.......................... 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] . ( 3 sec) [ -3249.7182] [ 287] [depth= 1] . ( 3 sec) [ -3249.6907] [ 287] [depth= 1] . ( 3 sec) [ -3249.6645] [ 287] [depth= 1] . ( 3 sec) [ -3249.5797] [ 287] [depth= 2] . ( 7 sec) [ -3249.5506] [ 287] [depth= 1] . ( 7 sec) [ -3249.4221] [ 287] [depth= 2] . ( 7 sec) [ -3249.0013] [ 287] [depth= 2] . ( 7 sec) [ -3244.7325] [ 287] [depth= 4] . ( 7 sec) [ -3244.2633] [ 287] [depth= 2] . ( 7 sec) [ -3243.7508] [ 287] [depth= 1] . ( 7 sec) [ -3243.7402] [ 287] [depth= 3] . ( 8 sec) [ -3237.5172] [ 286] [depth= 3] . ( 8 sec) [ -3236.8494] [ 286] [depth= 2] . ( 8 sec) [ -3236.8378] [ 286] [depth= 1] . ( 9 sec) [ -3236.7549] [ 286] [depth= 1] . ( 9 sec) [ -3236.2186] [ 286] [depth= 1] . ( 9 sec) [ -3236.1944] [ 286] [depth= 1] . ( 11 sec) [ -3235.2068] [ 286] [depth= 2] . ( 11 sec) [ -3232.8330] [ 286] [depth= 2] . ( 12 sec) [ -3232.8083] [ 286] [depth= 1] . ( 13 sec) [ -3232.7844] [ 286] [depth= 4] . ( 13 sec) [ -3232.7563] [ 286] [depth= 1] . ( 13 sec) [ -3232.7366] [ 286] [depth= 1] . ( 13 sec) [ -3232.5855] [ 286] [depth= 2] . ( 15 sec) [ -3232.4975] [ 286] [depth= 1] . ( 16 sec) [ -3232.4602] [ 286] [depth= 1] . ( 16 sec) [ -3232.4367] [ 286] [depth= 2] . ( 20 sec) [ -3232.4157] [ 286] [depth= 3] . ( 20 sec) [ -3232.2600] [ 286] [depth= 1] . ( 24 sec) [ -3232.1425] [ 286] [depth= 1] . ( 25 sec) [ -3231.3343] [ 286] [depth= 4] . ( 25 sec) [ -3230.5993] [ 286] [depth= 2] . ( 25 sec) [ -3230.5753] [ 286] [depth= 1] . ( 25 sec) [ -3230.4740] [ 286] [depth= 2] . ( 25 sec) [ -3230.4378] [ 286] [depth= 2] . ( 25 sec) [ -3229.9582] [ 286] [depth= 1] . ( 25 sec) [ -3229.7321] [ 286] [depth= 1] . ( 26 sec) [ -3229.6998] [ 286] [depth= 1] . ( 26 sec) [ -3229.6813] [ 286] [depth= 1] . ( 27 sec) [ -3229.5369] [ 286] [depth= 2] . ( 27 sec) [ -3229.5083] [ 286] [depth= 1] . ( 33 sec) [ -3218.7872] [Branch lengths ] . ( 34 sec) [ -3057.8348] [GTR parameters ] . ( 34 sec) [ -3044.6318] [Alpha ][ 0.250961] . ( 35 sec) [ -3044.0260] [ 284] [depth= 1] . ( 35 sec) [ -3043.7893] [ 286] [depth= 1] . ( 67 sec) [ -3042.3307] [ 286] [depth= 4] . ( 78 sec) [ -3039.5370] [Branch lengths ] . ( 79 sec) [ -3039.1025] [GTR parameters ] . ( 79 sec) [ -3034.3465] [Alpha ][ 0.133727] . ( 80 sec) [ -3034.3146] [ 288] [depth= 1] . ( 124 sec) [ -3033.9829] [Branch lengths ] . ( 125 sec) [ -3033.8365] [GTR parameters ] . ( 125 sec) [ -3033.8338] [Alpha ][ 0.131597] . ( 151 sec) [ -3033.8075] [Branch lengths ] . ( 151 sec) [ -3033.8075] [Topology ] . ( 151 sec) [ -3033.8064] [Topology ] . ( 152 sec) [ -3033.8062] [Topology ] . ( 152 sec) [ -3033.8053] [GTR parameters ] . ( 152 sec) [ -3033.8051] [Alpha ][ 0.132170] . ( 152 sec) [ -3033.8051] [Topology ] . ( 153 sec) [ -3033.8049] [Topology ] . ( 153 sec) [ -3033.8049] [GTR parameters ] . ( 153 sec) [ -3033.8049] [Alpha ][ 0.132170] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3033.804930. . Printing the most likely tree in file 'nucleic_M2922_77x1101_2006.phy_phyml_tree.txt'... . Time used 0h2m38s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 157.02user 0.00system 2:38.30elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps