Sequence filename : /auto/dufayard/res/bigdatasets_2.4.5_nucl/nucleic_M2839_470x829_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 . 52 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... . Nbytes = 225277288 . Log(lk) : * -> -46967.376787 . Log(lk) : -46967.376787 -> -45409.518543 71 swaps done . Log(lk) : -45409.518543 -> -45092.672905 53 swaps done . Log(lk) : -45092.672905 -> -44977.602337 42 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42649.621758 -> -42558.591452 31 swaps done . Log(lk) : -42558.591452 -> -42525.346069 26 swaps done . Log(lk) : -42525.346069 -> -42495.823330 24 swaps done . Log(lk) : -42495.823330 -> -42487.103934 21 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42482.514903 -> -42460.072958 19 swaps done . Log(lk) : -42460.072958 -> -42455.765644 14 swaps done . Log(lk) : -42455.765644 -> -42441.369475 12 swaps done . Log(lk) : -42441.369475 -> -42439.307334 12 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42439.090104 -> -42433.589776 12 swaps done . Log(lk) : -42433.589776 -> -42435.261364 12 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42433.589776 -> -42432.476935 12 swaps done . Log(lk) : -42432.476935 -> -42428.566003 11 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42428.562444 -> -42427.049979 10 swaps done . Log(lk) : -42427.049979 -> -42424.637413 9 swaps done . Log(lk) : -42424.637413 -> -42426.094243 12 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42424.637413 -> -42423.461335 12 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42423.461305 -> -42423.115036 10 swaps done . Log(lk) : -42423.115036 -> -42423.194070 9 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42423.115036 -> -42422.517300 9 swaps done . Log(lk) : -42422.517300 -> -42422.266989 7 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42422.265907 -> -42422.591572 8 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42422.265907 -> -42422.130155 8 swaps done . Log(lk) : -42422.130155 -> -42422.725868 6 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42422.130155 -> -42422.036479 6 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42422.036450 -> -42421.872101 6 swaps done . Log(lk) : -42421.872101 -> -42422.200907 7 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42421.872101 -> -42421.558255 7 swaps done . Log(lk) : -42421.558255 -> -42421.972089 8 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42421.558255 -> -42421.400628 8 swaps done . Log(lk) : -42421.400628 -> -42422.245693 8 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42421.400628 -> -42421.391865 8 swaps done . Log(lk) : -42421.391865 -> -42422.041456 8 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42421.391865 -> -42421.343390 8 swaps done . Log(lk) : -42421.343390 -> -42422.354218 9 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42421.343390 -> -42421.280189 9 swaps done . Log(lk) : -42421.280189 -> -42421.448167 9 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42421.280189 -> -42421.273199 9 swaps done . Log(lk) : -42421.273199 -> -42421.807387 8 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42421.273199 -> -42421.224858 8 swaps done . Log(lk) : -42421.224858 -> -42421.651927 7 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42421.224858 -> -42421.224473 7 swaps done . Last optimization step... . Log(lk) : * -> -42421.119536 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42421.119536 -> -42421.021971 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42421.021971 -> -42420.938739 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.938739 -> -42420.885250 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.885250 -> -42420.862227 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.862227 -> -42420.860570 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.860570 -> -42420.860180 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.860180 -> -42420.859973 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.859973 -> -42420.859840 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.859840 -> -42420.859739 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.859739 -> -42420.859651 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.859651 -> -42420.859568 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.859568 -> -42420.859489 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.859489 -> -42420.859410 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.859410 -> -42420.859331 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.859331 -> -42420.859252 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.859252 -> -42420.859173 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.859173 -> -42420.859093 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.859093 -> -42420.859013 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.859013 -> -42420.858933 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.858933 -> -42420.858852 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.858852 -> -42420.858772 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.858772 -> -42420.858690 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.858690 -> -42420.858609 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.858609 -> -42420.858527 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.858527 -> -42420.858445 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.858445 -> -42420.858395 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.858395 -> -42420.858364 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.858364 -> -42420.858333 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.858333 -> -42420.858301 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.858301 -> -42420.858270 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.858270 -> -42420.858238 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.858238 -> -42420.858206 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.858206 -> -42420.858174 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.858174 -> -42420.858142 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.858142 -> -42420.858110 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.858110 -> -42420.858078 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.858078 -> -42420.858045 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.858045 -> -42420.858013 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.858013 -> -42420.857980 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857980 -> -42420.857947 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857947 -> -42420.857914 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857914 -> -42420.857881 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857881 -> -42420.857848 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857848 -> -42420.857815 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857815 -> -42420.857781 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857781 -> -42420.857748 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857748 -> -42420.857714 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857714 -> -42420.857680 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857680 -> -42420.857646 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857646 -> -42420.857612 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857612 -> -42420.857578 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857578 -> -42420.857543 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857543 -> -42420.857512 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857512 -> -42420.857489 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857489 -> -42420.857468 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857468 -> -42420.857446 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857446 -> -42420.857424 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857424 -> -42420.857401 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857401 -> -42420.857379 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857379 -> -42420.857357 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857357 -> -42420.857335 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857335 -> -42420.857312 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857312 -> -42420.857290 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857290 -> -42420.857267 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857267 -> -42420.857245 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857245 -> -42420.857222 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857222 -> -42420.857199 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857199 -> -42420.857176 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857176 -> -42420.857154 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857154 -> -42420.857131 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857131 -> -42420.857108 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857108 -> -42420.857084 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857084 -> -42420.857061 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857061 -> -42420.857038 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857038 -> -42420.857015 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.857015 -> -42420.856991 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.856991 -> -42420.856967 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.856967 -> -42420.856943 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.856943 -> -42420.856919 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.856919 -> -42420.856895 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.856895 -> -42420.856871 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.856871 -> -42420.856846 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.856846 -> -42420.856822 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.856822 -> -42420.856797 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.856797 -> -42420.856773 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.856773 -> -42420.856748 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.856748 -> -42420.856723 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.856723 -> -42420.856698 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.856698 -> -42420.856674 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.856674 -> -42420.856648 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.856648 -> -42420.856623 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.856623 -> -42420.856598 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.856598 -> -42420.856573 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.856573 -> -42420.856547 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.856547 -> -42420.856522 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.856522 -> -42420.856496 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.856496 -> -42420.856471 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.856471 -> -42420.856444 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -42420.856444 -> -42420.856418 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Final Log(lk) : -42420.856418 . Time used 1h10m38s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 4198.01user 0.00system 1:10:39elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps