.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data55.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... . 368 patterns found. (out of a total of 500 sites) . 121 sites without polymorphism (24.20%). . 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=-6406.286429 . ( 1 sec) [ -6402.1884] [GTR parameters ] . ( 1 sec) [ -6401.7922] [Alpha ][ 1.092051] . ( 1 sec) [ -6401.7922] [Topology ] . ( 2 sec) [ -6375.9310] [Topology ] . ( 2 sec) [ -6372.7229] [Topology ] . ( 3 sec) [ -6372.0135] [Topology ] . ( 4 sec) [ -6371.8040] [Topology ] . ( 4 sec) [ -6371.7320] [Topology ] . ( 5 sec) [ -6371.7049] [Topology ] . ( 6 sec) [ -6371.6942] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-6371.694164 . ( 11 sec) [ -6371.6671] [GTR parameters ] . ( 11 sec) [ -6371.6314] [Alpha ][ 1.120840] . ( 11 sec) [ -6371.6314] [Topology ] . ( 12 sec) [ -6371.6239] [Topology ] . ( 12 sec) [ -6371.6210] [Topology ] . ( 13 sec) [ -6371.6198] [Topology ] . ( 14 sec) [ -6371.6193] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-6371.619333 . ( 18 sec) [ -6371.6193] [GTR parameters ] . ( 18 sec) [ -6371.6191] [Alpha ][ 1.122924] . ( 18 sec) [ -6371.6191] [Topology ] . ( 19 sec) [ -6371.6189] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 29 sec) [ -6402.1884] [GTR parameters ] . ( 29 sec) [ -6401.7922] [Alpha ][ 1.092051] . ( 29 sec) [ -6395.3228] [ 1195] [depth= 1] . ( 29 sec) [ -6395.0715] [ 1197] [depth= 1] . ( 29 sec) [ -6394.7013] [ 1195] [depth= 1] . ( 30 sec) [ -6393.9281] [ 1200] [depth= 1] . ( 30 sec) [ -6393.7546] [ 1198] [depth= 1] . ( 30 sec) [ -6393.4548] [ 1200] [depth= 1] . ( 31 sec) [ -6393.4358] [ 1202] [depth= 1] . ( 31 sec) [ -6392.7700] [ 1203] [depth= 2] . ( 31 sec) [ -6391.9102] [ 1200] [depth= 2] . ( 32 sec) [ -6374.3950] [Branch lengths ] . ( 32 sec) [ -6374.3706] [GTR parameters ] . ( 32 sec) [ -6374.3494] [Alpha ][ 1.114011] . ( 33 sec) [ -6374.2988] [ 1202] [depth= 1] . ( 34 sec) [ -6373.3996] [ 1198] [depth= 1] . ( 35 sec) [ -6373.1024] [ 1196] [depth= 1] . ( 36 sec) [ -6371.6723] [Branch lengths ] . ( 36 sec) [ -6371.6698] [GTR parameters ] . ( 36 sec) [ -6371.6677] [Alpha ][ 1.121213] . ( 40 sec) [ -6371.6228] [Branch lengths ] . ( 59 sec) [ -6371.6191] [Branch lengths ] . ( 59 sec) [ -6371.6191] [Topology ] . ( 60 sec) [ -6371.6189] [Topology ] . ( 60 sec) [ -6371.6189] [GTR parameters ] . ( 60 sec) [ -6371.6187] [Alpha ][ 1.122978] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -6371.618861 . Log likelihood obtained after SPR moves : -6371.618710 . Log likelihood of the current tree: -6371.618710. . Printing the most likely tree in file 'data55.phy_phyml_tree.txt'... . Time used 0h1m5s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo