Sequence filename : /auto/dufayard/res/2.4.5/proteic_M1990_35x153_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 Starting tree : BIONJ Optimise tree topology : yes Optimise branch lengths and rate parameters : yes . 5 sites are made from completely undetermined states ('X', '-', '?')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... . Nbytes = 9420736 . Log(lk) : * -> -1492.367914 . Log(lk) : -1492.367914 -> -1478.402024 3 swaps done . Log(lk) : -1478.402024 -> -1476.342129 0 swap done . Log(lk) : -1476.342129 -> -1475.940556 0 swap done . Optimisation of the gamma shape parameter... . Log(lk) : -1458.336171 -> -1455.610137 0 swap done . Log(lk) : -1455.610137 -> -1455.309787 0 swap done . Log(lk) : -1455.309787 -> -1455.125343 0 swap done . Log(lk) : -1455.125343 -> -1455.016739 0 swap done . Last optimization step... . Log(lk) : * -> -1454.947011 . Optimisation of the gamma shape parameter... . Log(lk) : -1454.947011 -> -1454.654320 . Optimisation of the gamma shape parameter... . Log(lk) : -1454.654320 -> -1454.584668 . Optimisation of the gamma shape parameter... . Log(lk) : -1454.584668 -> -1454.578668 . Optimisation of the gamma shape parameter... . Log(lk) : -1454.578668 -> -1454.576448 . Optimisation of the gamma shape parameter... . Log(lk) : -1454.576448 -> -1454.574958 . Optimisation of the gamma shape parameter... . Log(lk) : -1454.574958 -> -1454.573414 . Optimisation of the gamma shape parameter... . Log(lk) : -1454.573414 -> -1454.571621 . Optimisation of the gamma shape parameter... . Log(lk) : -1454.571621 -> -1454.569384 . Optimisation of the gamma shape parameter... . Log(lk) : -1454.569384 -> -1454.568541 . Optimisation of the gamma shape parameter... . Log(lk) : -1454.568541 -> -1454.568505 . Optimisation of the gamma shape parameter... . Log(lk) : -1454.568505 -> -1454.568505 . Optimisation of the gamma shape parameter... . Final Log(lk) : -1454.568505 . Time used 0h0m58s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 57.32user 0.00system 0:57.55elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps