.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2922_77x1101_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... . 173 patterns found. (out of a total of 1101 sites) . 906 sites without polymorphism (82.29%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 7Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -3268.3123] [GTR parameters ] . ( 0 sec) [ -3255.0160] [Alpha ][ 0.500960] . ( 0 sec) [ -3254.2192] [ 285] [depth= 1] . ( 0 sec) [ -3254.0206] [ 285] [depth= 1] . ( 1 sec) [ -3249.8435] [ 287] [depth= 1] . ( 1 sec) [ -3249.7182] [ 287] [depth= 1] . ( 1 sec) [ -3249.6907] [ 287] [depth= 1] . ( 1 sec) [ -3249.6645] [ 287] [depth= 1] . ( 1 sec) [ -3249.5797] [ 287] [depth= 2] . ( 2 sec) [ -3249.5506] [ 287] [depth= 1] . ( 2 sec) [ -3249.4221] [ 287] [depth= 2] . ( 2 sec) [ -3249.0013] [ 287] [depth= 2] . ( 2 sec) [ -3244.7325] [ 287] [depth= 4] . ( 2 sec) [ -3244.2633] [ 287] [depth= 2] . ( 2 sec) [ -3243.7508] [ 287] [depth= 1] . ( 2 sec) [ -3243.7402] [ 287] [depth= 3] . ( 2 sec) [ -3237.5172] [ 286] [depth= 3] . ( 2 sec) [ -3236.8494] [ 286] [depth= 2] . ( 2 sec) [ -3236.8378] [ 286] [depth= 1] . ( 2 sec) [ -3236.7549] [ 286] [depth= 1] . ( 2 sec) [ -3236.2186] [ 286] [depth= 1] . ( 2 sec) [ -3236.1944] [ 286] [depth= 1] . ( 2 sec) [ -3235.2068] [ 286] [depth= 2] . ( 2 sec) [ -3232.8330] [ 286] [depth= 2] . ( 2 sec) [ -3232.8083] [ 286] [depth= 1] . ( 3 sec) [ -3232.7844] [ 286] [depth= 4] . ( 3 sec) [ -3232.7563] [ 286] [depth= 1] . ( 3 sec) [ -3232.7366] [ 286] [depth= 1] . ( 3 sec) [ -3232.5855] [ 286] [depth= 2] . ( 3 sec) [ -3232.4975] [ 286] [depth= 1] . ( 3 sec) [ -3232.4602] [ 286] [depth= 1] . ( 3 sec) [ -3232.4367] [ 286] [depth= 2] . ( 3 sec) [ -3232.4157] [ 286] [depth= 3] . ( 3 sec) [ -3232.2600] [ 286] [depth= 1] . ( 4 sec) [ -3232.1425] [ 286] [depth= 1] . ( 4 sec) [ -3231.3343] [ 286] [depth= 4] . ( 4 sec) [ -3230.5993] [ 286] [depth= 2] . ( 4 sec) [ -3230.5753] [ 286] [depth= 1] . ( 4 sec) [ -3230.4740] [ 286] [depth= 2] . ( 4 sec) [ -3230.4378] [ 286] [depth= 2] . ( 4 sec) [ -3229.9582] [ 286] [depth= 1] . ( 4 sec) [ -3229.7321] [ 286] [depth= 1] . ( 4 sec) [ -3229.6998] [ 286] [depth= 1] . ( 4 sec) [ -3229.6813] [ 286] [depth= 1] . ( 4 sec) [ -3229.5369] [ 286] [depth= 2] . ( 5 sec) [ -3229.5083] [ 286] [depth= 1] . ( 5 sec) [ -3218.7872] [Branch lengths ] . ( 6 sec) [ -3057.8348] [GTR parameters ] . ( 6 sec) [ -3044.6318] [Alpha ][ 0.250961] . ( 7 sec) [ -3044.0260] [ 284] [depth= 1] . ( 7 sec) [ -3043.7893] [ 286] [depth= 1] . ( 10 sec) [ -3042.3307] [ 286] [depth= 4] . ( 11 sec) [ -3039.5370] [Branch lengths ] . ( 12 sec) [ -3039.1025] [GTR parameters ] . ( 13 sec) [ -3034.3465] [Alpha ][ 0.133727] . ( 17 sec) [ -3033.9865] [Branch lengths ] . ( 44 sec) [ -3033.9644] [Branch lengths ] . ( 44 sec) [ -3033.9644] [Topology ] . ( 44 sec) [ -3033.9642] [Topology ] . ( 45 sec) [ -3033.8173] [GTR parameters ] . ( 45 sec) [ -3033.8158] [Alpha ][ 0.132119] . ( 45 sec) [ -3033.8158] [Topology ] . ( 46 sec) [ -3033.8073] [Topology ] . ( 46 sec) [ -3033.8063] [Topology ] . ( 47 sec) [ -3033.8060] [Topology ] . ( 47 sec) [ -3033.8052] [GTR parameters ] . ( 47 sec) [ -3033.8052] [Alpha ][ 0.132119] . ( 47 sec) [ -3033.8052] [Topology ] . ( 48 sec) [ -3033.8050] [Topology ] . ( 48 sec) [ -3033.8049] [GTR parameters ] . ( 48 sec) [ -3033.8049] [Alpha ][ 0.132251] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3033.804946. . Printing the most likely tree in file 'nucleic_M2922_77x1101_2006.phy_phyml_tree.txt'... . Time used 0h0m52s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 51.47user 0.00system 0:52.27elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps