.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data34.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... . 357 patterns found. (out of a total of 500 sites) . 130 sites without polymorphism (26.00%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 7Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-5915.368272 . ( 1 sec) [ -5914.3337] [GTR parameters ] . ( 1 sec) [ -5914.2453] [Alpha ][ 1.044120] . ( 1 sec) [ -5914.2453] [Topology ] . ( 2 sec) [ -5884.5145] [Topology ] . ( 3 sec) [ -5879.8822] [Topology ] . ( 3 sec) [ -5878.8229] [Topology ] . ( 4 sec) [ -5878.5145] [Topology ] . ( 5 sec) [ -5878.4132] [Topology ] . ( 7 sec) [ -5878.3768] [Topology ] . ( 8 sec) [ -5878.3628] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-5878.362839 . ( 16 sec) [ -5878.3580] [GTR parameters ] . ( 16 sec) [ -5878.2915] [Alpha ][ 1.083518] . ( 16 sec) [ -5878.2915] [Topology ] . ( 18 sec) [ -5878.2828] [Topology ] . ( 19 sec) [ -5878.2795] [Topology ] . ( 20 sec) [ -5878.2782] [Topology ] . ( 20 sec) [ -5878.2777] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-5878.277650 . ( 26 sec) [ -5878.2776] [GTR parameters ] . ( 26 sec) [ -5878.2775] [Alpha ][ 1.084814] . ( 26 sec) [ -5878.2775] [Topology ] . ( 27 sec) [ -5878.2772] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 39 sec) [ -5914.3337] [GTR parameters ] . ( 39 sec) [ -5914.2453] [Alpha ][ 1.044120] . ( 39 sec) [ -5913.8418] [ 1089] [depth= 1] . ( 39 sec) [ -5913.7836] [ 1089] [depth= 1] . ( 40 sec) [ -5913.0286] [ 1089] [depth= 1] . ( 40 sec) [ -5908.3687] [ 1089] [depth= 1] . ( 40 sec) [ -5907.6441] [ 1089] [depth= 1] . ( 40 sec) [ -5907.4454] [ 1089] [depth= 1] . ( 40 sec) [ -5907.3233] [ 1089] [depth= 1] . ( 40 sec) [ -5907.3116] [ 1089] [depth= 2] . ( 40 sec) [ -5907.2691] [ 1089] [depth= 1] . ( 41 sec) [ -5906.9424] [ 1090] [depth= 1] . ( 42 sec) [ -5905.2974] [ 1094] [depth= 1] . ( 42 sec) [ -5904.4479] [ 1094] [depth= 1] . ( 42 sec) [ -5904.4147] [ 1094] [depth= 1] . ( 42 sec) [ -5904.3980] [ 1094] [depth= 1] . ( 43 sec) [ -5898.4707] [ 1091] [depth= 1] . ( 44 sec) [ -5882.9331] [Branch lengths ] . ( 45 sec) [ -5882.8961] [GTR parameters ] . ( 45 sec) [ -5882.8629] [Alpha ][ 1.071721] . ( 46 sec) [ -5879.8435] [ 1087] [depth= 1] . ( 46 sec) [ -5879.1989] [ 1086] [depth= 1] . ( 47 sec) [ -5879.1357] [ 1089] [depth= 1] . ( 48 sec) [ -5879.1199] [ 1089] [depth= 1] . ( 49 sec) [ -5878.4015] [Branch lengths ] . ( 50 sec) [ -5878.3863] [GTR parameters ] . ( 50 sec) [ -5878.3822] [Alpha ][ 1.081915] . ( 54 sec) [ -5878.3427] [Branch lengths ] . ( 77 sec) [ -5878.3397] [Branch lengths ] . ( 77 sec) [ -5878.3397] [Topology ] . ( 77 sec) [ -5878.3395] [Topology ] . ( 78 sec) [ -5878.3395] [GTR parameters ] . ( 78 sec) [ -5878.3393] [Alpha ][ 1.083706] . Checking for NNIs, optimizing five branches... . ( 82 sec) [ -5878.3321] [Topology ] . Checking for NNIs, optimizing five branches... . ( 87 sec) [ -5878.2923] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -5878.277241 . Log likelihood obtained after SPR moves : -5878.292255 . Log likelihood of the current tree: -5878.277241. . Printing the most likely tree in file 'data34.phy_phyml_tree.txt'... . Time used 0h1m32s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo