.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data43.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... . 428 patterns found. (out of a total of 500 sites) . 67 sites without polymorphism (13.40%). . 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=-10318.994783 . ( 1 sec) [ -10312.0688] [GTR parameters ] . ( 1 sec) [ -10311.6492] [Alpha ][ 0.935381] . ( 1 sec) [ -10311.6492] [Topology ] . ( 2 sec) [ -10271.7364] [Topology ] . ( 2 sec) [ -10265.0575] [Topology ] . ( 3 sec) [ -10263.2794] [Topology ] . ( 4 sec) [ -10262.6090] [Topology ] . ( 5 sec) [ -10262.2889] [Topology ] . ( 6 sec) [ -10262.1288] [Topology ] . ( 7 sec) [ -10262.0472] [Topology ] . ( 7 sec) [ -10262.0051] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10262.005059 . ( 14 sec) [ -10261.9510] [GTR parameters ] . ( 14 sec) [ -10261.6619] [Alpha ][ 0.986600] . ( 14 sec) [ -10261.6619] [Topology ] . ( 15 sec) [ -10261.6104] [Topology ] . ( 16 sec) [ -10261.5863] [Topology ] . ( 17 sec) [ -10261.5740] [Topology ] . ( 18 sec) [ -10261.5677] [Topology ] . ( 19 sec) [ -10261.5644] [Topology ] . ( 20 sec) [ -10261.5627] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10261.562735 . ( 26 sec) [ -10261.5626] [GTR parameters ] . ( 26 sec) [ -10261.5600] [Alpha ][ 0.991703] . ( 26 sec) [ -10261.5600] [Topology ] . ( 27 sec) [ -10261.5587] [Topology ] . ( 28 sec) [ -10261.5581] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10261.558104 . ( 34 sec) [ -10261.5581] [GTR parameters ] . ( 34 sec) [ -10261.5581] [Alpha ][ 0.991703] . ( 34 sec) [ -10261.5581] [Topology ] . ( 35 sec) [ -10261.5578] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 47 sec) [ -10312.0688] [GTR parameters ] . ( 47 sec) [ -10311.6492] [Alpha ][ 0.935381] . ( 47 sec) [ -10311.0174] [ 2257] [depth= 2] . ( 47 sec) [ -10310.7489] [ 2254] [depth= 2] . ( 47 sec) [ -10309.0195] [ 2255] [depth= 1] . ( 48 sec) [ -10308.5527] [ 2254] [depth= 1] . ( 48 sec) [ -10307.1233] [ 2255] [depth= 1] . ( 48 sec) [ -10305.9064] [ 2257] [depth= 1] . ( 49 sec) [ -10304.3128] [ 2258] [depth= 1] . ( 49 sec) [ -10303.9779] [ 2257] [depth= 1] . ( 49 sec) [ -10302.5236] [ 2260] [depth= 1] . ( 49 sec) [ -10301.9731] [ 2260] [depth= 1] . ( 49 sec) [ -10298.1291] [ 2258] [depth= 1] . ( 49 sec) [ -10295.3385] [ 2260] [depth= 1] . ( 49 sec) [ -10291.7170] [ 2261] [depth= 1] . ( 49 sec) [ -10291.0106] [ 2260] [depth= 1] . ( 49 sec) [ -10290.8519] [ 2264] [depth= 1] . ( 49 sec) [ -10288.3332] [ 2266] [depth= 1] . ( 49 sec) [ -10288.0158] [ 2264] [depth= 1] . ( 50 sec) [ -10287.9646] [ 2266] [depth= 1] . ( 50 sec) [ -10287.1933] [ 2265] [depth= 1] . ( 50 sec) [ -10263.9806] [Branch lengths ] . ( 51 sec) [ -10263.9422] [GTR parameters ] . ( 51 sec) [ -10263.7825] [Alpha ][ 0.973650] . ( 54 sec) [ -10262.3031] [Branch lengths ] . ( 77 sec) [ -10262.1239] [Branch lengths ] . ( 77 sec) [ -10262.1239] [Topology ] . ( 78 sec) [ -10261.6218] [Topology ] . ( 79 sec) [ -10261.6051] [Topology ] . ( 80 sec) [ -10261.6009] [Topology ] . ( 80 sec) [ -10261.5991] [Topology ] . ( 81 sec) [ -10261.5983] [Topology ] . ( 81 sec) [ -10261.5944] [GTR parameters ] . ( 81 sec) [ -10261.5616] [Alpha ][ 0.991689] . ( 81 sec) [ -10261.5616] [Topology ] . ( 82 sec) [ -10261.5593] [Topology ] . ( 83 sec) [ -10261.5584] [Topology ] . ( 83 sec) [ -10261.5584] [GTR parameters ] . ( 83 sec) [ -10261.5584] [Alpha ][ 0.991689] . ( 83 sec) [ -10261.5584] [Topology ] . ( 84 sec) [ -10261.5579] [Topology ] . ( 84 sec) [ -10261.5579] [GTR parameters ] . ( 84 sec) [ -10261.5579] [Alpha ][ 0.991689] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10261.557766 . Log likelihood obtained after SPR moves : -10261.557897 . Log likelihood of the current tree: -10261.557766. . Printing the most likely tree in file 'data43.phy_phyml_tree.txt'... . Time used 0h1m30s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo