.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1989_18x173_2004.phy . Data type : aa . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : WAG . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Amino acid equilibrium frequencies : model . 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 . 7 sites are made from completely undetermined states ('X', '-', '?')... . Compressing sequences... . 139 patterns found. (out of a total of 173 sites) . 46 sites without polymorphism (26.59%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 6Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -3205.9405] [Alpha ][ 0.715572] . ( 1 sec) [ -3204.8230] [ 588] [depth= 1] . ( 1 sec) [ -3204.4975] [ 588] [depth= 1] . ( 1 sec) [ -3202.1815] [ 588] [depth= 1] . ( 1 sec) [ -3201.6828] [ 588] [depth= 1] . ( 1 sec) [ -3201.4585] [ 588] [depth= 1] . ( 2 sec) [ -3201.3209] [ 588] [depth= 1] . ( 3 sec) [ -3200.3034] [ 590] [depth= 1] . ( 3 sec) [ -3196.8229] [ 588] [depth= 1] . ( 3 sec) [ -3194.9065] [ 588] [depth= 1] . ( 5 sec) [ -3194.8109] [ 590] [depth= 1] . ( 5 sec) [ -3194.0856] [ 588] [depth= 1] . ( 6 sec) [ -3192.5816] [ 587] [depth= 1] . ( 6 sec) [ -3188.0278] [ 586] [depth= 2] . ( 8 sec) [ -3187.7771] [ 587] [depth= 1] . ( 8 sec) [ -3181.9854] [Branch lengths ] . ( 8 sec) [ -3181.8290] [Alpha ][ 0.769967] . ( 11 sec) [ -3181.0234] [ 587] [depth= 1] . ( 18 sec) [ -3180.0617] [Branch lengths ] . ( 18 sec) [ -3180.0407] [Alpha ][ 0.790686] . ( 28 sec) [ -3179.9257] [Branch lengths ] . ( 28 sec) [ -3179.9257] [Topology ] . ( 28 sec) [ -3179.9121] [Topology ] . ( 29 sec) [ -3179.9069] [Topology ] . ( 29 sec) [ -3179.9042] [Topology ] . ( 30 sec) [ -3179.9027] [Topology ] . ( 31 sec) [ -3179.9018] [Topology ] . ( 31 sec) [ -3179.8986] [Alpha ][ 0.799119] . ( 31 sec) [ -3179.8986] [Topology ] . ( 31 sec) [ -3179.8978] [Topology ] . ( 31 sec) [ -3179.8978] [Alpha ][ 0.799119] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3179.897758. . Printing the most likely tree in file 'proteic_M1989_18x173_2004.phy_phyml_tree.txt'... . Time used 0h0m35s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 34.78user 0.00system 0:35.17elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps