.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data79.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... . 397 patterns found. (out of a total of 500 sites) . 92 sites without polymorphism (18.40%). . 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=-7990.949843 . ( 1 sec) [ -7988.1958] [GTR parameters ] . ( 1 sec) [ -7988.1956] [Alpha ][ 0.998171] . ( 1 sec) [ -7988.1956] [Topology ] . ( 2 sec) [ -7946.8898] [Topology ] . ( 3 sec) [ -7942.5047] [Topology ] . ( 3 sec) [ -7940.3008] [Topology ] . ( 4 sec) [ -7939.1196] [Topology ] . ( 5 sec) [ -7938.8803] [Topology ] . ( 6 sec) [ -7938.7734] [Topology ] . ( 6 sec) [ -7938.7010] [Topology ] . ( 7 sec) [ -7938.5453] [Topology ] . ( 8 sec) [ -7936.6980] [Topology ] . Before opt ts/t=1.000000 LK=-7935.798149 . ( 9 sec) [ -7935.7576] [GTR parameters ] . ( 9 sec) [ -7935.6997] [Alpha ][ 1.026029] . ( 9 sec) [ -7935.6997] [Topology ] . ( 10 sec) [ -7935.4675] [Topology ] . ( 11 sec) [ -7935.3702] [Topology ] . ( 12 sec) [ -7935.3500] [Topology ] . ( 13 sec) [ -7935.3422] [Topology ] . ( 14 sec) [ -7935.3386] [Topology ] . ( 15 sec) [ -7935.3369] [Topology ] . ( 15 sec) [ -7935.3360] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7935.336011 . ( 21 sec) [ -7935.3345] [GTR parameters ] . ( 21 sec) [ -7935.3344] [Alpha ][ 1.027305] . ( 21 sec) [ -7935.3344] [Topology ] . ( 22 sec) [ -7935.3339] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7935.333949 . ( 27 sec) [ -7935.3339] [GTR parameters ] . ( 27 sec) [ -7935.3339] [Alpha ][ 1.027305] . ( 27 sec) [ -7935.3339] [Topology ] . ( 28 sec) [ -7935.3337] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 39 sec) [ -7988.1958] [GTR parameters ] . ( 39 sec) [ -7988.1956] [Alpha ][ 0.998171] . ( 39 sec) [ -7988.1635] [ 1628] [depth= 1] . ( 39 sec) [ -7987.6224] [ 1628] [depth= 1] . ( 39 sec) [ -7987.3773] [ 1628] [depth= 1] . ( 39 sec) [ -7984.4829] [ 1628] [depth= 1] . ( 39 sec) [ -7984.0566] [ 1630] [depth= 1] . ( 39 sec) [ -7982.7212] [ 1630] [depth= 1] . ( 39 sec) [ -7981.1481] [ 1628] [depth= 1] . ( 39 sec) [ -7979.5774] [ 1632] [depth= 1] . ( 40 sec) [ -7976.7897] [ 1633] [depth= 1] . ( 40 sec) [ -7968.0716] [ 1638] [depth= 1] . ( 40 sec) [ -7966.7634] [ 1640] [depth= 1] . ( 40 sec) [ -7966.1916] [ 1638] [depth= 1] . ( 40 sec) [ -7964.7461] [ 1640] [depth= 1] . ( 40 sec) [ -7963.2952] [ 1641] [depth= 1] . ( 40 sec) [ -7963.1830] [ 1642] [depth= 1] . ( 40 sec) [ -7962.0833] [ 1639] [depth= 1] . ( 41 sec) [ -7961.4020] [ 1643] [depth= 1] . ( 42 sec) [ -7961.3089] [ 1645] [depth= 1] . ( 42 sec) [ -7961.2720] [ 1641] [depth= 1] . ( 42 sec) [ -7959.8943] [ 1641] [depth= 1] . ( 43 sec) [ -7939.1251] [Branch lengths ] . ( 43 sec) [ -7939.0429] [GTR parameters ] . ( 44 sec) [ -7939.0243] [Alpha ][ 1.014460] . ( 44 sec) [ -7939.0007] [ 1641] [depth= 1] . ( 44 sec) [ -7938.2809] [ 1639] [depth= 1] . ( 46 sec) [ -7937.1521] [ 1635] [depth= 1] . ( 48 sec) [ -7935.7476] [Branch lengths ] . ( 48 sec) [ -7935.7387] [GTR parameters ] . ( 49 sec) [ -7935.7299] [Alpha ][ 1.025762] . ( 53 sec) [ -7935.6495] [Branch lengths ] . ( 59 sec) [ -7935.5950] [ 1636] [depth= 1] . ( 73 sec) [ -7935.5171] [Branch lengths ] . ( 73 sec) [ -7935.5169] [GTR parameters ] . ( 73 sec) [ -7935.5167] [Alpha ][ 1.026997] . ( 73 sec) [ -7935.5167] [Topology ] . ( 74 sec) [ -7935.5149] [Topology ] . ( 74 sec) [ -7935.5144] [Topology ] . ( 74 sec) [ -7935.5144] [GTR parameters ] . ( 75 sec) [ -7935.5144] [Alpha ][ 1.026997] . ( 75 sec) [ -7935.5144] [Topology ] . ( 75 sec) [ -7935.5141] [Topology ] . ( 75 sec) [ -7935.5141] [GTR parameters ] . ( 75 sec) [ -7935.5141] [Alpha ][ 1.026997] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7935.333689 . Log likelihood obtained after SPR moves : -7935.514145 . Log likelihood of the current tree: -7935.333689. . Printing the most likely tree in file 'data79.phy_phyml_tree.txt'... . Time used 0h1m21s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo