.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data61.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... . 443 patterns found. (out of a total of 500 sites) . 54 sites without polymorphism (10.80%). . 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=-10669.048113 . ( 0 sec) [ -10666.4815] [GTR parameters ] . ( 0 sec) [ -10666.1551] [Alpha ][ 0.942575] . ( 0 sec) [ -10666.1551] [Topology ] . ( 2 sec) [ -10601.6847] [Topology ] . ( 3 sec) [ -10591.0335] [Topology ] . ( 5 sec) [ -10588.0682] [Topology ] . ( 6 sec) [ -10586.8013] [Topology ] . ( 7 sec) [ -10586.1775] [Topology ] . ( 8 sec) [ -10585.8506] [Topology ] . ( 9 sec) [ -10585.6740] [Topology ] . ( 11 sec) [ -10585.5769] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10585.576851 . ( 19 sec) [ -10585.4824] [GTR parameters ] . ( 19 sec) [ -10585.3893] [Alpha ][ 0.970827] . ( 19 sec) [ -10585.3893] [Topology ] . ( 20 sec) [ -10585.3253] [Topology ] . ( 21 sec) [ -10585.2917] [Topology ] . ( 22 sec) [ -10585.2731] [Topology ] . ( 23 sec) [ -10585.2627] [Topology ] . ( 24 sec) [ -10585.2568] [Topology ] . ( 25 sec) [ -10585.2535] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10585.253512 . ( 33 sec) [ -10585.2534] [GTR parameters ] . ( 33 sec) [ -10585.2530] [Alpha ][ 0.972592] . ( 33 sec) [ -10585.2530] [Topology ] . ( 34 sec) [ -10585.2511] [Topology ] . ( 35 sec) [ -10585.2501] [Topology ] . ( 36 sec) [ -10585.2495] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10585.249466 . ( 43 sec) [ -10585.2495] [GTR parameters ] . ( 43 sec) [ -10585.2495] [Alpha ][ 0.972592] . ( 43 sec) [ -10585.2495] [Topology ] . ( 44 sec) [ -10585.2491] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 58 sec) [ -10666.4815] [GTR parameters ] . ( 58 sec) [ -10666.1551] [Alpha ][ 0.942575] . ( 58 sec) [ -10666.0635] [ 2475] [depth= 1] . ( 59 sec) [ -10663.6758] [ 2475] [depth= 1] . ( 59 sec) [ -10663.2245] [ 2475] [depth= 1] . ( 59 sec) [ -10660.6480] [ 2476] [depth= 1] . ( 59 sec) [ -10660.5665] [ 2479] [depth= 1] . ( 59 sec) [ -10659.2284] [ 2473] [depth= 1] . ( 59 sec) [ -10652.4409] [ 2471] [depth= 1] . ( 59 sec) [ -10651.1805] [ 2470] [depth= 1] . ( 59 sec) [ -10649.2389] [ 2471] [depth= 1] . ( 60 sec) [ -10647.9733] [ 2472] [depth= 1] . ( 60 sec) [ -10644.8117] [ 2471] [depth= 1] . ( 60 sec) [ -10643.6844] [ 2473] [depth= 1] . ( 60 sec) [ -10640.8768] [ 2474] [depth= 1] . ( 60 sec) [ -10640.3771] [ 2473] [depth= 1] . ( 60 sec) [ -10632.6432] [ 2475] [depth= 1] . ( 60 sec) [ -10627.7592] [ 2473] [depth= 1] . ( 60 sec) [ -10622.9803] [ 2470] [depth= 1] . ( 61 sec) [ -10591.0249] [Branch lengths ] . ( 62 sec) [ -10590.9426] [GTR parameters ] . ( 62 sec) [ -10590.8769] [Alpha ][ 0.966371] . ( 62 sec) [ -10589.6656] [ 2471] [depth= 1] . ( 63 sec) [ -10589.6458] [ 2476] [depth= 1] . ( 64 sec) [ -10589.2784] [ 2477] [depth= 1] . ( 65 sec) [ -10587.1672] [Branch lengths ] . ( 65 sec) [ -10587.1644] [GTR parameters ] . ( 65 sec) [ -10587.1612] [Alpha ][ 0.971819] . ( 69 sec) [ -10586.8564] [Branch lengths ] . ( 90 sec) [ -10586.7962] [Branch lengths ] . ( 90 sec) [ -10586.7962] [Topology ] . ( 92 sec) [ -10586.6851] [Topology ] . ( 93 sec) [ -10586.5647] [Topology ] . ( 94 sec) [ -10586.5423] [Topology ] . ( 95 sec) [ -10586.5337] [Topology ] . ( 96 sec) [ -10586.5301] [Topology ] . ( 97 sec) [ -10586.5286] [Topology ] . ( 98 sec) [ -10586.5279] [Topology ] . ( 98 sec) [ -10586.5265] [GTR parameters ] . ( 98 sec) [ -10586.5265] [Alpha ][ 0.971819] . ( 98 sec) [ -10586.5265] [Topology ] . ( 99 sec) [ -10586.5262] [Topology ] . ( 99 sec) [ -10586.5262] [GTR parameters ] . ( 99 sec) [ -10586.5262] [Alpha ][ 0.971819] . Checking for NNIs, optimizing five branches... . ( 106 sec) [ -10585.2593] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10585.249115 . Log likelihood obtained after SPR moves : -10585.259349 . Log likelihood of the current tree: -10585.249115. . Printing the most likely tree in file 'data61.phy_phyml_tree.txt'... . Time used 0h1m52s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo