.......................... 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] . ( 2 sec) [ -7790.3934] [ 1390] [depth= 1] . ( 2 sec) [ -7780.7630] [ 1392] [depth= 1] . ( 2 sec) [ -7772.7156] [ 1390] [depth= 1] . ( 2 sec) [ -7770.5775] [ 1388] [depth= 1] . ( 2 sec) [ -7767.6349] [ 1390] [depth= 1] . ( 2 sec) [ -7762.5253] [ 1389] [depth= 1] . ( 2 sec) [ -7753.2366] [ 1384] [depth= 1] . ( 3 sec) [ -7751.6072] [ 1383] [depth= 1] . ( 3 sec) [ -7750.3527] [ 1384] [depth= 1] . ( 3 sec) [ -7750.1659] [ 1384] [depth= 1] . ( 3 sec) [ -7749.7937] [ 1380] [depth= 2] . ( 3 sec) [ -7746.6235] [ 1379] [depth= 1] . ( 3 sec) [ -7727.1260] [ 1379] [depth= 2] . ( 3 sec) [ -7725.1616] [ 1378] [depth= 2] . ( 3 sec) [ -7724.9374] [ 1375] [depth= 2] . ( 3 sec) [ -7721.9866] [ 1373] [depth= 1] . ( 4 sec) [ -7718.0482] [ 1371] [depth= 1] . ( 4 sec) [ -7716.0328] [ 1372] [depth= 2] . ( 4 sec) [ -7714.6230] [ 1374] [depth= 1] . ( 4 sec) [ -7712.6430] [ 1372] [depth= 1] . ( 4 sec) [ -7710.0737] [ 1370] [depth= 3] . ( 4 sec) [ -7706.1817] [ 1365] [depth= 1] . ( 4 sec) [ -7705.6485] [ 1366] [depth= 1] . ( 5 sec) [ -7692.6834] [ 1371] [depth= 1] . ( 5 sec) [ -7692.3938] [ 1371] [depth= 1] . ( 5 sec) [ -7691.9334] [ 1371] [depth= 1] . ( 5 sec) [ -7691.4335] [ 1371] [depth= 1] . ( 5 sec) [ -7691.4091] [ 1371] [depth= 3] . ( 5 sec) [ -7691.3212] [ 1371] [depth= 3] . ( 5 sec) [ -7690.8156] [ 1371] [depth= 1] . ( 5 sec) [ -7684.8985] [ 1366] [depth= 1] . ( 6 sec) [ -7682.6111] [ 1368] [depth= 2] . ( 6 sec) [ -7681.0068] [ 1366] [depth= 1] . ( 6 sec) [ -7672.1283] [ 1367] [depth= 4] . ( 6 sec) [ -7669.8978] [ 1366] [depth= 1] . ( 6 sec) [ -7665.4158] [ 1364] [depth= 1] . ( 6 sec) [ -7657.0635] [ 1363] [depth= 2] . ( 6 sec) [ -7652.0370] [ 1364] [depth= 4] . ( 7 sec) [ -7651.3717] [ 1364] [depth= 1] . ( 8 sec) [ -7650.4078] [ 1361] [depth= 2] . ( 9 sec) [ -7650.2644] [ 1360] [depth= 2] . ( 9 sec) [ -7649.2167] [ 1364] [depth= 1] . ( 12 sec) [ -7614.2902] [Branch lengths ] . ( 12 sec) [ -7612.3626] [GTR parameters ] . ( 12 sec) [ -7604.6228] [Alpha ][ 0.379693] . ( 12 sec) [ -7603.5880] [ 1360] [depth= 1] . ( 13 sec) [ -7602.9717] [ 1350] [depth= 4] . ( 13 sec) [ -7601.7044] [ 1349] [depth= 2] . ( 14 sec) [ -7601.3500] [ 1348] [depth= 1] . ( 14 sec) [ -7601.2784] [ 1350] [depth= 1] . ( 14 sec) [ -7590.8202] [ 1349] [depth= 7] . ( 14 sec) [ -7590.3864] [ 1350] [depth= 1] . ( 15 sec) [ -7590.3461] [ 1351] [depth= 1] . ( 17 sec) [ -7589.4481] [ 1349] [depth= 1] . ( 17 sec) [ -7589.1696] [ 1348] [depth= 1] . ( 17 sec) [ -7587.5993] [ 1348] [depth= 1] . ( 18 sec) [ -7587.5770] [ 1350] [depth= 1] . ( 18 sec) [ -7583.8405] [ 1351] [depth= 1] . ( 18 sec) [ -7582.9821] [ 1350] [depth= 2] . ( 18 sec) [ -7581.4845] [ 1349] [depth= 1] . ( 19 sec) [ -7581.1903] [ 1352] [depth= 1] . ( 24 sec) [ -7572.8917] [Branch lengths ] . ( 24 sec) [ -7572.5328] [GTR parameters ] . ( 24 sec) [ -7572.5008] [Alpha ][ 0.386412] . ( 27 sec) [ -7572.4363] [ 1355] [depth= 1] . ( 34 sec) [ -7572.3025] [ 1351] [depth= 1] . ( 35 sec) [ -7571.0906] [ 1352] [depth= 2] . ( 40 sec) [ -7570.2470] [Branch lengths ] . ( 41 sec) [ -7570.2305] [GTR parameters ] . ( 41 sec) [ -7570.2288] [Alpha ][ 0.384822] . ( 47 sec) [ -7570.1497] [ 1351] [depth= 2] . ( 56 sec) [ -7569.9900] [Branch lengths ] . ( 56 sec) [ -7569.9889] [GTR parameters ] . ( 56 sec) [ -7569.9887] [Alpha ][ 0.385219] . ( 98 sec) [ -7569.8696] [Branch lengths ] . ( 98 sec) [ -7569.8696] [Topology ] . ( 99 sec) [ -7569.8648] [Topology ] . ( 100 sec) [ -7569.8640] [Topology ] . ( 100 sec) [ -7569.8639] [GTR parameters ] . ( 100 sec) [ -7569.8639] [Alpha ][ 0.385219] . ( 100 sec) [ -7569.8639] [Topology ] . ( 101 sec) [ -7569.8637] [Topology ] . ( 101 sec) [ -7569.8637] [GTR parameters ] . ( 101 sec) [ -7569.8637] [Alpha ][ 0.385219] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7569.863686. . Printing the most likely tree in file 'nucleic_M2902_51x908_2006.phy_phyml_tree.txt'... . Time used 0h1m50s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 107.18user 0.00system 1:50.17elapsed 97%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps