.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data59.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... . 428 patterns found. (out of a total of 500 sites) . 69 sites without polymorphism (13.80%). . 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=-10186.540847 . ( 1 sec) [ -10185.4470] [GTR parameters ] . ( 1 sec) [ -10184.2698] [Alpha ][ 0.894321] . ( 1 sec) [ -10184.2698] [Topology ] . ( 2 sec) [ -10117.0407] [Topology ] . ( 3 sec) [ -10103.8503] [Topology ] . ( 3 sec) [ -10100.4331] [Topology ] . ( 4 sec) [ -10098.0463] [Topology ] . Moving backward . ( 5 sec) [ -10096.1225] [Topology ] . ( 6 sec) [ -10095.2812] [Topology ] . Moving backward . ( 7 sec) [ -10094.3631] [Topology ] . ( 8 sec) [ -10093.8820] [Topology ] . ( 8 sec) [ -10093.6541] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10093.529204 . ( 17 sec) [ -10093.4996] [GTR parameters ] . ( 17 sec) [ -10093.4945] [Alpha ][ 0.900666] . ( 17 sec) [ -10093.4945] [Topology ] . ( 18 sec) [ -10093.4231] [Topology ] . ( 19 sec) [ -10093.3824] [Topology ] . ( 20 sec) [ -10093.3592] [Topology ] . ( 21 sec) [ -10093.3458] [Topology ] . ( 22 sec) [ -10093.3379] [Topology ] . ( 22 sec) [ -10093.3334] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10093.333388 . ( 31 sec) [ -10093.3333] [GTR parameters ] . ( 31 sec) [ -10093.3329] [Alpha ][ 0.898930] . ( 31 sec) [ -10093.3329] [Topology ] . ( 32 sec) [ -10093.3301] [Topology ] . ( 33 sec) [ -10093.3285] [Topology ] . ( 34 sec) [ -10093.3276] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10093.327553 . ( 43 sec) [ -10093.3275] [GTR parameters ] . ( 44 sec) [ -10093.3275] [Alpha ][ 0.898930] . ( 44 sec) [ -10093.3275] [Topology ] . ( 45 sec) [ -10093.3269] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 60 sec) [ -10185.4470] [GTR parameters ] . ( 60 sec) [ -10184.2698] [Alpha ][ 0.894321] . ( 61 sec) [ -10182.9740] [ 2299] [depth= 1] . ( 61 sec) [ -10180.0792] [ 2297] [depth= 1] . ( 61 sec) [ -10179.8263] [ 2299] [depth= 1] . ( 61 sec) [ -10177.7849] [ 2304] [depth= 1] . ( 61 sec) [ -10167.5027] [ 2299] [depth= 1] . ( 61 sec) [ -10167.3872] [ 2304] [depth= 1] . ( 61 sec) [ -10163.7342] [ 2307] [depth= 1] . ( 61 sec) [ -10160.2715] [ 2304] [depth= 1] . ( 61 sec) [ -10160.1251] [ 2307] [depth= 1] . ( 61 sec) [ -10159.3992] [ 2314] [depth= 1] . ( 62 sec) [ -10155.2995] [ 2313] [depth= 1] . ( 62 sec) [ -10152.6096] [ 2310] [depth= 1] . ( 62 sec) [ -10146.4321] [ 2316] [depth= 1] . ( 62 sec) [ -10145.0402] [ 2316] [depth= 2] . ( 62 sec) [ -10144.7030] [ 2316] [depth= 1] . ( 63 sec) [ -10142.8602] [ 2321] [depth= 1] . ( 63 sec) [ -10138.1476] [ 2317] [depth= 2] . ( 63 sec) [ -10134.4438] [ 2314] [depth= 1] . ( 63 sec) [ -10134.1396] [ 2314] [depth= 1] . ( 63 sec) [ -10132.4188] [ 2313] [depth= 4] . ( 63 sec) [ -10132.1312] [ 2317] [depth= 1] . ( 63 sec) [ -10130.4604] [ 2319] [depth= 2] . ( 64 sec) [ -10130.1124] [ 2314] [depth= 2] . ( 64 sec) [ -10105.3413] [Branch lengths ] . ( 64 sec) [ -10105.3144] [GTR parameters ] . ( 64 sec) [ -10105.3039] [Alpha ][ 0.903639] . ( 65 sec) [ -10102.2877] [ 2307] [depth= 1] . ( 65 sec) [ -10102.0767] [ 2307] [depth= 1] . ( 65 sec) [ -10102.0398] [ 2307] [depth= 1] . ( 65 sec) [ -10100.0875] [ 2309] [depth= 1] . ( 67 sec) [ -10098.1574] [ 2308] [depth= 1] . ( 67 sec) [ -10097.9835] [ 2308] [depth= 1] . ( 68 sec) [ -10097.9547] [ 2311] [depth= 1] . ( 68 sec) [ -10094.1137] [Branch lengths ] . ( 68 sec) [ -10094.1131] [GTR parameters ] . ( 68 sec) [ -10094.1123] [Alpha ][ 0.900992] . ( 71 sec) [ -10091.1737] [ 2313] [depth= 5] . ( 71 sec) [ -10091.0091] [ 2313] [depth= 2] . ( 71 sec) [ -10090.9158] [ 2313] [depth= 1] . ( 71 sec) [ -10090.8286] [ 2313] [depth= 1] . ( 71 sec) [ -10090.7076] [ 2311] [depth= 1] . ( 72 sec) [ -10090.6932] [ 2311] [depth= 1] . ( 72 sec) [ -10089.5990] [Branch lengths ] . ( 73 sec) [ -10089.5622] [GTR parameters ] . ( 73 sec) [ -10089.5594] [Alpha ][ 0.896189] . ( 78 sec) [ -10089.3765] [Branch lengths ] . ( 105 sec) [ -10089.3522] [Branch lengths ] . ( 105 sec) [ -10089.3522] [Topology ] . ( 106 sec) [ -10089.3101] [Topology ] . ( 107 sec) [ -10089.3008] [Topology ] . ( 108 sec) [ -10089.2996] [Topology ] . ( 109 sec) [ -10089.2992] [Topology ] . ( 109 sec) [ -10089.2991] [GTR parameters ] . ( 109 sec) [ -10089.2987] [Alpha ][ 0.894264] . ( 109 sec) [ -10089.2987] [Topology ] . ( 110 sec) [ -10089.2985] [Topology ] . ( 110 sec) [ -10089.2985] [GTR parameters ] . ( 110 sec) [ -10089.2985] [Alpha ][ 0.894264] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10093.326949 . Log likelihood obtained after SPR moves : -10089.298461 . Log likelihood of the current tree: -10089.298461. . Printing the most likely tree in file 'data59.phy_phyml_tree.txt'... . Time used 0h1m58s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo