Sequence filename : /auto/dufayard/res/2.4.5/nucleic_M2932_68x1712_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 . 5 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... . Nbytes = 55140736 . Log(lk) : * -> -15903.491730 . Log(lk) : -15903.491730 -> -15635.776138 10 swaps done . Log(lk) : -15635.776138 -> -15531.190368 9 swaps done . Log(lk) : -15531.190368 -> -15502.523868 8 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -15006.738944 -> -14964.673342 8 swaps done . Log(lk) : -14964.673342 -> -14954.400024 3 swaps done . Log(lk) : -14954.400024 -> -14952.065974 3 swaps done . Log(lk) : -14952.065974 -> -14950.437645 2 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14942.145897 -> -14940.384584 1 swap done . Log(lk) : -14940.384584 -> -14939.060390 1 swap done . Log(lk) : -14939.060390 -> -14939.173773 1 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14939.060390 -> -14937.948925 1 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14937.945682 -> -14937.591866 2 swaps done . Log(lk) : -14937.591866 -> -14937.233704 1 swap done . Log(lk) : -14937.233704 -> -14937.183925 3 swaps done . Log(lk) : -14937.183925 -> -14935.303892 2 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14935.245375 -> -14932.693019 1 swap done . Log(lk) : -14932.693019 -> -14931.984555 2 swaps done . Log(lk) : -14931.984555 -> -14931.722583 1 swap done . Log(lk) : -14931.722583 -> -14931.604938 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.521053 -> -14931.436599 0 swap done . Log(lk) : -14931.436599 -> -14931.399906 0 swap done . Log(lk) : -14931.399906 -> -14931.386201 0 swap done . Log(lk) : -14931.386201 -> -14931.379627 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.365521 -> -14931.368558 0 swap done . Last optimization step... . Log(lk) : * -> -14931.320980 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.320980 -> -14931.315291 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.315291 -> -14931.313246 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.313246 -> -14931.312523 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.312523 -> -14931.312234 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.312234 -> -14931.312119 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.312119 -> -14931.312063 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.312063 -> -14931.312027 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.312027 -> -14931.311997 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311997 -> -14931.311970 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311970 -> -14931.311943 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311943 -> -14931.311916 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311916 -> -14931.311889 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311889 -> -14931.311862 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311862 -> -14931.311834 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311834 -> -14931.311807 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311807 -> -14931.311779 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311779 -> -14931.311750 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311750 -> -14931.311722 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311722 -> -14931.311693 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311693 -> -14931.311663 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311663 -> -14931.311634 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311634 -> -14931.311604 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311604 -> -14931.311574 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311574 -> -14931.311543 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311543 -> -14931.311512 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311512 -> -14931.311481 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311481 -> -14931.311449 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311449 -> -14931.311418 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311418 -> -14931.311385 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311385 -> -14931.311353 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311353 -> -14931.311320 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311320 -> -14931.311287 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311287 -> -14931.311253 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311253 -> -14931.311220 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311220 -> -14931.311185 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311185 -> -14931.311151 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311151 -> -14931.311116 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311116 -> -14931.311081 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311081 -> -14931.311045 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311045 -> -14931.311009 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.311009 -> -14931.310972 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.310972 -> -14931.310935 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.310935 -> -14931.310898 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.310898 -> -14931.310861 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.310861 -> -14931.310823 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.310823 -> -14931.310784 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.310784 -> -14931.310745 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.310745 -> -14931.310706 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.310706 -> -14931.310666 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.310666 -> -14931.310627 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.310627 -> -14931.310587 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.310587 -> -14931.310547 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.310547 -> -14931.310507 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.310507 -> -14931.310466 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.310466 -> -14931.310424 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.310424 -> -14931.310382 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.310382 -> -14931.310340 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.310340 -> -14931.310297 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.310297 -> -14931.310254 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.310254 -> -14931.310210 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.310210 -> -14931.310166 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.310166 -> -14931.310121 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.310121 -> -14931.310076 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.310076 -> -14931.310030 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.310030 -> -14931.309984 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.309984 -> -14931.309938 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.309938 -> -14931.309890 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.309890 -> -14931.309843 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.309843 -> -14931.309795 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.309795 -> -14931.309746 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.309746 -> -14931.309697 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.309697 -> -14931.309647 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.309647 -> -14931.309597 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.309597 -> -14931.309546 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.309546 -> -14931.309495 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.309495 -> -14931.309443 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.309443 -> -14931.309390 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.309390 -> -14931.309337 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.309337 -> -14931.309284 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.309284 -> -14931.309230 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.309230 -> -14931.309175 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.309175 -> -14931.309119 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.309119 -> -14931.309063 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.309063 -> -14931.309007 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.309007 -> -14931.308950 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.308950 -> -14931.308892 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.308892 -> -14931.308834 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.308834 -> -14931.308775 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.308775 -> -14931.308715 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.308715 -> -14931.308655 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.308655 -> -14931.308594 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.308594 -> -14931.308532 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.308532 -> -14931.308470 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.308470 -> -14931.308407 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.308407 -> -14931.308343 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.308343 -> -14931.308279 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.308279 -> -14931.308214 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.308214 -> -14931.308148 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -14931.308148 -> -14931.305300 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Final Log(lk) : -14931.305300 . Time used 0h17m25s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 1043.87user 0.00system 17:25.67elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps