Sequence filename : /auto/dufayard/res/2.4.5/nucleic_M2711_123x1181_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 . 18 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... . Nbytes = 49177368 . Log(lk) : * -> -11876.785652 . Log(lk) : -11876.785652 -> -11594.789857 16 swaps done . Log(lk) : -11594.789857 -> -11547.867523 12 swaps done . Log(lk) : -11547.867523 -> -11531.620072 9 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10722.805621 -> -10694.739464 6 swaps done . Log(lk) : -10694.739464 -> -10686.961949 4 swaps done . Log(lk) : -10686.961949 -> -10683.525572 5 swaps done . Log(lk) : -10683.525572 -> -10681.176039 1 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10672.905143 -> -10670.953288 1 swap done . Log(lk) : -10670.953288 -> -10669.986947 1 swap done . Log(lk) : -10669.986947 -> -10669.532406 2 swaps done . Log(lk) : -10669.532406 -> -10669.297171 1 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10669.188696 -> -10669.027694 0 swap done . Log(lk) : -10669.027694 -> -10668.917399 1 swap done . Log(lk) : -10668.917399 -> -10668.842799 0 swap done . Log(lk) : -10668.842799 -> -10668.808575 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.801190 -> -10668.779678 0 swap done . Log(lk) : -10668.779678 -> -10668.767886 0 swap done . Log(lk) : -10668.767886 -> -10668.761293 0 swap done . Log(lk) : -10668.761293 -> -10668.757557 0 swap done . Last optimization step... . Log(lk) : * -> -10668.754302 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.754302 -> -10668.751688 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.751688 -> -10668.751099 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.751099 -> -10668.750916 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750916 -> -10668.750852 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750852 -> -10668.750833 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750833 -> -10668.750825 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750825 -> -10668.750820 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750820 -> -10668.750815 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750815 -> -10668.750811 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750811 -> -10668.750807 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750807 -> -10668.750803 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750803 -> -10668.750799 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750799 -> -10668.750795 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750795 -> -10668.750791 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750791 -> -10668.750787 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750787 -> -10668.750784 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750784 -> -10668.750780 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750780 -> -10668.750776 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750776 -> -10668.750772 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750772 -> -10668.750768 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750768 -> -10668.750764 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750764 -> -10668.750760 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750760 -> -10668.750756 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750756 -> -10668.750752 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750752 -> -10668.750748 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750748 -> -10668.750744 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750744 -> -10668.750740 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750740 -> -10668.750737 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750737 -> -10668.750733 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750733 -> -10668.750729 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750729 -> -10668.750725 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750725 -> -10668.750721 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750721 -> -10668.750717 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750717 -> -10668.750713 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750713 -> -10668.750709 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750709 -> -10668.750705 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750705 -> -10668.750701 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750701 -> -10668.750697 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750697 -> -10668.750693 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750693 -> -10668.750689 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750689 -> -10668.750685 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750685 -> -10668.750681 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750681 -> -10668.750677 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750677 -> -10668.750673 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750673 -> -10668.750669 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750669 -> -10668.750665 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750665 -> -10668.750662 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750662 -> -10668.750658 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750658 -> -10668.750654 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750654 -> -10668.750650 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750650 -> -10668.750646 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750646 -> -10668.750642 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750642 -> -10668.750638 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750638 -> -10668.750634 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750634 -> -10668.750630 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750630 -> -10668.750626 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750626 -> -10668.750622 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750622 -> -10668.750618 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750618 -> -10668.750614 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750614 -> -10668.750610 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750610 -> -10668.750606 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750606 -> -10668.750602 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750602 -> -10668.750598 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750598 -> -10668.750594 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750594 -> -10668.750590 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750590 -> -10668.750586 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750586 -> -10668.750582 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750582 -> -10668.750578 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750578 -> -10668.750574 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750574 -> -10668.750570 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750570 -> -10668.750566 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750566 -> -10668.750562 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750562 -> -10668.750558 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750558 -> -10668.750554 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750554 -> -10668.750550 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750550 -> -10668.750546 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750546 -> -10668.750542 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750542 -> -10668.750537 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750537 -> -10668.750533 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750533 -> -10668.750529 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750529 -> -10668.750525 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750525 -> -10668.750521 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750521 -> -10668.750517 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750517 -> -10668.750513 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750513 -> -10668.750509 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750509 -> -10668.750505 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750505 -> -10668.750501 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750501 -> -10668.750497 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750497 -> -10668.750493 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750493 -> -10668.750489 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750489 -> -10668.750485 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750485 -> -10668.750481 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750481 -> -10668.750477 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750477 -> -10668.750473 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750473 -> -10668.750469 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750469 -> -10668.750465 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750465 -> -10668.750461 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750461 -> -10668.750456 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -10668.750456 -> -10668.750452 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Final Log(lk) : -10668.750452 . Time used 0h16m1s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 952.89user 0.00system 16:01.46elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps