Sequence filename : /auto/dufayard/res/2.4.5/nucleic_M2944_80x1495_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 Starting tree : BIONJ Optimise tree topology : yes Optimise branch lengths and rate parameters : yes . 3 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... . Nbytes = 25439024 . Log(lk) : * -> -9741.271185 . Log(lk) : -9741.271185 -> -9624.385302 12 swaps done . Log(lk) : -9624.385302 -> -9603.323757 8 swaps done . Log(lk) : -9603.323757 -> -9595.635519 3 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9067.524630 -> -9043.034560 6 swaps done . Log(lk) : -9043.034560 -> -9028.373007 5 swaps done . Log(lk) : -9028.373007 -> -9024.227604 2 swaps done . Log(lk) : -9024.227604 -> -9022.549874 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9020.748569 -> -9019.663703 1 swap done . Log(lk) : -9019.663703 -> -9019.020287 0 swap done . Log(lk) : -9019.020287 -> -9018.621927 0 swap done . Log(lk) : -9018.621927 -> -9018.370797 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9018.359009 -> -9018.192688 0 swap done . Log(lk) : -9018.192688 -> -9018.085694 0 swap done . Log(lk) : -9018.085694 -> -9018.016378 0 swap done . Last optimization step... . Log(lk) : * -> -9017.941185 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9017.941185 -> -9017.900738 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9017.900738 -> -9017.885509 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9017.885509 -> -9017.879505 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9017.879505 -> -9017.877128 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9017.877128 -> -9017.876208 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9017.876208 -> -9017.875837 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9017.875837 -> -9017.875693 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9017.875693 -> -9017.875635 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9017.875635 -> -9017.875612 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9017.875612 -> -9017.875602 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9017.875602 -> -9017.875598 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9017.875598 -> -9017.875597 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9017.875597 -> -9017.875596 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Final Log(lk) : -9017.875596 . Time used 0h1m4s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 63.15user 0.00system 1:03.66elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps