.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data2.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... . 454 patterns found. (out of a total of 500 sites) . 40 sites without polymorphism (8.00%). . 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=-9801.144178 . ( 1 sec) [ -9799.9617] [GTR parameters ] . ( 1 sec) [ -9797.1449] [Alpha ][ 1.202689] . ( 1 sec) [ -9797.1449] [Topology ] . ( 2 sec) [ -9743.9815] [Topology ] . ( 2 sec) [ -9735.8535] [Topology ] . ( 3 sec) [ -9733.2210] [Topology ] . ( 4 sec) [ -9732.0913] [Topology ] . ( 5 sec) [ -9731.5407] [Topology ] . ( 6 sec) [ -9731.2519] [Topology ] . ( 7 sec) [ -9730.9560] [Topology ] . ( 7 sec) [ -9729.8822] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9729.882213 . ( 15 sec) [ -9729.8433] [GTR parameters ] . ( 15 sec) [ -9729.8272] [Alpha ][ 1.186224] . ( 15 sec) [ -9729.8272] [Topology ] . ( 16 sec) [ -9726.3677] [Topology ] . ( 17 sec) [ -9724.1515] [Topology ] . ( 18 sec) [ -9723.9354] [Topology ] . ( 19 sec) [ -9723.8862] [Topology ] . ( 20 sec) [ -9723.8718] [Topology ] . ( 21 sec) [ -9723.8666] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9723.866603 . ( 31 sec) [ -9723.8661] [GTR parameters ] . ( 31 sec) [ -9723.8658] [Alpha ][ 1.183900] . ( 31 sec) [ -9723.8658] [Topology ] . ( 33 sec) [ -9723.8635] [Topology ] . ( 34 sec) [ -9723.8622] [Topology ] . ( 35 sec) [ -9723.8615] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9723.861484 . ( 43 sec) [ -9723.8615] [GTR parameters ] . ( 43 sec) [ -9723.8615] [Alpha ][ 1.183900] . ( 43 sec) [ -9723.8615] [Topology ] . ( 44 sec) [ -9723.8611] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9723.861076. . Printing the most likely tree in file 'data2.phy_phyml_tree.txt'... . Time used 0h1m1s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo