.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data87.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... . 388 patterns found. (out of a total of 500 sites) . 107 sites without polymorphism (21.40%). . 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=-7943.507673 . ( 1 sec) [ -7939.9700] [GTR parameters ] . ( 1 sec) [ -7937.9644] [Alpha ][ 0.846040] . ( 1 sec) [ -7937.9644] [Topology ] . ( 2 sec) [ -7904.9970] [Topology ] . ( 3 sec) [ -7899.3218] [Topology ] . ( 5 sec) [ -7897.8608] [Topology ] . ( 6 sec) [ -7897.2441] [Topology ] . ( 7 sec) [ -7896.9520] [Topology ] . ( 8 sec) [ -7896.8081] [Topology ] . ( 9 sec) [ -7896.7358] [Topology ] . ( 11 sec) [ -7896.6992] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7896.699227 . ( 19 sec) [ -7896.6594] [GTR parameters ] . ( 19 sec) [ -7896.5871] [Alpha ][ 0.871821] . ( 19 sec) [ -7896.5871] [Topology ] . ( 20 sec) [ -7896.5615] [Topology ] . ( 21 sec) [ -7896.5494] [Topology ] . ( 22 sec) [ -7896.5433] [Topology ] . ( 24 sec) [ -7896.5403] [Topology ] . ( 25 sec) [ -7896.5387] [Topology ] . ( 26 sec) [ -7896.5379] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7896.537893 . ( 33 sec) [ -7896.5379] [GTR parameters ] . ( 33 sec) [ -7896.5374] [Alpha ][ 0.873929] . ( 33 sec) [ -7896.5374] [Topology ] . ( 34 sec) [ -7896.5369] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 52 sec) [ -7939.9700] [GTR parameters ] . ( 52 sec) [ -7937.9644] [Alpha ][ 0.846040] . ( 53 sec) [ -7934.8492] [ 1615] [depth= 1] . ( 53 sec) [ -7930.6520] [ 1640] [depth= 2] . ( 53 sec) [ -7929.7377] [ 1641] [depth= 1] . ( 53 sec) [ -7927.4369] [ 1640] [depth= 1] . ( 55 sec) [ -7927.0405] [ 1641] [depth= 1] . ( 56 sec) [ -7924.5552] [ 1640] [depth= 1] . ( 56 sec) [ -7922.1555] [ 1638] [depth= 1] . ( 56 sec) [ -7921.0597] [ 1638] [depth= 1] . ( 56 sec) [ -7920.5539] [ 1641] [depth= 2] . ( 56 sec) [ -7918.6026] [ 1643] [depth= 1] . ( 56 sec) [ -7918.4087] [ 1645] [depth= 1] . ( 56 sec) [ -7916.1650] [ 1643] [depth= 1] . ( 56 sec) [ -7914.2709] [ 1646] [depth= 1] . ( 57 sec) [ -7902.3233] [Branch lengths ] . ( 58 sec) [ -7902.2813] [GTR parameters ] . ( 58 sec) [ -7902.2779] [Alpha ][ 0.851645] . ( 58 sec) [ -7902.1786] [ 1643] [depth= 1] . ( 59 sec) [ -7900.1373] [ 1618] [depth= 2] . ( 59 sec) [ -7900.1078] [ 1619] [depth= 1] . ( 62 sec) [ -7900.0651] [ 1621] [depth= 1] . ( 63 sec) [ -7896.9257] [Branch lengths ] . ( 63 sec) [ -7896.9155] [GTR parameters ] . ( 63 sec) [ -7896.8794] [Alpha ][ 0.870496] . ( 66 sec) [ -7896.6762] [ 1624] [depth= 1] . ( 68 sec) [ -7896.5537] [Branch lengths ] . ( 68 sec) [ -7896.5534] [GTR parameters ] . ( 68 sec) [ -7896.5522] [Alpha ][ 0.866934] . ( 85 sec) [ -7896.5090] [ 1622] [depth= 1] . ( 94 sec) [ -7896.4323] [Branch lengths ] . ( 94 sec) [ -7896.4322] [GTR parameters ] . ( 94 sec) [ -7896.4322] [Alpha ][ 0.866068] . ( 94 sec) [ -7896.4322] [Topology ] . ( 95 sec) [ -7896.3948] [Topology ] . ( 97 sec) [ -7896.3725] [Topology ] . ( 98 sec) [ -7896.3689] [Topology ] . ( 99 sec) [ -7896.3679] [Topology ] . ( 100 sec) [ -7896.3676] [Topology ] . ( 100 sec) [ -7896.3675] [GTR parameters ] . ( 100 sec) [ -7896.3672] [Alpha ][ 0.867513] . ( 100 sec) [ -7896.3672] [Topology ] . ( 102 sec) [ -7896.3671] [Topology ] . ( 102 sec) [ -7896.3671] [GTR parameters ] . ( 102 sec) [ -7896.3671] [Alpha ][ 0.867513] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7896.536936 . Log likelihood obtained after SPR moves : -7896.367109 . Log likelihood of the current tree: -7896.367109. . Printing the most likely tree in file 'data87.phy_phyml_tree.txt'... . Time used 0h1m49s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo