.......................... 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 : 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... . 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 NNI moves)... . ( 2 sec) [ -7873.6472] [GTR parameters ] . ( 2 sec) [ -7790.9479] [Alpha ][ 0.500960] . ( 2 sec) [ -7790.9479] [Topology ] . ( 3 sec) [ -7695.8151] [Topology ] . ( 4 sec) [ -7654.2234] [Topology ] . ( 5 sec) [ -7635.8857] [Topology ] . ( 6 sec) [ -7621.9400] [Topology ] . ( 7 sec) [ -7616.0972] [Topology ] . ( 8 sec) [ -7614.9800] [Topology ] . ( 9 sec) [ -7614.7148] [Topology ] . ( 10 sec) [ -7614.5517] [Topology ] . ( 11 sec) [ -7613.9240] [Topology ] . Checking for NNIs, optimizing five branches... . ( 19 sec) [ -7608.2048] [GTR parameters ] . ( 20 sec) [ -7600.3742] [Alpha ][ 0.381413] . ( 20 sec) [ -7600.3742] [Topology ] . ( 21 sec) [ -7595.2839] [Topology ] . ( 22 sec) [ -7593.6950] [Topology ] . ( 22 sec) [ -7593.3087] [Topology ] . ( 23 sec) [ -7593.2116] [Topology ] . ( 24 sec) [ -7593.1863] [Topology ] . ( 25 sec) [ -7593.1793] [Topology ] . Checking for NNIs, optimizing five branches... . ( 33 sec) [ -7593.1100] [GTR parameters ] . ( 33 sec) [ -7593.1097] [Alpha ][ 0.382068] . ( 33 sec) [ -7593.1097] [Topology ] . ( 34 sec) [ -7593.1069] [Topology ] . ( 35 sec) [ -7593.1060] [Topology ] . Checking for NNIs, optimizing five branches... . ( 43 sec) [ -7593.1060] [GTR parameters ] . ( 43 sec) [ -7593.1060] [Alpha ][ 0.382068] . ( 43 sec) [ -7593.1060] [Topology ] . ( 44 sec) [ -7593.1057] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 60 sec) [ -7873.6472] [GTR parameters ] . ( 60 sec) [ -7790.9479] [Alpha ][ 0.500960] . ( 60 sec) [ -7790.3934] [ 1390] [depth= 1] . ( 60 sec) [ -7780.7630] [ 1392] [depth= 1] . ( 61 sec) [ -7772.7156] [ 1390] [depth= 1] . ( 61 sec) [ -7770.5775] [ 1388] [depth= 1] . ( 61 sec) [ -7767.6349] [ 1390] [depth= 1] . ( 61 sec) [ -7762.5253] [ 1389] [depth= 1] . ( 61 sec) [ -7753.2366] [ 1384] [depth= 1] . ( 61 sec) [ -7751.6072] [ 1383] [depth= 1] . ( 61 sec) [ -7750.3527] [ 1384] [depth= 1] . ( 61 sec) [ -7750.1659] [ 1384] [depth= 1] . ( 61 sec) [ -7749.7937] [ 1380] [depth= 2] . ( 62 sec) [ -7746.6235] [ 1379] [depth= 1] . ( 62 sec) [ -7727.1260] [ 1379] [depth= 2] . ( 62 sec) [ -7725.1616] [ 1378] [depth= 2] . ( 62 sec) [ -7724.9374] [ 1375] [depth= 2] . ( 62 sec) [ -7721.9866] [ 1373] [depth= 1] . ( 62 sec) [ -7718.0482] [ 1371] [depth= 1] . ( 62 sec) [ -7716.0328] [ 1372] [depth= 2] . ( 63 sec) [ -7714.6230] [ 1374] [depth= 1] . ( 63 sec) [ -7712.6430] [ 1372] [depth= 1] . ( 63 sec) [ -7710.0737] [ 1370] [depth= 3] . ( 63 sec) [ -7706.1817] [ 1365] [depth= 1] . ( 63 sec) [ -7705.6485] [ 1366] [depth= 1] . ( 63 sec) [ -7692.6834] [ 1371] [depth= 1] . ( 63 sec) [ -7692.3938] [ 1371] [depth= 1] . ( 63 sec) [ -7691.9334] [ 1371] [depth= 1] . ( 63 sec) [ -7691.4335] [ 1371] [depth= 1] . ( 63 sec) [ -7691.4091] [ 1371] [depth= 3] . ( 63 sec) [ -7691.3212] [ 1371] [depth= 3] . ( 64 sec) [ -7690.8156] [ 1371] [depth= 1] . ( 64 sec) [ -7684.8985] [ 1366] [depth= 1] . ( 64 sec) [ -7682.6111] [ 1368] [depth= 2] . ( 64 sec) [ -7681.0068] [ 1366] [depth= 1] . ( 64 sec) [ -7672.1283] [ 1367] [depth= 4] . ( 65 sec) [ -7669.8978] [ 1366] [depth= 1] . ( 65 sec) [ -7665.4158] [ 1364] [depth= 1] . ( 65 sec) [ -7657.0635] [ 1363] [depth= 2] . ( 65 sec) [ -7652.0370] [ 1364] [depth= 4] . ( 66 sec) [ -7651.3717] [ 1364] [depth= 1] . ( 67 sec) [ -7650.4078] [ 1361] [depth= 2] . ( 67 sec) [ -7650.2644] [ 1360] [depth= 2] . ( 68 sec) [ -7649.2167] [ 1364] [depth= 1] . ( 70 sec) [ -7614.2902] [Branch lengths ] . ( 71 sec) [ -7612.3626] [GTR parameters ] . ( 71 sec) [ -7604.6228] [Alpha ][ 0.379693] . ( 71 sec) [ -7603.5880] [ 1360] [depth= 1] . ( 71 sec) [ -7602.9717] [ 1350] [depth= 4] . ( 72 sec) [ -7601.7044] [ 1349] [depth= 2] . ( 73 sec) [ -7601.3500] [ 1348] [depth= 1] . ( 73 sec) [ -7601.2784] [ 1350] [depth= 1] . ( 73 sec) [ -7590.8202] [ 1349] [depth= 7] . ( 73 sec) [ -7590.3864] [ 1350] [depth= 1] . ( 73 sec) [ -7590.3461] [ 1351] [depth= 1] . ( 76 sec) [ -7589.4481] [ 1349] [depth= 1] . ( 76 sec) [ -7589.1696] [ 1348] [depth= 1] . ( 76 sec) [ -7587.5993] [ 1348] [depth= 1] . ( 77 sec) [ -7587.5770] [ 1350] [depth= 1] . ( 77 sec) [ -7583.8405] [ 1351] [depth= 1] . ( 77 sec) [ -7582.9821] [ 1350] [depth= 2] . ( 77 sec) [ -7581.4845] [ 1349] [depth= 1] . ( 77 sec) [ -7581.1903] [ 1352] [depth= 1] . ( 82 sec) [ -7572.8917] [Branch lengths ] . ( 83 sec) [ -7572.5328] [GTR parameters ] . ( 83 sec) [ -7572.5008] [Alpha ][ 0.386412] . ( 86 sec) [ -7572.4363] [ 1355] [depth= 1] . ( 91 sec) [ -7572.3025] [ 1351] [depth= 1] . ( 92 sec) [ -7571.0906] [ 1352] [depth= 2] . ( 97 sec) [ -7570.2470] [Branch lengths ] . ( 98 sec) [ -7570.2305] [GTR parameters ] . ( 98 sec) [ -7570.2288] [Alpha ][ 0.384822] . ( 105 sec) [ -7570.1497] [ 1351] [depth= 2] . ( 113 sec) [ -7569.9900] [Branch lengths ] . ( 113 sec) [ -7569.9889] [GTR parameters ] . ( 113 sec) [ -7569.9887] [Alpha ][ 0.385219] . ( 156 sec) [ -7569.8696] [Branch lengths ] . ( 156 sec) [ -7569.8696] [Topology ] . ( 157 sec) [ -7569.8648] [Topology ] . ( 158 sec) [ -7569.8640] [Topology ] . ( 158 sec) [ -7569.8639] [GTR parameters ] . ( 158 sec) [ -7569.8639] [Alpha ][ 0.385219] . ( 158 sec) [ -7569.8639] [Topology ] . ( 159 sec) [ -7569.8637] [Topology ] . ( 159 sec) [ -7569.8637] [GTR parameters ] . ( 159 sec) [ -7569.8637] [Alpha ][ 0.385219] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7593.105691 . Log likelihood obtained after SPR moves : -7569.863686 . 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 0h2m48s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 163.41user 0.00system 2:47.89elapsed 97%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps