.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2588_68x1196_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 : NNIs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 6 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 730 patterns found. (out of a total of 1196 sites) . 526 sites without polymorphism (43.98%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 26Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 5 sec) [ -12703.7048] [GTR parameters ] . ( 5 sec) [ -12506.3721] [Alpha ][ 0.500960] . ( 5 sec) [ -12506.3721] [Topology ] . ( 7 sec) [ -12215.6080] [Topology ] . ( 9 sec) [ -12152.0977] [Topology ] . ( 11 sec) [ -12139.1352] [Topology ] . ( 13 sec) [ -12126.7129] [Topology ] . ( 15 sec) [ -12130.9985] [Topology ] . Moving backward . ( 15 sec) [ -12121.4353] [Topology ] . ( 17 sec) [ -12122.7329] [Topology ] . Moving backward . ( 18 sec) [ -12118.4950] [Topology ] . ( 19 sec) [ -12116.6881] [Topology ] . ( 24 sec) [ -12094.3714] [GTR parameters ] . ( 24 sec) [ -12054.0715] [Alpha ][ 0.324674] . ( 24 sec) [ -12054.0715] [Topology ] . ( 26 sec) [ -12046.5550] [Topology ] . ( 28 sec) [ -12049.9254] [Topology ] . Moving backward . ( 28 sec) [ -12041.0508] [Topology ] . ( 30 sec) [ -12039.5299] [Topology ] . ( 32 sec) [ -12040.3282] [Topology ] . Moving backward . ( 32 sec) [ -12035.7717] [Topology ] . ( 34 sec) [ -12034.7699] [Topology ] . ( 36 sec) [ -12034.6451] [Topology ] . ( 38 sec) [ -12034.0025] [Topology ] . Checking for NNIs, optimizing five branches... . ( 54 sec) [ -12034.0255] [Topology ] . ( 56 sec) [ -12030.5971] [GTR parameters ] . ( 56 sec) [ -12029.8024] [Alpha ][ 0.306568] . ( 56 sec) [ -12029.8024] [Topology ] . ( 58 sec) [ -12029.0738] [Topology ] . ( 60 sec) [ -12029.0786] [Topology ] . Moving backward . ( 60 sec) [ -12028.8782] [Topology ] . ( 62 sec) [ -12028.8209] [Topology ] . ( 64 sec) [ -12029.0361] [Topology ] . Moving backward . ( 64 sec) [ -12028.6691] [Topology ] . ( 66 sec) [ -12028.6702] [Topology ] . Moving backward . ( 66 sec) [ -12028.5546] [Topology ] . ( 68 sec) [ -12028.4954] [Topology ] . Checking for NNIs, optimizing five branches... . ( 83 sec) [ -12028.4944] [Topology ] . ( 84 sec) [ -12028.2370] [GTR parameters ] . ( 85 sec) [ -12028.1961] [Alpha ][ 0.302803] . ( 85 sec) [ -12028.1961] [Topology ] . ( 87 sec) [ -12028.0997] [Topology ] . ( 88 sec) [ -12028.1125] [Topology ] . Moving backward . ( 88 sec) [ -12028.0660] [Topology ] . ( 90 sec) [ -12028.1322] [Topology ] . Moving backward . ( 90 sec) [ -12028.0427] [Topology ] . ( 92 sec) [ -12028.0742] [Topology ] . Moving backward . ( 92 sec) [ -12028.0259] [Topology ] . ( 94 sec) [ -12028.1259] [Topology ] . Moving backward . ( 94 sec) [ -12028.0120] [Topology ] . Checking for NNIs, optimizing five branches... . ( 111 sec) [ -12028.0710] [Topology ] . ( 112 sec) [ -12028.0401] [GTR parameters ] . ( 113 sec) [ -12028.0365] [Alpha ][ 0.301588] . ( 113 sec) [ -12028.0365] [Topology ] . ( 115 sec) [ -12028.0205] [Topology ] . ( 116 sec) [ -12028.4083] [Topology ] . Moving backward . ( 117 sec) [ -12027.9769] [Topology ] . ( 119 sec) [ -12028.0037] [Topology ] . Moving backward . ( 119 sec) [ -12027.8763] [Topology ] . ( 121 sec) [ -12027.8675] [Topology ] . ( 122 sec) [ -12027.9072] [Topology ] . Moving backward . ( 123 sec) [ -12027.8644] [Topology ] . ( 124 sec) [ -12027.9897] [Topology ] . Checking for NNIs, optimizing five branches... . ( 139 sec) [ -12027.8083] [Topology ] . ( 141 sec) [ -12027.8011] [GTR parameters ] . ( 141 sec) [ -12027.8005] [Alpha ][ 0.301093] . ( 141 sec) [ -12027.8005] [Topology ] . ( 143 sec) [ -12027.7950] [Topology ] . ( 144 sec) [ -12027.8067] [Topology ] . Moving backward . ( 145 sec) [ -12027.7946] [Topology ] . Checking for NNIs, optimizing five branches... . ( 159 sec) [ -12027.7925] [Topology ] . ( 160 sec) [ -12027.7921] [GTR parameters ] . ( 160 sec) [ -12027.7921] [Alpha ][ 0.301093] . ( 160 sec) [ -12027.7921] [Topology ] . ( 162 sec) [ -12027.7894] [Topology ] . ( 164 sec) [ -12027.7894] [Topology ] . Checking for NNIs, optimizing five branches... . ( 178 sec) [ -12027.7807] [Topology ] . ( 179 sec) [ -12027.7806] [GTR parameters ] . ( 179 sec) [ -12027.7806] [Alpha ][ 0.301093] . ( 179 sec) [ -12027.7806] [Topology ] . ( 181 sec) [ -12027.7797] [Topology ] . Checking for NNIs, optimizing five branches... . ( 195 sec) [ -12027.7796] [Topology ] . ( 196 sec) [ -12027.7796] [GTR parameters ] . ( 196 sec) [ -12027.7796] [Alpha ][ 0.301093] . ( 196 sec) [ -12027.7796] [Topology ] . ( 198 sec) [ -12027.7790] [Topology ] . Checking for NNIs, optimizing five branches... . ( 212 sec) [ -12027.7789] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12027.778921. . Printing the most likely tree in file 'nucleic_M2588_68x1196_2006.phy_phyml_tree.txt'... . Time used 0h3m47s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 226.38user 0.00system 3:47.95elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps