Sequence filename : /auto/dufayard/res/bigdatasets_2.4.5_nucl/nucleic_M3459_407x1707_2007.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 . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... . Nbytes = 284894568 . Log(lk) : * -> -22692.670281 . Log(lk) : -22692.670281 -> -22159.417870 61 swaps done . Log(lk) : -22159.417870 -> -22077.455169 34 swaps done . Log(lk) : -22077.455169 -> -22050.786214 29 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19570.645340 -> -19497.392013 23 swaps done . Log(lk) : -19497.392013 -> -19484.594734 18 swaps done . Log(lk) : -19484.594734 -> -19462.928113 12 swaps done . Log(lk) : -19462.928113 -> -19449.223940 9 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19423.296942 -> -19391.868689 8 swaps done . Log(lk) : -19391.868689 -> -19386.403005 7 swaps done . Log(lk) : -19386.403005 -> -19385.512559 4 swaps done . Log(lk) : -19385.512559 -> -19385.667650 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19385.512559 -> -19384.536757 3 swaps done . Log(lk) : -19384.536757 -> -19384.957264 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.536757 -> -19384.361791 2 swaps done . Log(lk) : -19384.361791 -> -19384.240827 2 swaps done . Log(lk) : -19384.240827 -> -19384.231119 2 swaps done . Log(lk) : -19384.231119 -> -19384.298205 1 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.231119 -> -19384.164929 1 swap done . Log(lk) : -19384.164929 -> -19384.177700 0 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.164929 -> -19384.141870 0 swap done . Log(lk) : -19384.141870 -> -19384.127131 0 swap done . Log(lk) : -19384.127131 -> -19384.153830 0 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.127131 -> -19384.111835 0 swap done . Log(lk) : -19384.111835 -> -19384.106995 0 swap done . Log(lk) : -19384.106995 -> -19384.137400 0 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.106995 -> -19384.095256 0 swap done . Log(lk) : -19384.095256 -> -19384.095262 0 swap done . Last optimization step... . Log(lk) : * -> -19384.080080 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.080080 -> -19384.077322 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.077322 -> -19384.075376 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.075376 -> -19384.073854 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.073854 -> -19384.072455 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.072455 -> -19384.071090 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.071090 -> -19384.069796 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.069796 -> -19384.068526 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.068526 -> -19384.067254 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.067254 -> -19384.065982 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.065982 -> -19384.064721 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.064721 -> -19384.063525 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.063525 -> -19384.062328 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.062328 -> -19384.061129 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.061129 -> -19384.059929 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.059929 -> -19384.058740 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.058740 -> -19384.057557 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.057557 -> -19384.056371 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.056371 -> -19384.050694 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.050694 -> -19384.049740 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.049740 -> -19384.048786 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.048786 -> -19384.047832 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.047832 -> -19384.046891 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.046891 -> -19384.046497 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.046497 -> -19384.046400 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.046400 -> -19384.046303 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.046303 -> -19384.046207 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.046207 -> -19384.046110 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.046110 -> -19384.046013 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.046013 -> -19384.045916 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.045916 -> -19384.045818 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.045818 -> -19384.045724 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.045724 -> -19384.045641 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.045641 -> -19384.045562 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.045562 -> -19384.045483 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.045483 -> -19384.045404 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.045404 -> -19384.045325 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.045325 -> -19384.045245 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.045245 -> -19384.045166 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.045166 -> -19384.045086 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.045086 -> -19384.045006 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.045006 -> -19384.044927 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.044927 -> -19384.044847 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.044847 -> -19384.044767 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.044767 -> -19384.044687 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.044687 -> -19384.044612 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.044612 -> -19384.044549 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.044549 -> -19384.044486 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.044486 -> -19384.044423 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.044423 -> -19384.044360 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.044360 -> -19384.044297 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.044297 -> -19384.044233 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.044233 -> -19384.044170 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.044170 -> -19384.044107 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.044107 -> -19384.044043 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.044043 -> -19384.043980 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.043980 -> -19384.043916 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.043916 -> -19384.043853 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.043853 -> -19384.043801 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.043801 -> -19384.043749 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.043749 -> -19384.043698 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.043698 -> -19384.043647 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.043647 -> -19384.043595 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.043595 -> -19384.043544 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.043544 -> -19384.043492 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.043492 -> -19384.043441 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.043441 -> -19384.043389 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.043389 -> -19384.043337 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.043337 -> -19384.043285 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.043285 -> -19384.043234 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.043234 -> -19384.043182 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.043182 -> -19384.043130 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.043130 -> -19384.043078 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.043078 -> -19384.043026 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.043026 -> -19384.042973 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.042973 -> -19384.042921 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.042921 -> -19384.042869 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.042869 -> -19384.042817 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.042817 -> -19384.042764 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.042764 -> -19384.042712 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.042712 -> -19384.042660 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.042660 -> -19384.042607 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.042607 -> -19384.042555 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.042555 -> -19384.042502 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.042502 -> -19384.042450 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.042450 -> -19384.042397 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.042397 -> -19384.042345 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.042345 -> -19384.042292 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.042292 -> -19384.042239 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.042239 -> -19384.042186 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.042186 -> -19384.042133 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.042133 -> -19384.042080 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.042080 -> -19384.042027 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.042027 -> -19384.041974 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.041974 -> -19384.041921 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.041921 -> -19384.041868 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.041868 -> -19384.041814 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.041814 -> -19384.041761 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.041761 -> -19384.041707 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -19384.041707 -> -19384.041654 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Final Log(lk) : -19384.041654 . Time used 1h31m4s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 5396.42user 0.00system 1:31:04elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps