.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data18.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... . 417 patterns found. (out of a total of 500 sites) . 78 sites without polymorphism (15.60%). . 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=-8350.364615 . ( 1 sec) [ -8348.2932] [GTR parameters ] . ( 2 sec) [ -8348.1523] [Alpha ][ 1.044806] . ( 2 sec) [ -8348.1523] [Topology ] . ( 3 sec) [ -8296.9542] [Topology ] . ( 5 sec) [ -8286.8915] [Topology ] . ( 6 sec) [ -8284.3275] [Topology ] . ( 8 sec) [ -8282.5314] [Topology ] . ( 9 sec) [ -8282.0722] [Topology ] . ( 10 sec) [ -8281.8788] [Topology ] . ( 12 sec) [ -8281.7891] [Topology ] . ( 13 sec) [ -8281.7461] [Topology ] . ( 15 sec) [ -8281.7251] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8281.725051 . ( 26 sec) [ -8281.6764] [GTR parameters ] . ( 26 sec) [ -8281.6695] [Alpha ][ 1.034679] . ( 26 sec) [ -8281.6695] [Topology ] . ( 27 sec) [ -8281.6579] [Topology ] . ( 28 sec) [ -8281.6524] [Topology ] . ( 30 sec) [ -8281.6496] [Topology ] . ( 31 sec) [ -8281.6482] [Topology ] . ( 32 sec) [ -8281.6475] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8281.647510 . ( 41 sec) [ -8281.6474] [GTR parameters ] . ( 41 sec) [ -8281.6474] [Alpha ][ 1.034679] . ( 41 sec) [ -8281.6474] [Topology ] . ( 42 sec) [ -8281.6470] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 62 sec) [ -8348.2932] [GTR parameters ] . ( 62 sec) [ -8348.1523] [Alpha ][ 1.044806] . ( 62 sec) [ -8345.9422] [ 1799] [depth= 1] . ( 62 sec) [ -8342.9652] [ 1804] [depth= 1] . ( 62 sec) [ -8340.3662] [ 1799] [depth= 1] . ( 63 sec) [ -8329.5668] [ 1811] [depth= 1] . ( 63 sec) [ -8327.5249] [ 1812] [depth= 1] . ( 63 sec) [ -8325.0888] [ 1812] [depth= 1] . ( 64 sec) [ -8324.0027] [ 1811] [depth= 1] . ( 64 sec) [ -8323.8872] [ 1812] [depth= 1] . ( 64 sec) [ -8323.2903] [ 1812] [depth= 1] . ( 64 sec) [ -8321.7625] [ 1810] [depth= 1] . ( 64 sec) [ -8317.9600] [ 1812] [depth= 1] . ( 65 sec) [ -8312.2771] [ 1807] [depth= 1] . ( 65 sec) [ -8312.1923] [ 1811] [depth= 1] . ( 65 sec) [ -8311.2178] [ 1807] [depth= 1] . ( 65 sec) [ -8311.1213] [ 1811] [depth= 1] . ( 65 sec) [ -8308.7561] [ 1809] [depth= 2] . ( 66 sec) [ -8307.9129] [ 1809] [depth= 1] . ( 66 sec) [ -8300.6023] [ 1809] [depth= 1] . ( 68 sec) [ -8282.8520] [Branch lengths ] . ( 68 sec) [ -8282.8017] [GTR parameters ] . ( 68 sec) [ -8282.7776] [Alpha ][ 1.027091] . ( 68 sec) [ -8282.7041] [ 1808] [depth= 1] . ( 73 sec) [ -8281.8116] [Branch lengths ] . ( 73 sec) [ -8281.8111] [GTR parameters ] . ( 74 sec) [ -8281.8087] [Alpha ][ 1.032721] . ( 100 sec) [ -8281.7002] [Branch lengths ] . ( 101 sec) [ -8281.7002] [Topology ] . ( 101 sec) [ -8281.6911] [Topology ] . ( 102 sec) [ -8281.6880] [Topology ] . ( 103 sec) [ -8281.6865] [Topology ] . ( 104 sec) [ -8281.6858] [Topology ] . ( 104 sec) [ -8281.6858] [GTR parameters ] . ( 104 sec) [ -8281.6854] [Alpha ][ 1.034755] . ( 104 sec) [ -8281.6854] [Topology ] . ( 105 sec) [ -8281.6850] [Topology ] . ( 105 sec) [ -8281.6850] [GTR parameters ] . ( 105 sec) [ -8281.6850] [Alpha ][ 1.034755] . Checking for NNIs, optimizing five branches... . ( 112 sec) [ -8281.6543] [Topology ] . Checking for NNIs, optimizing five branches... . ( 122 sec) [ -8281.6541] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -8281.646982 . Log likelihood obtained after SPR moves : -8281.654128 . Log likelihood of the current tree: -8281.646982. . Printing the most likely tree in file 'data18.phy_phyml_tree.txt'... . Time used 0h2m11s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo