.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data23.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... . 442 patterns found. (out of a total of 500 sites) . 57 sites without polymorphism (11.40%). . 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=-11139.762588 . ( 2 sec) [ -11134.8438] [GTR parameters ] . ( 2 sec) [ -11133.7157] [Alpha ][ 0.897560] . ( 2 sec) [ -11133.7157] [Topology ] . ( 3 sec) [ -11071.6927] [Topology ] . ( 4 sec) [ -11062.4220] [Topology ] . ( 6 sec) [ -11059.6633] [Topology ] . ( 6 sec) [ -11058.5159] [Topology ] . ( 7 sec) [ -11057.9695] [Topology ] . ( 8 sec) [ -11057.7608] [Topology ] . ( 9 sec) [ -11057.6626] [Topology ] . ( 10 sec) [ -11057.6133] [Topology ] . ( 11 sec) [ -11057.5878] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-11057.574544 . ( 21 sec) [ -11057.4909] [GTR parameters ] . ( 21 sec) [ -11057.2749] [Alpha ][ 0.939065] . ( 21 sec) [ -11057.2749] [Topology ] . ( 22 sec) [ -11057.2482] [Topology ] . ( 24 sec) [ -11057.2386] [Topology ] . ( 25 sec) [ -11057.2339] [Topology ] . ( 27 sec) [ -11057.2316] [Topology ] . ( 28 sec) [ -11057.2304] [Topology ] . ( 29 sec) [ -11057.2297] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-11057.229712 . ( 41 sec) [ -11057.2296] [GTR parameters ] . ( 41 sec) [ -11057.2280] [Alpha ][ 0.942620] . ( 41 sec) [ -11057.2280] [Topology ] . ( 43 sec) [ -11057.2275] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-11057.227516 . ( 52 sec) [ -11057.2275] [GTR parameters ] . ( 52 sec) [ -11057.2275] [Alpha ][ 0.942620] . ( 52 sec) [ -11057.2275] [Topology ] . ( 53 sec) [ -11057.2273] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 75 sec) [ -11134.8438] [GTR parameters ] . ( 75 sec) [ -11133.7157] [Alpha ][ 0.897560] . ( 75 sec) [ -11125.5894] [ 2561] [depth= 1] . ( 76 sec) [ -11123.1740] [ 2569] [depth= 1] . ( 77 sec) [ -11123.0787] [ 2573] [depth= 1] . ( 77 sec) [ -11120.7119] [ 2569] [depth= 1] . ( 77 sec) [ -11119.8083] [ 2574] [depth= 1] . ( 77 sec) [ -11113.5648] [ 2569] [depth= 1] . ( 77 sec) [ -11113.0493] [ 2567] [depth= 1] . ( 78 sec) [ -11111.2409] [ 2566] [depth= 1] . ( 78 sec) [ -11111.1637] [ 2570] [depth= 1] . ( 79 sec) [ -11103.3330] [ 2575] [depth= 1] . ( 79 sec) [ -11102.3404] [ 2575] [depth= 1] . ( 79 sec) [ -11096.4944] [ 2580] [depth= 1] . ( 79 sec) [ -11095.2693] [ 2581] [depth= 1] . ( 79 sec) [ -11094.8994] [ 2582] [depth= 1] . ( 80 sec) [ -11091.3796] [ 2584] [depth= 1] . ( 80 sec) [ -11090.2215] [ 2587] [depth= 1] . ( 80 sec) [ -11090.0575] [ 2592] [depth= 1] . ( 81 sec) [ -11067.7339] [Branch lengths ] . ( 81 sec) [ -11067.5809] [GTR parameters ] . ( 81 sec) [ -11067.4411] [Alpha ][ 0.930639] . ( 82 sec) [ -11066.6179] [ 2582] [depth= 1] . ( 83 sec) [ -11066.2286] [ 2578] [depth= 1] . ( 84 sec) [ -11066.0335] [ 2573] [depth= 1] . ( 84 sec) [ -11065.9066] [ 2572] [depth= 1] . ( 84 sec) [ -11065.8336] [ 2565] [depth= 1] . ( 85 sec) [ -11065.6937] [ 2560] [depth= 1] . ( 85 sec) [ -11065.2189] [ 2563] [depth= 1] . ( 85 sec) [ -11058.9520] [Branch lengths ] . ( 86 sec) [ -11058.9407] [GTR parameters ] . ( 86 sec) [ -11058.9340] [Alpha ][ 0.938137] . ( 92 sec) [ -11058.2824] [Branch lengths ] . ( 121 sec) [ -11058.2307] [Branch lengths ] . ( 121 sec) [ -11058.2307] [Topology ] . ( 123 sec) [ -11057.7048] [Topology ] . ( 124 sec) [ -11057.4067] [Topology ] . ( 125 sec) [ -11057.3452] [Topology ] . ( 126 sec) [ -11057.3231] [Topology ] . ( 127 sec) [ -11057.3145] [Topology ] . ( 128 sec) [ -11057.3110] [Topology ] . ( 130 sec) [ -11057.3095] [Topology ] . ( 130 sec) [ -11057.3075] [GTR parameters ] . ( 130 sec) [ -11057.3051] [Alpha ][ 0.942669] . ( 130 sec) [ -11057.3051] [Topology ] . ( 131 sec) [ -11057.3043] [Topology ] . ( 131 sec) [ -11057.3043] [GTR parameters ] . ( 132 sec) [ -11057.3043] [Alpha ][ 0.942669] . Checking for NNIs, optimizing five branches... . ( 142 sec) [ -11057.2458] [Topology ] . Checking for NNIs, optimizing five branches... . ( 154 sec) [ -11057.2456] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -11057.227268 . Log likelihood obtained after SPR moves : -11057.245610 . Log likelihood of the current tree: -11057.227268. . Printing the most likely tree in file 'data23.phy_phyml_tree.txt'... . Time used 0h2m44s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo