.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data57.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... . 398 patterns found. (out of a total of 500 sites) . 97 sites without polymorphism (19.40%). . 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=-7252.857742 . ( 1 sec) [ -7242.8403] [GTR parameters ] . ( 2 sec) [ -7242.1885] [Alpha ][ 1.109718] . ( 2 sec) [ -7242.1885] [Topology ] . ( 3 sec) [ -7202.1609] [Topology ] . ( 5 sec) [ -7198.2279] [Topology ] . ( 6 sec) [ -7197.5078] [Topology ] . ( 7 sec) [ -7197.2985] [Topology ] . ( 7 sec) [ -7197.2249] [Topology ] . ( 8 sec) [ -7197.1964] [Topology ] . ( 9 sec) [ -7197.1847] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7197.184696 . ( 14 sec) [ -7197.1380] [GTR parameters ] . ( 14 sec) [ -7197.1167] [Alpha ][ 1.131102] . ( 14 sec) [ -7197.1167] [Topology ] . ( 15 sec) [ -7197.1086] [Topology ] . ( 16 sec) [ -7197.1054] [Topology ] . ( 17 sec) [ -7197.1040] [Topology ] . ( 18 sec) [ -7197.1034] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7197.103429 . ( 25 sec) [ -7197.1034] [GTR parameters ] . ( 25 sec) [ -7197.1034] [Alpha ][ 1.132233] . ( 25 sec) [ -7197.1034] [Topology ] . ( 26 sec) [ -7197.1031] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 39 sec) [ -7242.8403] [GTR parameters ] . ( 39 sec) [ -7242.1885] [Alpha ][ 1.109718] . ( 40 sec) [ -7239.0080] [ 1435] [depth= 1] . ( 40 sec) [ -7238.7123] [ 1436] [depth= 1] . ( 41 sec) [ -7227.8420] [ 1434] [depth= 1] . ( 41 sec) [ -7227.7182] [ 1435] [depth= 1] . ( 42 sec) [ -7227.0615] [ 1433] [depth= 1] . ( 42 sec) [ -7226.0591] [ 1438] [depth= 1] . ( 43 sec) [ -7225.3600] [ 1433] [depth= 1] . ( 44 sec) [ -7202.3762] [Branch lengths ] . ( 45 sec) [ -7202.3382] [GTR parameters ] . ( 45 sec) [ -7202.3331] [Alpha ][ 1.120024] . ( 45 sec) [ -7201.6025] [ 1432] [depth= 1] . ( 46 sec) [ -7201.5705] [ 1433] [depth= 1] . ( 46 sec) [ -7201.4926] [ 1432] [depth= 1] . ( 47 sec) [ -7200.9370] [ 1431] [depth= 1] . ( 48 sec) [ -7200.3871] [ 1433] [depth= 1] . ( 49 sec) [ -7200.2393] [ 1438] [depth= 1] . ( 49 sec) [ -7199.1105] [ 1436] [depth= 1] . ( 51 sec) [ -7197.2316] [Branch lengths ] . ( 51 sec) [ -7197.2201] [GTR parameters ] . ( 51 sec) [ -7197.2149] [Alpha ][ 1.130556] . ( 56 sec) [ -7197.1087] [Branch lengths ] . ( 79 sec) [ -7197.1037] [Branch lengths ] . ( 79 sec) [ -7197.1037] [Topology ] . ( 80 sec) [ -7197.1032] [Topology ] . ( 80 sec) [ -7197.1032] [GTR parameters ] . ( 80 sec) [ -7197.1031] [Alpha ][ 1.132044] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7197.103097 . Log likelihood obtained after SPR moves : -7197.103094 . Log likelihood of the current tree: -7197.103094. . Printing the most likely tree in file 'data57.phy_phyml_tree.txt'... . Time used 0h1m28s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo