.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data17.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... . 394 patterns found. (out of a total of 500 sites) . 90 sites without polymorphism (18.00%). . 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=-7947.170164 . ( 1 sec) [ -7944.4534] [GTR parameters ] . ( 1 sec) [ -7943.8676] [Alpha ][ 0.913664] . ( 1 sec) [ -7943.8676] [Topology ] . ( 2 sec) [ -7907.6242] [Topology ] . ( 3 sec) [ -7899.5631] [Topology ] . ( 4 sec) [ -7895.5710] [Topology ] . ( 4 sec) [ -7894.5882] [Topology ] . ( 5 sec) [ -7894.2081] [Topology ] . ( 6 sec) [ -7894.0524] [Topology ] . ( 7 sec) [ -7893.9831] [Topology ] . ( 7 sec) [ -7893.9520] [Topology ] . Checking for NNIs, optimizing five branches... . ( 15 sec) [ -7893.8894] [Topology ] . Before opt ts/t=1.000000 LK=-7893.889429 . ( 15 sec) [ -7893.8379] [GTR parameters ] . ( 15 sec) [ -7893.5614] [Alpha ][ 0.969457] . ( 15 sec) [ -7893.5614] [Topology ] . ( 16 sec) [ -7893.5239] [Topology ] . ( 17 sec) [ -7893.5111] [Topology ] . ( 17 sec) [ -7893.5055] [Topology ] . ( 18 sec) [ -7893.5029] [Topology ] . ( 19 sec) [ -7893.5016] [Topology ] . ( 20 sec) [ -7893.5010] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7893.501048 . ( 26 sec) [ -7893.5008] [GTR parameters ] . ( 26 sec) [ -7893.4986] [Alpha ][ 0.974705] . ( 26 sec) [ -7893.4986] [Topology ] . ( 27 sec) [ -7893.4980] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7893.498049 . ( 34 sec) [ -7893.4980] [GTR parameters ] . ( 34 sec) [ -7893.4980] [Alpha ][ 0.974705] . ( 34 sec) [ -7893.4980] [Topology ] . ( 35 sec) [ -7893.4978] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 49 sec) [ -7944.4534] [GTR parameters ] . ( 49 sec) [ -7943.8676] [Alpha ][ 0.913664] . ( 50 sec) [ -7943.5295] [ 1648] [depth= 1] . ( 50 sec) [ -7942.5763] [ 1648] [depth= 1] . ( 51 sec) [ -7941.5718] [ 1650] [depth= 1] . ( 51 sec) [ -7941.5588] [ 1653] [depth= 1] . ( 51 sec) [ -7940.4075] [ 1652] [depth= 1] . ( 51 sec) [ -7932.3731] [ 1649] [depth= 1] . ( 51 sec) [ -7930.6840] [ 1649] [depth= 1] . ( 51 sec) [ -7928.2296] [ 1649] [depth= 1] . ( 51 sec) [ -7927.6559] [ 1645] [depth= 2] . ( 51 sec) [ -7926.9617] [ 1650] [depth= 1] . ( 51 sec) [ -7926.1280] [ 1645] [depth= 1] . ( 51 sec) [ -7925.4974] [ 1647] [depth= 1] . ( 52 sec) [ -7921.7899] [ 1647] [depth= 2] . ( 52 sec) [ -7921.7274] [ 1649] [depth= 1] . ( 52 sec) [ -7920.2920] [ 1647] [depth= 1] . ( 52 sec) [ -7920.1528] [ 1646] [depth= 1] . ( 52 sec) [ -7920.1230] [ 1647] [depth= 1] . ( 52 sec) [ -7919.1391] [ 1646] [depth= 1] . ( 53 sec) [ -7918.6228] [ 1647] [depth= 1] . ( 53 sec) [ -7910.8072] [ 1646] [depth= 3] . ( 53 sec) [ -7908.4620] [ 1647] [depth= 2] . ( 53 sec) [ -7907.8269] [ 1649] [depth= 1] . ( 54 sec) [ -7906.7101] [ 1648] [depth= 1] . ( 54 sec) [ -7906.3968] [ 1647] [depth= 1] . ( 54 sec) [ -7906.2626] [ 1648] [depth= 1] . ( 54 sec) [ -7905.3765] [ 1647] [depth= 1] . ( 54 sec) [ -7904.6535] [ 1651] [depth= 1] . ( 54 sec) [ -7903.6269] [ 1647] [depth= 1] . ( 54 sec) [ -7903.2113] [ 1648] [depth= 1] . ( 55 sec) [ -7885.3570] [Branch lengths ] . ( 55 sec) [ -7885.3084] [GTR parameters ] . ( 55 sec) [ -7885.1269] [Alpha ][ 0.959010] . ( 57 sec) [ -7884.8654] [ 1646] [depth= 1] . ( 59 sec) [ -7883.8589] [Branch lengths ] . ( 59 sec) [ -7883.8576] [GTR parameters ] . ( 59 sec) [ -7883.8534] [Alpha ][ 0.966145] . ( 63 sec) [ -7883.7885] [Branch lengths ] . ( 70 sec) [ -7883.7131] [ 1643] [depth= 1] . ( 87 sec) [ -7883.6394] [ 1642] [depth= 1] . ( 88 sec) [ -7883.5837] [Branch lengths ] . ( 89 sec) [ -7883.5830] [GTR parameters ] . ( 89 sec) [ -7883.5819] [Alpha ][ 0.969631] . ( 89 sec) [ -7883.5819] [Topology ] . ( 90 sec) [ -7883.5747] [Topology ] . ( 91 sec) [ -7883.5729] [Topology ] . ( 91 sec) [ -7883.5723] [Topology ] . ( 92 sec) [ -7883.5722] [GTR parameters ] . ( 92 sec) [ -7883.5722] [Alpha ][ 0.970600] . ( 92 sec) [ -7883.5722] [Topology ] . ( 93 sec) [ -7883.5719] [Topology ] . ( 93 sec) [ -7883.5719] [GTR parameters ] . ( 93 sec) [ -7883.5719] [Alpha ][ 0.970600] . Checking for NNIs, optimizing five branches... . ( 100 sec) [ -7883.5420] [Topology ] . Checking for NNIs, optimizing five branches... . ( 108 sec) [ -7883.5063] [Topology ] . Checking for NNIs, optimizing five branches... . ( 117 sec) [ -7883.5060] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7893.497825 . Log likelihood obtained after SPR moves : -7883.506001 . Log likelihood of the current tree: -7883.506001. . Printing the most likely tree in file 'data17.phy_phyml_tree.txt'... . Time used 0h2m4s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo