.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2655_50x872_2006.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 . 1 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 374 patterns found. (out of a total of 872 sites) . 550 sites without polymorphism (63.07%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 10Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 2 sec) [ -6841.6794] [GTR parameters ] . ( 2 sec) [ -6721.7547] [Alpha ][ 0.500960] . ( 2 sec) [ -6721.7547] [Topology ] . ( 3 sec) [ -6612.7666] [Topology ] . ( 4 sec) [ -6594.7043] [Topology ] . ( 5 sec) [ -6588.9103] [Topology ] . ( 5 sec) [ -6587.3875] [Topology ] . ( 6 sec) [ -6586.8383] [Topology ] . ( 7 sec) [ -6586.3648] [Topology ] . ( 8 sec) [ -6586.2689] [Topology ] . ( 9 sec) [ -6586.2243] [Topology ] . ( 10 sec) [ -6586.1240] [Topology ] . Checking for NNIs, optimizing five branches... . ( 16 sec) [ -6584.3212] [Topology ] . ( 18 sec) [ -6582.0995] [GTR parameters ] . ( 18 sec) [ -6525.0173] [Alpha ][ 0.250961] . ( 18 sec) [ -6525.0173] [Topology ] . ( 19 sec) [ -6522.2195] [Topology ] . ( 19 sec) [ -6520.3490] [Topology ] . ( 20 sec) [ -6519.9884] [Topology ] . ( 21 sec) [ -6519.8839] [Topology ] . ( 22 sec) [ -6519.8444] [Topology ] . ( 23 sec) [ -6519.8279] [Topology ] . ( 24 sec) [ -6519.8204] [Topology ] . Checking for NNIs, optimizing five branches... . ( 31 sec) [ -6518.8123] [GTR parameters ] . ( 31 sec) [ -6518.2445] [Alpha ][ 0.234545] . ( 31 sec) [ -6518.2445] [Topology ] . ( 32 sec) [ -6518.2141] [Topology ] . ( 33 sec) [ -6518.2079] [Topology ] . ( 34 sec) [ -6518.2054] [Topology ] . ( 34 sec) [ -6518.2043] [Topology ] . ( 35 sec) [ -6518.2038] [Topology ] . Checking for NNIs, optimizing five branches... . ( 42 sec) [ -6518.1914] [GTR parameters ] . ( 42 sec) [ -6518.1893] [Alpha ][ 0.233524] . ( 43 sec) [ -6518.1893] [Topology ] . ( 43 sec) [ -6518.1887] [Topology ] . Checking for NNIs, optimizing five branches... . ( 50 sec) [ -6518.1886] [GTR parameters ] . ( 50 sec) [ -6518.1886] [Alpha ][ 0.233524] . ( 50 sec) [ -6518.1886] [Topology ] . ( 51 sec) [ -6518.1884] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 66 sec) [ -6841.6794] [GTR parameters ] . ( 66 sec) [ -6721.7547] [Alpha ][ 0.500960] . ( 66 sec) [ -6719.2727] [ 1115] [depth= 1] . ( 66 sec) [ -6718.1728] [ 1115] [depth= 1] . ( 66 sec) [ -6713.9543] [ 1115] [depth= 1] . ( 66 sec) [ -6713.8010] [ 1115] [depth= 1] . ( 67 sec) [ -6709.1247] [ 1118] [depth= 1] . ( 67 sec) [ -6708.8321] [ 1121] [depth= 1] . ( 67 sec) [ -6705.1067] [ 1118] [depth= 1] . ( 67 sec) [ -6700.9852] [ 1118] [depth= 1] . ( 67 sec) [ -6699.3761] [ 1116] [depth= 1] . ( 68 sec) [ -6693.9948] [ 1117] [depth= 1] . ( 68 sec) [ -6691.2533] [ 1116] [depth= 1] . ( 68 sec) [ -6691.2330] [ 1117] [depth= 1] . ( 68 sec) [ -6691.1180] [ 1116] [depth= 1] . ( 68 sec) [ -6690.6112] [ 1118] [depth= 1] . ( 68 sec) [ -6686.5190] [ 1116] [depth= 1] . ( 68 sec) [ -6686.3195] [ 1115] [depth= 1] . ( 69 sec) [ -6676.8829] [ 1115] [depth= 1] . ( 69 sec) [ -6674.2944] [ 1114] [depth= 3] . ( 69 sec) [ -6670.7428] [ 1117] [depth= 2] . ( 69 sec) [ -6670.3121] [ 1117] [depth= 1] . ( 69 sec) [ -6666.3950] [ 1115] [depth= 2] . ( 69 sec) [ -6663.4249] [ 1112] [depth= 1] . ( 69 sec) [ -6655.0619] [ 1122] [depth= 1] . ( 69 sec) [ -6653.8756] [ 1126] [depth= 1] . ( 70 sec) [ -6650.9100] [ 1122] [depth= 1] . ( 70 sec) [ -6649.2546] [ 1122] [depth= 3] . ( 70 sec) [ -6648.1506] [ 1124] [depth= 1] . ( 70 sec) [ -6643.1100] [ 1123] [depth= 1] . ( 71 sec) [ -6637.6858] [ 1121] [depth= 1] . ( 71 sec) [ -6636.7553] [ 1120] [depth= 1] . ( 71 sec) [ -6634.2796] [ 1121] [depth= 1] . ( 72 sec) [ -6632.7635] [ 1120] [depth= 1] . ( 72 sec) [ -6591.5811] [Branch lengths ] . ( 73 sec) [ -6589.6343] [GTR parameters ] . ( 73 sec) [ -6531.5745] [Alpha ][ 0.250961] . ( 74 sec) [ -6531.5263] [ 1120] [depth= 1] . ( 74 sec) [ -6530.3439] [ 1112] [depth= 3] . ( 74 sec) [ -6529.3058] [ 1112] [depth= 1] . ( 74 sec) [ -6525.2579] [ 1111] [depth= 2] . ( 75 sec) [ -6523.6616] [ 1113] [depth= 1] . ( 76 sec) [ -6523.5481] [ 1113] [depth= 1] . ( 76 sec) [ -6522.7050] [ 1112] [depth= 2] . ( 77 sec) [ -6518.7362] [ 1111] [depth= 1] . ( 80 sec) [ -6514.0203] [Branch lengths ] . ( 81 sec) [ -6512.7762] [GTR parameters ] . ( 81 sec) [ -6512.1188] [Alpha ][ 0.233131] . ( 81 sec) [ -6512.0400] [ 1111] [depth= 1] . ( 82 sec) [ -6511.9404] [ 1111] [depth= 1] . ( 88 sec) [ -6511.5722] [Branch lengths ] . ( 89 sec) [ -6511.5536] [GTR parameters ] . ( 89 sec) [ -6511.5531] [Alpha ][ 0.232627] . ( 118 sec) [ -6511.5248] [Branch lengths ] . ( 118 sec) [ -6511.5248] [Topology ] . ( 119 sec) [ -6511.5234] [Topology ] . ( 120 sec) [ -6511.5229] [Topology ] . ( 121 sec) [ -6511.5227] [GTR parameters ] . ( 121 sec) [ -6511.5227] [Alpha ][ 0.232627] . ( 121 sec) [ -6511.5227] [Topology ] . ( 122 sec) [ -6511.5225] [Topology ] . ( 122 sec) [ -6511.5225] [GTR parameters ] . ( 122 sec) [ -6511.5225] [Alpha ][ 0.232627] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -6518.188398 . Log likelihood obtained after SPR moves : -6511.522478 . Log likelihood of the current tree: -6511.522478. . Printing the most likely tree in file 'nucleic_M2655_50x872_2006.phy_phyml_tree.txt'... . Time used 0h2m8s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 127.44user 0.00system 2:08.35elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps