.......................... 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)... . ( 1 sec) [ -7873.6472] [GTR parameters ] . ( 1 sec) [ -7790.9479] [Alpha ][ 0.500960] . ( 8 sec) [ -7790.3934] [ 1390] [depth= 1] . ( 12 sec) [ -7780.7630] [ 1392] [depth= 1] . ( 12 sec) [ -7772.7156] [ 1390] [depth= 1] . ( 12 sec) [ -7770.5775] [ 1388] [depth= 1] . ( 12 sec) [ -7767.6349] [ 1390] [depth= 1] . ( 17 sec) [ -7762.5253] [ 1389] [depth= 1] . ( 17 sec) [ -7753.2366] [ 1384] [depth= 1] . ( 17 sec) [ -7751.6072] [ 1383] [depth= 1] . ( 18 sec) [ -7750.3527] [ 1384] [depth= 1] . ( 21 sec) [ -7750.1659] [ 1384] [depth= 1] . ( 21 sec) [ -7749.7937] [ 1380] [depth= 2] . ( 21 sec) [ -7746.6235] [ 1379] [depth= 1] . ( 21 sec) [ -7727.1260] [ 1379] [depth= 2] . ( 23 sec) [ -7725.1616] [ 1378] [depth= 2] . ( 23 sec) [ -7724.9374] [ 1375] [depth= 2] . ( 24 sec) [ -7721.9866] [ 1373] [depth= 1] . ( 24 sec) [ -7718.0482] [ 1371] [depth= 1] . ( 26 sec) [ -7716.0328] [ 1372] [depth= 2] . ( 27 sec) [ -7715.4329] [ 1379] [depth= 2] . ( 27 sec) [ -7715.0499] [ 1381] [depth= 1] . ( 27 sec) [ -7712.6170] [ 1378] [depth= 1] . ( 27 sec) [ -7706.1897] [ 1375] [depth= 3] . ( 27 sec) [ -7704.0621] [ 1373] [depth= 1] . ( 28 sec) [ -7701.2816] [ 1380] [depth= 4] . ( 28 sec) [ -7700.9341] [ 1381] [depth= 1] . ( 28 sec) [ -7696.5966] [ 1383] [depth= 1] . ( 28 sec) [ -7695.9466] [ 1380] [depth= 1] . ( 30 sec) [ -7695.6604] [ 1380] [depth= 1] . ( 30 sec) [ -7695.2065] [ 1380] [depth= 1] . ( 30 sec) [ -7694.7098] [ 1380] [depth= 1] . ( 30 sec) [ -7694.6843] [ 1380] [depth= 3] . ( 30 sec) [ -7694.5932] [ 1380] [depth= 3] . ( 30 sec) [ -7694.1328] [ 1380] [depth= 1] . ( 32 sec) [ -7690.2874] [ 1381] [depth= 3] . ( 33 sec) [ -7686.6427] [ 1380] [depth= 2] . ( 37 sec) [ -7685.9227] [ 1377] [depth= 5] . ( 37 sec) [ -7678.1237] [ 1379] [depth= 4] . ( 39 sec) [ -7675.3396] [ 1376] [depth= 1] . ( 39 sec) [ -7674.4039] [ 1379] [depth= 1] . ( 39 sec) [ -7667.7934] [ 1379] [depth= 4] . ( 39 sec) [ -7667.5132] [ 1378] [depth= 3] . ( 40 sec) [ -7660.7561] [ 1379] [depth= 3] . ( 40 sec) [ -7660.0274] [ 1378] [depth= 1] . ( 42 sec) [ -7659.5109] [ 1381] [depth= 1] . ( 42 sec) [ -7657.9344] [ 1378] [depth= 1] . ( 43 sec) [ -7657.1421] [ 1378] [depth= 2] . ( 43 sec) [ -7655.7267] [ 1378] [depth= 2] . ( 43 sec) [ -7654.6506] [ 1378] [depth= 1] . ( 43 sec) [ -7654.4838] [ 1378] [depth= 1] . ( 43 sec) [ -7652.6917] [ 1376] [depth= 1] . ( 45 sec) [ -7652.0236] [ 1378] [depth= 1] . ( 46 sec) [ -7648.5132] [ 1376] [depth= 1] . ( 55 sec) [ -7620.6210] [Branch lengths ] . ( 55 sec) [ -7618.0346] [GTR parameters ] . ( 55 sec) [ -7609.7658] [Alpha ][ 0.378092] . ( 59 sec) [ -7609.5357] [ 1375] [depth= 1] . ( 60 sec) [ -7607.7914] [ 1371] [depth= 1] . ( 65 sec) [ -7606.1986] [ 1370] [depth= 1] . ( 73 sec) [ -7605.2991] [ 1367] [depth= 4] . ( 73 sec) [ -7604.8996] [ 1369] [depth= 1] . ( 77 sec) [ -7603.2499] [ 1364] [depth= 3] . ( 79 sec) [ -7602.8702] [ 1366] [depth= 1] . ( 82 sec) [ -7601.2019] [ 1364] [depth= 1] . ( 83 sec) [ -7600.8697] [ 1362] [depth= 1] . ( 84 sec) [ -7598.5831] [ 1364] [depth= 1] . ( 90 sec) [ -7598.2472] [ 1364] [depth= 2] . ( 92 sec) [ -7596.1387] [ 1363] [depth= 1] . ( 92 sec) [ -7596.0331] [ 1362] [depth= 1] . ( 99 sec) [ -7595.2280] [ 1360] [depth= 1] . ( 99 sec) [ -7594.4646] [ 1350] [depth= 6] . ( 99 sec) [ -7592.4459] [ 1351] [depth= 1] . ( 108 sec) [ -7591.9897] [ 1350] [depth= 1] . ( 110 sec) [ -7591.6984] [ 1351] [depth= 1] . ( 112 sec) [ -7591.3975] [ 1350] [depth= 1] . ( 117 sec) [ -7590.5286] [ 1348] [depth= 4] . ( 117 sec) [ -7589.6581] [ 1348] [depth= 1] . ( 119 sec) [ -7586.7212] [ 1348] [depth= 1] . ( 134 sec) [ -7577.3900] [Branch lengths ] . ( 134 sec) [ -7577.1511] [GTR parameters ] . ( 134 sec) [ -7577.1430] [Alpha ][ 0.381400] . ( 175 sec) [ -7576.7636] [ 1347] [depth= 2] . ( 187 sec) [ -7576.7478] [ 1350] [depth= 1] . ( 198 sec) [ -7576.4498] [ 1349] [depth= 1] . ( 200 sec) [ -7574.9511] [ 1351] [depth= 1] . ( 209 sec) [ -7574.8454] [ 1351] [depth= 1] . ( 226 sec) [ -7572.9438] [Branch lengths ] . ( 227 sec) [ -7572.9106] [GTR parameters ] . ( 227 sec) [ -7572.9082] [Alpha ][ 0.383176] . ( 254 sec) [ -7572.8413] [ 1350] [depth= 3] . ( 294 sec) [ -7571.5299] [ 1351] [depth= 2] . ( 320 sec) [ -7570.5455] [Branch lengths ] . ( 321 sec) [ -7570.5397] [GTR parameters ] . ( 321 sec) [ -7570.5369] [Alpha ][ 0.385121] . ( 355 sec) [ -7570.5108] [ 1349] [depth= 1] . ( 373 sec) [ -7570.4471] [ 1348] [depth= 2] . ( 415 sec) [ -7570.2402] [Branch lengths ] . ( 415 sec) [ -7570.2383] [GTR parameters ] . ( 416 sec) [ -7570.2381] [Alpha ][ 0.385533] . ( 440 sec) [ -7570.0803] [ 1349] [depth= 1] . ( 458 sec) [ -7569.8740] [Branch lengths ] . ( 458 sec) [ -7569.8735] [GTR parameters ] . ( 458 sec) [ -7569.8735] [Alpha ][ 0.385533] . ( 458 sec) [ -7569.8735] [Topology ] . ( 459 sec) [ -7569.8654] [Topology ] . ( 460 sec) [ -7569.8641] [Topology ] . ( 461 sec) [ -7569.8639] [Topology ] . ( 461 sec) [ -7569.8638] [GTR parameters ] . ( 462 sec) [ -7569.8638] [Alpha ][ 0.385533] . ( 462 sec) [ -7569.8638] [Topology ] . ( 463 sec) [ -7569.8638] [Topology ] . ( 463 sec) [ -7569.8638] [GTR parameters ] . ( 463 sec) [ -7569.8638] [Alpha ][ 0.385533] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7569.863765. . Printing the most likely tree in file 'nucleic_M2902_51x908_2006.phy_phyml_tree.txt'... . Time used 0h7m51s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 470.14user 0.00system 7:51.50elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps