.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2902_51x908_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 : 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... . 467 patterns found. (out of a total of 908 sites) . 480 sites without polymorphism (52.86%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 12Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -7873.6472] [GTR parameters ] . ( 3 sec) [ -7790.9479] [Alpha ][ 0.500960] . ( 3 sec) [ -7790.3934] [ 1390] [depth= 1] . ( 4 sec) [ -7780.7630] [ 1392] [depth= 1] . ( 4 sec) [ -7772.7156] [ 1390] [depth= 1] . ( 4 sec) [ -7770.5775] [ 1388] [depth= 1] . ( 4 sec) [ -7767.6349] [ 1390] [depth= 1] . ( 4 sec) [ -7762.5253] [ 1389] [depth= 1] . ( 4 sec) [ -7753.2366] [ 1384] [depth= 1] . ( 4 sec) [ -7751.6072] [ 1383] [depth= 1] . ( 4 sec) [ -7750.3527] [ 1384] [depth= 1] . ( 4 sec) [ -7750.1659] [ 1384] [depth= 1] . ( 4 sec) [ -7749.7937] [ 1380] [depth= 2] . ( 5 sec) [ -7746.6235] [ 1379] [depth= 1] . ( 5 sec) [ -7727.1260] [ 1379] [depth= 2] . ( 5 sec) [ -7725.1616] [ 1378] [depth= 2] . ( 5 sec) [ -7724.9374] [ 1375] [depth= 2] . ( 5 sec) [ -7721.9866] [ 1373] [depth= 1] . ( 5 sec) [ -7718.0482] [ 1371] [depth= 1] . ( 5 sec) [ -7716.0328] [ 1372] [depth= 2] . ( 5 sec) [ -7714.6230] [ 1374] [depth= 1] . ( 5 sec) [ -7712.6430] [ 1372] [depth= 1] . ( 5 sec) [ -7710.0737] [ 1370] [depth= 3] . ( 5 sec) [ -7706.1817] [ 1365] [depth= 1] . ( 6 sec) [ -7692.1199] [ 1369] [depth= 1] . ( 6 sec) [ -7691.8303] [ 1369] [depth= 1] . ( 6 sec) [ -7691.3709] [ 1369] [depth= 1] . ( 6 sec) [ -7690.8701] [ 1369] [depth= 1] . ( 6 sec) [ -7690.8456] [ 1369] [depth= 3] . ( 6 sec) [ -7690.7580] [ 1369] [depth= 3] . ( 6 sec) [ -7690.2570] [ 1369] [depth= 1] . ( 6 sec) [ -7685.9903] [ 1365] [depth= 1] . ( 7 sec) [ -7677.4637] [ 1365] [depth= 1] . ( 7 sec) [ -7668.9488] [ 1364] [depth= 4] . ( 7 sec) [ -7667.2448] [ 1361] [depth= 4] . ( 7 sec) [ -7666.2868] [ 1359] [depth= 1] . ( 7 sec) [ -7658.3515] [ 1357] [depth= 1] . ( 7 sec) [ -7653.6061] [ 1359] [depth= 3] . ( 7 sec) [ -7649.3271] [ 1355] [depth= 1] . ( 7 sec) [ -7647.9412] [ 1358] [depth= 3] . ( 7 sec) [ -7647.2593] [ 1357] [depth= 2] . ( 7 sec) [ -7646.6216] [ 1357] [depth= 3] . ( 7 sec) [ -7646.2918] [ 1357] [depth= 2] . ( 7 sec) [ -7645.1015] [ 1356] [depth= 1] . ( 8 sec) [ -7644.0135] [ 1355] [depth= 2] . ( 8 sec) [ -7643.9099] [ 1355] [depth= 1] . ( 8 sec) [ -7643.5433] [ 1355] [depth= 1] . ( 8 sec) [ -7642.9601] [ 1353] [depth= 1] . ( 9 sec) [ -7608.8392] [Branch lengths ] . ( 9 sec) [ -7606.0962] [GTR parameters ] . ( 9 sec) [ -7598.7962] [Alpha ][ 0.381924] . ( 10 sec) [ -7595.3386] [ 1351] [depth= 1] . ( 11 sec) [ -7583.3268] [ 1348] [depth= 7] . ( 11 sec) [ -7583.2747] [ 1348] [depth= 1] . ( 11 sec) [ -7583.2380] [ 1348] [depth= 1] . ( 11 sec) [ -7582.8153] [ 1348] [depth= 1] . ( 12 sec) [ -7582.5148] [ 1348] [depth= 1] . ( 12 sec) [ -7582.2633] [ 1348] [depth= 1] . ( 13 sec) [ -7580.6249] [ 1348] [depth= 1] . ( 14 sec) [ -7580.4872] [ 1348] [depth= 1] . ( 15 sec) [ -7575.3138] [Branch lengths ] . ( 15 sec) [ -7575.2424] [GTR parameters ] . ( 15 sec) [ -7575.2414] [Alpha ][ 0.383088] . ( 18 sec) [ -7575.1678] [ 1347] [depth= 2] . ( 20 sec) [ -7574.3789] [Branch lengths ] . ( 20 sec) [ -7574.3753] [GTR parameters ] . ( 20 sec) [ -7574.3747] [Alpha ][ 0.383944] . ( 38 sec) [ -7574.0978] [ 1348] [depth= 2] . ( 40 sec) [ -7573.3961] [ 1347] [depth= 1] . ( 44 sec) [ -7573.3662] [ 1347] [depth= 1] . ( 47 sec) [ -7573.2601] [ 1350] [depth= 1] . ( 55 sec) [ -7571.8603] [ 1349] [depth= 2] . ( 62 sec) [ -7569.3726] [Branch lengths ] . ( 62 sec) [ -7569.3506] [GTR parameters ] . ( 62 sec) [ -7569.3496] [Alpha ][ 0.385082] . ( 104 sec) [ -7569.2718] [Branch lengths ] . ( 104 sec) [ -7569.2718] [Topology ] . ( 105 sec) [ -7569.2695] [Topology ] . ( 106 sec) [ -7569.2691] [Topology ] . ( 106 sec) [ -7569.2691] [GTR parameters ] . ( 106 sec) [ -7569.2691] [Alpha ][ 0.385082] . ( 106 sec) [ -7569.2691] [Topology ] . ( 107 sec) [ -7569.2690] [Topology ] . ( 107 sec) [ -7569.2690] [GTR parameters ] . ( 107 sec) [ -7569.2690] [Alpha ][ 0.385082] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7569.268973. . Printing the most likely tree in file 'nucleic_M2902_51x908_2006.phy_phyml_tree.txt'... . Time used 0h1m55s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 112.29user 0.00system 1:54.99elapsed 97%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps