Sequence filename : /auto/dufayard/res/2.4.5/nucleic_M2913_81x897_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 . 84 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... . Nbytes = 10273944 . Log(lk) : * -> -2596.101443 . Log(lk) : -2596.101443 -> -2558.831273 10 swaps done . Log(lk) : -2558.831273 -> -2544.427675 12 swaps done . Log(lk) : -2544.427675 -> -2544.412837 9 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2450.594343 -> -2444.217921 8 swaps done . Log(lk) : -2444.217921 -> -2444.524624 5 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2444.217921 -> -2436.483318 5 swaps done . Log(lk) : -2436.483318 -> -2435.466433 6 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2435.442745 -> -2435.834054 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2435.442745 -> -2433.692567 3 swaps done . Log(lk) : -2433.692567 -> -2433.623664 3 swaps done . Log(lk) : -2433.623664 -> -2433.644117 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2433.623664 -> -2433.000174 2 swaps done . Log(lk) : -2433.000174 -> -2432.834626 3 swaps done . Log(lk) : -2432.834626 -> -2432.851975 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2432.834626 -> -2432.619417 2 swaps done . Log(lk) : -2432.619417 -> -2432.489339 2 swaps done . Log(lk) : -2432.489339 -> -2432.523252 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2432.489339 -> -2432.448393 2 swaps done . Log(lk) : -2432.448393 -> -2432.492022 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2432.448393 -> -2432.405227 2 swaps done . Log(lk) : -2432.405227 -> -2429.082661 3 swaps done . Log(lk) : -2429.082661 -> -2427.253005 3 swaps done . Log(lk) : -2427.253005 -> -2426.971325 2 swaps done . Log(lk) : -2426.971325 -> -2426.907984 1 swap done . Log(lk) : -2426.907984 -> -2426.975456 0 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.907984 -> -2426.781413 0 swap done . Log(lk) : -2426.781413 -> -2426.775879 0 swap done . Log(lk) : -2426.775879 -> -2426.783005 0 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.775879 -> -2426.772445 0 swap done . Log(lk) : -2426.772445 -> -2426.773120 0 swap done . Last optimization step... . Log(lk) : * -> -2426.769798 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.769798 -> -2426.769614 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.769614 -> -2426.769437 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.769437 -> -2426.769255 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.769255 -> -2426.769065 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.769065 -> -2426.768867 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.768867 -> -2426.768661 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.768661 -> -2426.768446 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.768446 -> -2426.768222 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.768222 -> -2426.767988 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.767988 -> -2426.767744 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.767744 -> -2426.767489 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.767489 -> -2426.767222 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.767222 -> -2426.766954 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.766954 -> -2426.766701 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.766701 -> -2426.766454 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.766454 -> -2426.766195 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.766195 -> -2426.765923 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.765923 -> -2426.765636 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.765636 -> -2426.765335 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.765335 -> -2426.765018 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.765018 -> -2426.764685 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.764685 -> -2426.764333 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.764333 -> -2426.763964 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.763964 -> -2426.763574 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.763574 -> -2426.763164 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.763164 -> -2426.762732 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.762732 -> -2426.762277 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.762277 -> -2426.761797 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.761797 -> -2426.761292 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.761292 -> -2426.760748 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.760748 -> -2426.760171 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.760171 -> -2426.759562 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.759562 -> -2426.758921 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.758921 -> -2426.758265 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.758265 -> -2426.757584 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.757584 -> -2426.756865 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.756865 -> -2426.756106 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.756106 -> -2426.755346 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.755346 -> -2426.754629 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.754629 -> -2426.753872 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.753872 -> -2426.753139 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.753139 -> -2426.752873 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.752873 -> -2426.752705 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.752705 -> -2426.752534 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.752534 -> -2426.752360 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.752360 -> -2426.752247 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.752247 -> -2426.752219 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.752219 -> -2426.752192 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.752192 -> -2426.752165 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.752165 -> -2426.752137 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.752137 -> -2426.752108 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.752108 -> -2426.752078 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.752078 -> -2426.752048 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.752048 -> -2426.752017 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.752017 -> -2426.751985 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.751985 -> -2426.751953 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.751953 -> -2426.751919 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.751919 -> -2426.751885 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.751885 -> -2426.751850 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.751850 -> -2426.751814 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.751814 -> -2426.751778 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.751778 -> -2426.751740 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.751740 -> -2426.751702 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.751702 -> -2426.751663 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.751663 -> -2426.751622 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.751622 -> -2426.751581 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.751581 -> -2426.751539 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.751539 -> -2426.751496 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.751496 -> -2426.751451 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.751451 -> -2426.751406 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.751406 -> -2426.751360 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.751360 -> -2426.751313 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.751313 -> -2426.751266 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.751266 -> -2426.751218 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.751218 -> -2426.751168 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.751168 -> -2426.751117 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.751117 -> -2426.751065 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.751065 -> -2426.751011 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.751011 -> -2426.750957 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.750957 -> -2426.750905 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.750905 -> -2426.750851 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.750851 -> -2426.750796 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.750796 -> -2426.750740 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.750740 -> -2426.750682 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.750682 -> -2426.750623 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.750623 -> -2426.750563 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.750563 -> -2426.750500 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.750500 -> -2426.750437 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.750437 -> -2426.750371 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.750371 -> -2426.750304 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.750304 -> -2426.750236 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.750236 -> -2426.750165 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.750165 -> -2426.750093 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.750093 -> -2426.750019 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.750019 -> -2426.749943 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.749943 -> -2426.749866 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.749866 -> -2426.749786 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.749786 -> -2426.749704 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -2426.749704 -> -2426.749620 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Final Log(lk) : -2426.749620 . Time used 0h2m46s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 165.83user 0.00system 2:46.21elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps