.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2738_53x1538_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... . 762 patterns found. (out of a total of 1538 sites) . 828 sites without polymorphism (53.84%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 21Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -14871.4533] [GTR parameters ] . ( 2 sec) [ -14653.1273] [Alpha ][ 0.500960] . ( 4 sec) [ -14651.0565] [ 2609] [depth= 1] . ( 4 sec) [ -14639.3400] [ 2603] [depth= 1] . ( 4 sec) [ -14635.1647] [ 2613] [depth= 1] . ( 4 sec) [ -14631.7424] [ 2615] [depth= 1] . ( 4 sec) [ -14622.2766] [ 2606] [depth= 1] . ( 7 sec) [ -14611.9354] [ 2603] [depth= 1] . ( 7 sec) [ -14601.9686] [ 2606] [depth= 1] . ( 9 sec) [ -14598.7739] [ 2603] [depth= 1] . ( 27 sec) [ -14598.6469] [ 2603] [depth= 1] . ( 27 sec) [ -14598.2706] [ 2603] [depth= 1] . ( 27 sec) [ -14595.5765] [ 2603] [depth= 1] . ( 38 sec) [ -14595.4355] [ 2603] [depth= 1] . ( 58 sec) [ -14589.4629] [ 2605] [depth= 1] . ( 58 sec) [ -14578.9078] [ 2603] [depth= 1] . ( 62 sec) [ -14573.5053] [ 2605] [depth= 1] . ( 62 sec) [ -14569.9585] [ 2611] [depth= 2] . ( 62 sec) [ -14567.4775] [ 2609] [depth= 1] . ( 63 sec) [ -14565.6817] [ 2610] [depth= 1] . ( 63 sec) [ -14565.5737] [ 2611] [depth= 1] . ( 63 sec) [ -14563.5728] [ 2610] [depth= 1] . ( 63 sec) [ -14559.0835] [ 2612] [depth= 2] . ( 72 sec) [ -14552.5326] [ 2614] [depth= 1] . ( 72 sec) [ -14549.2055] [ 2612] [depth= 1] . ( 72 sec) [ -14544.2122] [ 2614] [depth= 1] . ( 75 sec) [ -14539.0937] [ 2611] [depth= 2] . ( 75 sec) [ -14538.8965] [ 2613] [depth= 2] . ( 75 sec) [ -14530.2641] [ 2616] [depth= 1] . ( 75 sec) [ -14525.4702] [ 2616] [depth= 1] . ( 77 sec) [ -14524.2362] [ 2609] [depth= 1] . ( 79 sec) [ -14522.9864] [ 2608] [depth= 1] . ( 79 sec) [ -14521.6785] [ 2609] [depth= 1] . ( 79 sec) [ -14521.1463] [ 2606] [depth= 1] . ( 87 sec) [ -14520.7791] [ 2609] [depth= 1] . ( 89 sec) [ -14520.6001] [ 2609] [depth= 3] . ( 89 sec) [ -14516.1899] [ 2609] [depth= 2] . ( 90 sec) [ -14509.8839] [ 2609] [depth= 3] . ( 90 sec) [ -14506.4224] [ 2610] [depth= 2] . ( 91 sec) [ -14504.7795] [ 2612] [depth= 1] . ( 94 sec) [ -14504.2876] [ 2610] [depth= 1] . ( 95 sec) [ -14497.4749] [ 2607] [depth= 1] . ( 98 sec) [ -14441.5016] [Branch lengths ] . ( 102 sec) [ -13990.0416] [GTR parameters ] . ( 102 sec) [ -13933.9042] [Alpha ][ 0.304092] . ( 111 sec) [ -13932.2268] [ 2613] [depth= 1] . ( 112 sec) [ -13931.4523] [ 2607] [depth= 1] . ( 112 sec) [ -13930.2946] [ 2613] [depth= 1] . ( 112 sec) [ -13928.0891] [ 2613] [depth= 1] . ( 112 sec) [ -13926.8213] [ 2608] [depth= 1] . ( 174 sec) [ -13926.1140] [ 2606] [depth= 1] . ( 188 sec) [ -13925.5672] [ 2608] [depth= 1] . ( 198 sec) [ -13924.3663] [ 2616] [depth= 3] . ( 198 sec) [ -13924.2543] [ 2615] [depth= 1] . ( 198 sec) [ -13921.6454] [ 2614] [depth= 1] . ( 200 sec) [ -13920.9643] [ 2617] [depth= 1] . ( 219 sec) [ -13920.4063] [ 2616] [depth= 1] . ( 228 sec) [ -13912.7632] [Branch lengths ] . ( 232 sec) [ -13910.3890] [GTR parameters ] . ( 232 sec) [ -13910.2901] [Alpha ][ 0.298282] . ( 371 sec) [ -13909.2868] [Branch lengths ] . ( 374 sec) [ -13908.2389] [ 2616] [depth= 1] . ( 436 sec) [ -13907.9035] [Branch lengths ] . ( 439 sec) [ -13907.8177] [GTR parameters ] . ( 439 sec) [ -13907.8175] [Alpha ][ 0.298580] . ( 499 sec) [ -13907.7881] [Branch lengths ] . ( 499 sec) [ -13907.7881] [Topology ] . ( 501 sec) [ -13907.7846] [Topology ] . ( 502 sec) [ -13907.7834] [Topology ] . ( 504 sec) [ -13907.7828] [Topology ] . ( 505 sec) [ -13907.7795] [GTR parameters ] . ( 505 sec) [ -13907.7795] [Alpha ][ 0.298580] . ( 505 sec) [ -13907.7795] [Topology ] . ( 507 sec) [ -13907.7786] [Topology ] . ( 509 sec) [ -13907.7773] [GTR parameters ] . ( 509 sec) [ -13907.7773] [Alpha ][ 0.298580] . ( 509 sec) [ -13907.7773] [Topology ] . ( 511 sec) [ -13907.7769] [Topology ] . ( 512 sec) [ -13907.7766] [GTR parameters ] . ( 512 sec) [ -13907.7766] [Alpha ][ 0.298580] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -13907.776649. . Printing the most likely tree in file 'nucleic_M2738_53x1538_2006.phy_phyml_tree.txt'... . Time used 0h8m46s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 523.95user 0.00system 8:46.04elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps