.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data75.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... . 452 patterns found. (out of a total of 500 sites) . 45 sites without polymorphism (9.00%). . 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=-11926.345408 . ( 1 sec) [ -11920.9976] [GTR parameters ] . ( 1 sec) [ -11920.2947] [Alpha ][ 0.921942] . ( 1 sec) [ -11920.2947] [Topology ] . ( 2 sec) [ -11833.5228] [Topology ] . ( 3 sec) [ -11820.3464] [Topology ] . ( 4 sec) [ -11817.2226] [Topology ] . ( 5 sec) [ -11815.9974] [Topology ] . ( 6 sec) [ -11815.4346] [Topology ] . ( 7 sec) [ -11815.1196] [Topology ] . ( 8 sec) [ -11814.7511] [Topology ] . ( 9 sec) [ -11814.6249] [Topology ] . ( 10 sec) [ -11814.5406] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-11814.427333 . ( 18 sec) [ -11814.3787] [GTR parameters ] . ( 18 sec) [ -11814.1596] [Alpha ][ 0.962056] . ( 18 sec) [ -11814.1596] [Topology ] . ( 19 sec) [ -11814.1196] [Topology ] . ( 20 sec) [ -11814.1055] [Topology ] . ( 21 sec) [ -11814.0985] [Topology ] . ( 22 sec) [ -11814.0949] [Topology ] . ( 23 sec) [ -11814.0930] [Topology ] . ( 24 sec) [ -11814.0919] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-11814.091919 . ( 33 sec) [ -11814.0918] [GTR parameters ] . ( 33 sec) [ -11814.0911] [Alpha ][ 0.964293] . ( 33 sec) [ -11814.0911] [Topology ] . ( 34 sec) [ -11814.0905] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-11814.090495 . ( 44 sec) [ -11814.0905] [GTR parameters ] . ( 44 sec) [ -11814.0905] [Alpha ][ 0.964293] . ( 44 sec) [ -11814.0905] [Topology ] . ( 46 sec) [ -11814.0902] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 67 sec) [ -11920.9976] [GTR parameters ] . ( 67 sec) [ -11920.2947] [Alpha ][ 0.921942] . ( 68 sec) [ -11914.3240] [ 2871] [depth= 1] . ( 68 sec) [ -11914.2976] [ 2869] [depth= 1] . ( 68 sec) [ -11908.1470] [ 2884] [depth= 1] . ( 68 sec) [ -11906.9168] [ 2869] [depth= 1] . ( 68 sec) [ -11896.3047] [ 2887] [depth= 1] . ( 68 sec) [ -11895.6716] [ 2879] [depth= 1] . ( 69 sec) [ -11892.5120] [ 2884] [depth= 1] . ( 69 sec) [ -11891.3093] [ 2885] [depth= 1] . ( 69 sec) [ -11884.4806] [ 2884] [depth= 1] . ( 69 sec) [ -11883.8250] [ 2877] [depth= 2] . ( 70 sec) [ -11883.3826] [ 2879] [depth= 1] . ( 70 sec) [ -11879.9963] [ 2877] [depth= 1] . ( 70 sec) [ -11876.7966] [ 2876] [depth= 1] . ( 70 sec) [ -11863.8751] [ 2855] [depth= 1] . ( 71 sec) [ -11862.8002] [ 2857] [depth= 1] . ( 71 sec) [ -11861.6249] [ 2855] [depth= 1] . ( 71 sec) [ -11861.3189] [ 2862] [depth= 1] . ( 72 sec) [ -11861.0463] [ 2855] [depth= 1] . ( 72 sec) [ -11819.9309] [Branch lengths ] . ( 73 sec) [ -11819.9001] [GTR parameters ] . ( 73 sec) [ -11819.7776] [Alpha ][ 0.952221] . ( 74 sec) [ -11819.3410] [ 2857] [depth= 1] . ( 76 sec) [ -11818.2117] [ 2861] [depth= 1] . ( 76 sec) [ -11818.1267] [ 2866] [depth= 1] . ( 78 sec) [ -11815.0661] [Branch lengths ] . ( 79 sec) [ -11815.0633] [GTR parameters ] . ( 79 sec) [ -11815.0514] [Alpha ][ 0.961827] . ( 84 sec) [ -11814.7572] [Branch lengths ] . ( 119 sec) [ -11814.7187] [Branch lengths ] . ( 119 sec) [ -11814.7187] [Topology ] . ( 120 sec) [ -11814.6991] [Topology ] . ( 122 sec) [ -11814.6023] [Topology ] . ( 123 sec) [ -11814.2848] [Topology ] . ( 124 sec) [ -11814.1693] [Topology ] . ( 125 sec) [ -11814.1245] [Topology ] . ( 126 sec) [ -11814.1059] [Topology ] . ( 128 sec) [ -11814.0982] [Topology ] . ( 128 sec) [ -11814.0969] [GTR parameters ] . ( 128 sec) [ -11814.0959] [Alpha ][ 0.964479] . ( 128 sec) [ -11814.0959] [Topology ] . ( 129 sec) [ -11814.0925] [Topology ] . ( 131 sec) [ -11814.0911] [Topology ] . ( 132 sec) [ -11814.0904] [Topology ] . ( 132 sec) [ -11814.0904] [GTR parameters ] . ( 132 sec) [ -11814.0904] [Alpha ][ 0.964479] . ( 132 sec) [ -11814.0904] [Topology ] . ( 133 sec) [ -11814.0901] [Topology ] . ( 134 sec) [ -11814.0901] [GTR parameters ] . ( 134 sec) [ -11814.0901] [Alpha ][ 0.964479] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -11814.090161 . Log likelihood obtained after SPR moves : -11814.090054 . Log likelihood of the current tree: -11814.090054. . Printing the most likely tree in file 'data75.phy_phyml_tree.txt'... . Time used 0h2m24s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo