.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data4.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... . 431 patterns found. (out of a total of 500 sites) . 63 sites without polymorphism (12.60%). . 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=-9072.110483 . ( 0 sec) [ -9071.6770] [GTR parameters ] . ( 0 sec) [ -9071.6595] [Alpha ][ 1.015113] . ( 0 sec) [ -9071.6595] [Topology ] . ( 1 sec) [ -9038.0496] [Topology ] . ( 2 sec) [ -9032.4404] [Topology ] . ( 3 sec) [ -9030.4804] [Topology ] . ( 5 sec) [ -9029.5590] [Topology ] . ( 6 sec) [ -9029.0788] [Topology ] . ( 7 sec) [ -9028.8183] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9028.818253 . ( 13 sec) [ -9028.8056] [GTR parameters ] . ( 13 sec) [ -9028.7296] [Alpha ][ 1.045040] . ( 13 sec) [ -9028.7296] [Topology ] . ( 14 sec) [ -9028.5755] [Topology ] . ( 15 sec) [ -9028.4903] [Topology ] . ( 15 sec) [ -9028.4411] [Topology ] . ( 16 sec) [ -9028.4126] [Topology ] . ( 17 sec) [ -9028.3958] [Topology ] . ( 18 sec) [ -9028.3858] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9028.385785 . ( 24 sec) [ -9028.3856] [GTR parameters ] . ( 24 sec) [ -9028.3853] [Alpha ][ 1.047166] . ( 24 sec) [ -9028.3853] [Topology ] . ( 25 sec) [ -9028.3792] [Topology ] . ( 25 sec) [ -9028.3756] [Topology ] . ( 26 sec) [ -9028.3735] [Topology ] . ( 27 sec) [ -9028.3721] [Topology ] . ( 28 sec) [ -9028.3713] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9028.371347 . ( 34 sec) [ -9028.3713] [GTR parameters ] . ( 34 sec) [ -9028.3713] [Alpha ][ 1.047166] . ( 34 sec) [ -9028.3713] [Topology ] . ( 35 sec) [ -9028.3708] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 47 sec) [ -9071.6770] [GTR parameters ] . ( 47 sec) [ -9071.6595] [Alpha ][ 1.015113] . ( 47 sec) [ -9070.9707] [ 1959] [depth= 1] . ( 48 sec) [ -9070.6104] [ 1961] [depth= 1] . ( 49 sec) [ -9066.8071] [ 1969] [depth= 2] . ( 49 sec) [ -9065.9874] [ 1970] [depth= 1] . ( 50 sec) [ -9065.8700] [ 1969] [depth= 1] . ( 50 sec) [ -9065.7317] [ 1972] [depth= 1] . ( 50 sec) [ -9063.6382] [ 1974] [depth= 1] . ( 50 sec) [ -9063.3347] [ 1960] [depth= 2] . ( 50 sec) [ -9061.1474] [ 1962] [depth= 3] . ( 50 sec) [ -9060.8712] [ 1963] [depth= 1] . ( 50 sec) [ -9058.7227] [ 1961] [depth= 1] . ( 51 sec) [ -9034.5647] [Branch lengths ] . ( 51 sec) [ -9034.5580] [GTR parameters ] . ( 51 sec) [ -9034.5164] [Alpha ][ 1.037201] . ( 52 sec) [ -9031.1392] [ 1959] [depth= 1] . ( 55 sec) [ -9028.8280] [Branch lengths ] . ( 55 sec) [ -9028.8252] [GTR parameters ] . ( 55 sec) [ -9028.8204] [Alpha ][ 1.045035] . ( 60 sec) [ -9028.4482] [Branch lengths ] . ( 87 sec) [ -9028.3840] [Branch lengths ] . ( 87 sec) [ -9028.3840] [Topology ] . ( 88 sec) [ -9028.3767] [Topology ] . ( 89 sec) [ -9028.3741] [Topology ] . ( 90 sec) [ -9028.3727] [Topology ] . ( 91 sec) [ -9028.3720] [Topology ] . ( 91 sec) [ -9028.3714] [GTR parameters ] . ( 91 sec) [ -9028.3711] [Alpha ][ 1.046770] . ( 91 sec) [ -9028.3711] [Topology ] . ( 92 sec) [ -9028.3707] [Topology ] . ( 92 sec) [ -9028.3706] [GTR parameters ] . ( 92 sec) [ -9028.3706] [Alpha ][ 1.046770] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9028.370844 . Log likelihood obtained after SPR moves : -9028.370644 . Log likelihood of the current tree: -9028.370644. . Printing the most likely tree in file 'data4.phy_phyml_tree.txt'... . Time used 0h1m38s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo