.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2675_51x1537_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 . Compressing sequences... . 607 patterns found. (out of a total of 1537 sites) . 978 sites without polymorphism (63.63%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 16Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -8178.2748] [GTR parameters ] . ( 3 sec) [ -8087.4232] [Alpha ][ 0.500960] . ( 3 sec) [ -8087.0972] [ 1200] [depth= 1] . ( 4 sec) [ -8084.7754] [ 1202] [depth= 1] . ( 4 sec) [ -8082.7059] [ 1201] [depth= 1] . ( 4 sec) [ -8082.5110] [ 1201] [depth= 1] . ( 5 sec) [ -8082.2716] [ 1201] [depth= 1] . ( 5 sec) [ -8081.9018] [ 1200] [depth= 2] . ( 5 sec) [ -8079.7678] [ 1200] [depth= 1] . ( 5 sec) [ -8078.9041] [ 1200] [depth= 1] . ( 5 sec) [ -8078.5930] [ 1200] [depth= 1] . ( 5 sec) [ -8078.4987] [ 1200] [depth= 1] . ( 5 sec) [ -8078.4207] [ 1200] [depth= 2] . ( 6 sec) [ -8069.1232] [ 1200] [depth= 1] . ( 6 sec) [ -8055.0493] [ 1198] [depth= 1] . ( 6 sec) [ -8053.5396] [ 1198] [depth= 2] . ( 6 sec) [ -8053.5137] [ 1198] [depth= 2] . ( 6 sec) [ -8049.2586] [ 1197] [depth= 1] . ( 7 sec) [ -8047.0850] [ 1197] [depth= 1] . ( 7 sec) [ -8046.9941] [ 1197] [depth= 2] . ( 7 sec) [ -8046.6394] [ 1197] [depth= 2] . ( 7 sec) [ -8046.5629] [ 1197] [depth= 1] . ( 7 sec) [ -8043.9070] [ 1197] [depth= 5] . ( 7 sec) [ -8034.1401] [ 1195] [depth= 2] . ( 7 sec) [ -8029.8403] [ 1195] [depth= 1] . ( 7 sec) [ -7981.5911] [ 1193] [depth= 1] . ( 8 sec) [ -7981.2213] [ 1193] [depth= 1] . ( 8 sec) [ -7979.5751] [ 1194] [depth= 1] . ( 9 sec) [ -7973.7832] [ 1193] [depth= 1] . ( 9 sec) [ -7973.5404] [ 1193] [depth= 1] . ( 9 sec) [ -7973.5261] [ 1193] [depth= 1] . ( 9 sec) [ -7954.2323] [ 1201] [depth= 1] . ( 10 sec) [ -7948.9275] [ 1193] [depth= 1] . ( 10 sec) [ -7946.7991] [ 1192] [depth= 1] . ( 10 sec) [ -7946.3610] [ 1192] [depth= 1] . ( 11 sec) [ -7940.7708] [ 1191] [depth= 2] . ( 11 sec) [ -7940.7599] [ 1191] [depth= 1] . ( 11 sec) [ -7940.7331] [ 1191] [depth= 2] . ( 13 sec) [ -7940.2547] [ 1191] [depth= 1] . ( 13 sec) [ -7907.8719] [Branch lengths ] . ( 16 sec) [ -7906.5357] [GTR parameters ] . ( 16 sec) [ -7866.3443] [Alpha ][ 0.263319] . ( 16 sec) [ -7866.3339] [ 1191] [depth= 1] . ( 17 sec) [ -7866.1460] [ 1189] [depth= 1] . ( 18 sec) [ -7866.1043] [ 1189] [depth= 2] . ( 19 sec) [ -7865.9958] [ 1189] [depth= 1] . ( 22 sec) [ -7865.4892] [ 1189] [depth= 1] . ( 23 sec) [ -7864.2086] [ 1189] [depth= 1] . ( 25 sec) [ -7859.8106] [Branch lengths ] . ( 27 sec) [ -7859.2250] [GTR parameters ] . ( 27 sec) [ -7858.9970] [Alpha ][ 0.251696] . ( 31 sec) [ -7858.9731] [ 1189] [depth= 1] . ( 34 sec) [ -7858.7156] [Branch lengths ] . ( 36 sec) [ -7858.7043] [GTR parameters ] . ( 36 sec) [ -7858.7028] [Alpha ][ 0.252600] . ( 69 sec) [ -7857.0559] [ 1190] [depth= 1] . ( 81 sec) [ -7856.0819] [Branch lengths ] . ( 83 sec) [ -7856.0501] [GTR parameters ] . ( 83 sec) [ -7856.0498] [Alpha ][ 0.252980] . ( 160 sec) [ -7855.8748] [Branch lengths ] . ( 160 sec) [ -7855.8748] [Topology ] . ( 163 sec) [ -7855.8419] [Topology ] . ( 165 sec) [ -7855.8275] [Topology ] . ( 167 sec) [ -7855.8194] [Topology ] . ( 169 sec) [ -7855.8146] [Topology ] . ( 172 sec) [ -7855.8119] [Topology ] . ( 174 sec) [ -7855.8103] [Topology ] . ( 175 sec) [ -7855.8101] [GTR parameters ] . ( 175 sec) [ -7855.8081] [Alpha ][ 0.254050] . ( 175 sec) [ -7855.8081] [Topology ] . ( 177 sec) [ -7855.8069] [Topology ] . ( 180 sec) [ -7855.8063] [Topology ] . ( 180 sec) [ -7855.8063] [GTR parameters ] . ( 181 sec) [ -7855.8063] [Alpha ][ 0.254050] . ( 181 sec) [ -7855.8063] [Topology ] . ( 183 sec) [ -7855.8059] [Topology ] . ( 184 sec) [ -7855.8059] [GTR parameters ] . ( 184 sec) [ -7855.8059] [Alpha ][ 0.254050] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7855.805880. . Printing the most likely tree in file 'nucleic_M2675_51x1537_2006.phy_phyml_tree.txt'... . Time used 0h3m22s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 153.07user 0.00system 3:22.60elapsed 75%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps