.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data76.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 : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 391 patterns found. (out of a total of 500 sites) . 102 sites without polymorphism (20.40%). . 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=-7436.387967 . ( 0 sec) [ -7433.1227] [GTR parameters ] . ( 0 sec) [ -7432.9847] [Alpha ][ 1.048573] . ( 0 sec) [ -7432.9847] [Topology ] . ( 1 sec) [ -7418.7794] [Topology ] . ( 2 sec) [ -7416.8646] [Topology ] . ( 3 sec) [ -7416.3286] [Topology ] . ( 3 sec) [ -7416.1296] [Topology ] . ( 4 sec) [ -7416.0462] [Topology ] . ( 5 sec) [ -7416.0093] [Topology ] . ( 6 sec) [ -7415.9925] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7415.992527 . ( 11 sec) [ -7415.9864] [GTR parameters ] . ( 11 sec) [ -7415.8865] [Alpha ][ 1.090665] . ( 11 sec) [ -7415.8865] [Topology ] . ( 12 sec) [ -7415.8713] [Topology ] . ( 13 sec) [ -7415.8647] [Topology ] . ( 14 sec) [ -7415.8617] [Topology ] . ( 14 sec) [ -7415.8603] [Topology ] . ( 15 sec) [ -7415.8597] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7415.859668 . ( 20 sec) [ -7415.8596] [GTR parameters ] . ( 20 sec) [ -7415.8590] [Alpha ][ 1.093839] . ( 20 sec) [ -7415.8590] [Topology ] . ( 21 sec) [ -7415.8586] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7415.858641 . ( 27 sec) [ -7415.8586] [GTR parameters ] . ( 27 sec) [ -7415.8586] [Alpha ][ 1.093839] . ( 27 sec) [ -7415.8586] [Topology ] . ( 28 sec) [ -7415.8585] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 38 sec) [ -7433.1227] [GTR parameters ] . ( 38 sec) [ -7432.9847] [Alpha ][ 1.048573] . ( 40 sec) [ -7432.6038] [ 1416] [depth= 2] . ( 40 sec) [ -7432.4633] [ 1415] [depth= 1] . ( 41 sec) [ -7431.5506] [ 1418] [depth= 1] . ( 42 sec) [ -7431.4944] [ 1417] [depth= 1] . ( 42 sec) [ -7431.3212] [ 1418] [depth= 1] . ( 42 sec) [ -7431.0753] [ 1417] [depth= 1] . ( 42 sec) [ -7420.2776] [Branch lengths ] . ( 43 sec) [ -7420.2627] [GTR parameters ] . ( 43 sec) [ -7420.2281] [Alpha ][ 1.073037] . ( 44 sec) [ -7418.6845] [ 1414] [depth= 2] . ( 45 sec) [ -7417.6300] [ 1408] [depth= 1] . ( 46 sec) [ -7415.9768] [Branch lengths ] . ( 47 sec) [ -7415.9709] [GTR parameters ] . ( 47 sec) [ -7415.9536] [Alpha ][ 1.091420] . ( 50 sec) [ -7415.8670] [Branch lengths ] . ( 70 sec) [ -7415.8598] [Branch lengths ] . ( 70 sec) [ -7415.8598] [Topology ] . ( 71 sec) [ -7415.8592] [Topology ] . ( 71 sec) [ -7415.8591] [GTR parameters ] . ( 71 sec) [ -7415.8587] [Alpha ][ 1.093940] . ( 71 sec) [ -7415.8587] [Topology ] . ( 72 sec) [ -7415.8585] [Topology ] . ( 72 sec) [ -7415.8585] [GTR parameters ] . ( 72 sec) [ -7415.8585] [Alpha ][ 1.093940] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7415.858458 . Log likelihood obtained after SPR moves : -7415.858484 . Log likelihood of the current tree: -7415.858458. . Printing the most likely tree in file 'data76.phy_phyml_tree.txt'... . Time used 0h1m18s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo