.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data7.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... . 288 patterns found. (out of a total of 500 sites) . 188 sites without polymorphism (37.60%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 6Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-4321.356122 . ( 0 sec) [ -4317.7470] [GTR parameters ] . ( 1 sec) [ -4317.7006] [Alpha ][ 1.041435] . ( 1 sec) [ -4317.7006] [Topology ] . ( 2 sec) [ -4310.8662] [Topology ] . ( 3 sec) [ -4310.0336] [Topology ] . ( 4 sec) [ -4309.9103] [Topology ] . ( 4 sec) [ -4309.8799] [Topology ] . ( 5 sec) [ -4309.8710] [Topology ] . ( 5 sec) [ -4309.8682] [Topology ] . ( 6 sec) [ -4309.8671] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4309.867116 . ( 11 sec) [ -4309.8394] [GTR parameters ] . ( 11 sec) [ -4309.8274] [Alpha ][ 1.062573] . ( 11 sec) [ -4309.8274] [Topology ] . ( 11 sec) [ -4309.8264] [Topology ] . ( 12 sec) [ -4309.8261] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4309.826070 . ( 15 sec) [ -4309.8260] [GTR parameters ] . ( 15 sec) [ -4309.8260] [Alpha ][ 1.063635] . ( 15 sec) [ -4309.8260] [Topology ] . ( 16 sec) [ -4309.8259] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 25 sec) [ -4317.7470] [GTR parameters ] . ( 25 sec) [ -4317.7006] [Alpha ][ 1.041435] . ( 27 sec) [ -4316.8262] [ 700] [depth= 1] . ( 28 sec) [ -4316.1976] [ 700] [depth= 1] . ( 28 sec) [ -4315.9168] [ 700] [depth= 1] . ( 28 sec) [ -4315.8543] [ 700] [depth= 1] . ( 29 sec) [ -4314.4693] [ 703] [depth= 2] . ( 29 sec) [ -4313.5571] [ 704] [depth= 2] . ( 29 sec) [ -4313.3107] [ 704] [depth= 1] . ( 29 sec) [ -4313.1471] [ 704] [depth= 1] . ( 30 sec) [ -4311.8275] [ 703] [depth= 3] . ( 31 sec) [ -4308.0539] [Branch lengths ] . ( 32 sec) [ -4308.0027] [GTR parameters ] . ( 32 sec) [ -4308.0025] [Alpha ][ 1.043809] . ( 36 sec) [ -4307.9155] [ 703] [depth= 1] . ( 39 sec) [ -4307.8029] [Branch lengths ] . ( 39 sec) [ -4307.7999] [GTR parameters ] . ( 39 sec) [ -4307.7996] [Alpha ][ 1.047006] . ( 60 sec) [ -4307.7979] [Branch lengths ] . ( 60 sec) [ -4307.7979] [Topology ] . ( 61 sec) [ -4307.7978] [Topology ] . ( 61 sec) [ -4307.7978] [GTR parameters ] . ( 61 sec) [ -4307.7978] [Alpha ][ 1.048053] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -4309.825920 . Log likelihood obtained after SPR moves : -4307.797803 . Log likelihood of the current tree: -4307.797803. . Printing the most likely tree in file 'data7.phy_phyml_tree.txt'... . Time used 0h1m5s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo