Sequence filename : /auto/dufayard/res/parc_wim/proteic_M2304_31x429_2005.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 . 35 sites are made from completely undetermined states ('X', '-', '?')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... N_RGRFT: 11 N_GLOBL: 5 MAX_DIST: 5 . Log(lk) : * -> -5528.369025 . Log(lk) : -5528.369025 -> -5520.408271 5 swaps done . Log(lk) : -5520.408271 -> -5519.456810 1 swap done . Log(lk) : -5519.456810 -> -5519.308664 0 swap done . Optimisation of the gamma shape parameter... . Log(lk) : -5506.934478 -> -5506.469890 0 swap done . Log(lk) : -5506.469890 -> -5506.419811 0 swap done . Log(lk) : -5506.419811 -> -5506.406885 0 swap done . Log(lk) : -5506.406885 -> -5506.402528 0 swap done . Optimisation of the gamma shape parameter... . Log(lk) : -5506.391608 -> -5506.389601 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization Log (lk): -5506.389601 . Last optimization step... . Log(lk) : * -> -5506.389601 . Optimisation of the gamma shape parameter... . Log(lk) : -5506.389601 -> -5506.389592 . Optimisation of the gamma shape parameter... . Log(lk) : -5506.389592 -> -5506.389592 . Optimisation of the gamma shape parameter... nr_d_L: 1672 nr_d_lk: 757 nr_loc: 100 nr_glb: 5 . Time used 0h1m23s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 80.38user 0.00system 1:22.55elapsed 97%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps