Sequence filename : /auto/dufayard/res/2.4.5/nucleic_M2916_143x897_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 . 73 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... . Nbytes = 28125672 . Log(lk) : * -> -3700.553428 . Log(lk) : -3700.553428 -> -3649.035576 23 swaps done . Log(lk) : -3649.035576 -> -3635.906530 16 swaps done . Log(lk) : -3635.906530 -> -3633.981553 13 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3504.728412 -> -3501.025625 15 swaps done . Log(lk) : -3501.025625 -> -3498.285579 9 swaps done . Log(lk) : -3498.285579 -> -3495.048629 10 swaps done . Log(lk) : -3495.048629 -> -3494.615843 7 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3492.935059 -> -3492.543731 7 swaps done . Log(lk) : -3492.543731 -> -3491.755908 6 swaps done . Log(lk) : -3491.755908 -> -3491.973227 6 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3491.755908 -> -3491.130484 6 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3491.130483 -> -3491.492701 5 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3491.130483 -> -3491.118078 5 swaps done . Log(lk) : -3491.118078 -> -3491.744641 5 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3491.118078 -> -3490.952409 5 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3490.952408 -> -3491.145172 6 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3490.952408 -> -3490.936715 6 swaps done . Log(lk) : -3490.936715 -> -3490.859566 4 swaps done . Log(lk) : -3490.859566 -> -3490.717140 3 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3490.716818 -> -3490.208273 3 swaps done . Log(lk) : -3490.208273 -> -3491.069627 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3490.208273 -> -3490.142982 2 swaps done . Log(lk) : -3490.142982 -> -3490.220022 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3490.142982 -> -3489.820361 2 swaps done . Log(lk) : -3489.820361 -> -3489.966611 5 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.820361 -> -3489.818884 5 swaps done . Log(lk) : -3489.818884 -> -3490.159857 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.818884 -> -3489.804534 3 swaps done . Log(lk) : -3489.804534 -> -3490.026934 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.804534 -> -3489.785915 3 swaps done . Log(lk) : -3489.785915 -> -3489.790168 1 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.785915 -> -3489.781396 1 swap done . Log(lk) : -3489.781396 -> -3489.814295 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.781396 -> -3489.778258 2 swaps done . Log(lk) : -3489.778258 -> -3489.788768 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.778258 -> -3489.776638 2 swaps done . Log(lk) : -3489.776638 -> -3489.820672 1 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.776638 -> -3489.774278 1 swap done . Log(lk) : -3489.774278 -> -3489.792582 0 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.774278 -> -3489.773730 0 swap done . Last optimization step... . Log(lk) : * -> -3489.764362 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.764362 -> -3489.754314 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.754314 -> -3489.743622 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.743622 -> -3489.739980 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.739980 -> -3489.739494 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.739494 -> -3489.739150 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.739150 -> -3489.738802 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.738802 -> -3489.738463 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.738463 -> -3489.738118 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.738118 -> -3489.737765 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.737765 -> -3489.737405 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.737405 -> -3489.737037 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.737037 -> -3489.736662 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.736662 -> -3489.736279 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.736279 -> -3489.735888 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.735888 -> -3489.735489 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.735489 -> -3489.735126 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.735126 -> -3489.734800 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.734800 -> -3489.734466 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.734466 -> -3489.734123 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.734123 -> -3489.733772 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.733772 -> -3489.733418 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.733418 -> -3489.733061 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.733061 -> -3489.732695 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.732695 -> -3489.732319 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.732319 -> -3489.731933 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.731933 -> -3489.731538 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.731538 -> -3489.731132 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.731132 -> -3489.730715 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.730715 -> -3489.730316 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.730316 -> -3489.729925 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.729925 -> -3489.729525 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.729525 -> -3489.729114 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.729114 -> -3489.728692 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.728692 -> -3489.728259 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.728259 -> -3489.727815 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.727815 -> -3489.727359 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.727359 -> -3489.726892 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.726892 -> -3489.726658 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.726658 -> -3489.726560 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.726560 -> -3489.726462 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.726462 -> -3489.726411 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.726411 -> -3489.726359 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.726359 -> -3489.726307 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.726307 -> -3489.726254 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.726254 -> -3489.726200 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.726200 -> -3489.726146 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.726146 -> -3489.726091 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.726091 -> -3489.726035 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.726035 -> -3489.725979 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.725979 -> -3489.725922 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.725922 -> -3489.725865 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.725865 -> -3489.725806 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.725806 -> -3489.725747 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.725747 -> -3489.725688 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.725688 -> -3489.725627 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.725627 -> -3489.725566 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.725566 -> -3489.725504 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.725504 -> -3489.725441 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.725441 -> -3489.725378 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.725378 -> -3489.725313 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.725313 -> -3489.725248 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.725248 -> -3489.725182 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.725182 -> -3489.725116 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.725116 -> -3489.725048 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.725048 -> -3489.724980 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.724980 -> -3489.724911 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.724911 -> -3489.724841 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.724841 -> -3489.724770 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.724770 -> -3489.724698 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.724698 -> -3489.724625 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.724625 -> -3489.724551 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.724551 -> -3489.724477 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.724477 -> -3489.724401 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.724401 -> -3489.724336 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.724336 -> -3489.724273 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.724273 -> -3489.724210 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.724210 -> -3489.724147 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.724147 -> -3489.724082 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.724082 -> -3489.724017 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.724017 -> -3489.723951 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.723951 -> -3489.723884 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.723884 -> -3489.723817 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.723817 -> -3489.723748 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.723748 -> -3489.723679 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.723679 -> -3489.723609 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.723609 -> -3489.723538 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.723538 -> -3489.723466 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.723466 -> -3489.723393 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.723393 -> -3489.723320 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.723320 -> -3489.723245 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.723245 -> -3489.723170 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.723170 -> -3489.723094 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.723094 -> -3489.723017 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.723017 -> -3489.722939 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.722939 -> -3489.722860 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.722860 -> -3489.722779 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.722779 -> -3489.722698 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.722698 -> -3489.722616 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -3489.722616 -> -3489.722533 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Final Log(lk) : -3489.722533 . Time used 0h11m23s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 678.91user 0.00system 11:23.32elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps