.4643] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9348.464309. . Printing the most likely tree in file 'data80.phy_phyml_tree.txt'... . Time used 0h0m44s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo