Sequence filename : /auto/dufayard/res/2.4.5/nucleic_M2879_70x800_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 . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... . Nbytes = 20940176 . Log(lk) : * -> -6106.102230 . Log(lk) : -6106.102230 -> -6047.952435 8 swaps done . Log(lk) : -6047.952435 -> -6037.492218 5 swaps done . Log(lk) : -6037.492218 -> -6035.172122 3 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5795.270876 -> -5791.763523 3 swaps done . Log(lk) : -5791.763523 -> -5791.063712 1 swap done . Log(lk) : -5791.063712 -> -5790.859166 0 swap done . Log(lk) : -5790.859166 -> -5790.775886 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.303836 -> -5790.242776 0 swap done . Log(lk) : -5790.242776 -> -5790.216820 0 swap done . Log(lk) : -5790.216820 -> -5790.204261 0 swap done . Log(lk) : -5790.204261 -> -5790.198512 0 swap done . Last optimization step... . Log(lk) : * -> -5790.194923 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.194923 -> -5790.191342 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.191342 -> -5790.190874 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190874 -> -5790.190711 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190711 -> -5790.190639 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190639 -> -5790.190602 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190602 -> -5790.190581 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190581 -> -5790.190568 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190568 -> -5790.190558 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190558 -> -5790.190551 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190551 -> -5790.190545 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190545 -> -5790.190539 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190539 -> -5790.190534 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190534 -> -5790.190529 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190529 -> -5790.190524 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190524 -> -5790.190518 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190518 -> -5790.190513 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190513 -> -5790.190508 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190508 -> -5790.190503 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190503 -> -5790.190498 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190498 -> -5790.190493 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190493 -> -5790.190487 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190487 -> -5790.190482 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190482 -> -5790.190477 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190477 -> -5790.190471 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190471 -> -5790.190466 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190466 -> -5790.190461 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190461 -> -5790.190455 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190455 -> -5790.190450 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190450 -> -5790.190445 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190445 -> -5790.190439 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190439 -> -5790.190434 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190434 -> -5790.190428 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190428 -> -5790.190423 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190423 -> -5790.190417 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190417 -> -5790.190411 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190411 -> -5790.190406 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190406 -> -5790.190400 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190400 -> -5790.190395 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190395 -> -5790.190389 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190389 -> -5790.190383 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190383 -> -5790.190377 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190377 -> -5790.190372 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190372 -> -5790.190366 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190366 -> -5790.190360 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190360 -> -5790.190354 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190354 -> -5790.190348 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190348 -> -5790.190342 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190342 -> -5790.190336 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190336 -> -5790.190330 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190330 -> -5790.190324 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190324 -> -5790.190318 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190318 -> -5790.190312 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190312 -> -5790.190306 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190306 -> -5790.190300 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190300 -> -5790.190294 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190294 -> -5790.190288 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190288 -> -5790.190282 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190282 -> -5790.190275 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190275 -> -5790.190269 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190269 -> -5790.190263 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190263 -> -5790.190257 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190257 -> -5790.190250 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190250 -> -5790.190244 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190244 -> -5790.190238 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190238 -> -5790.190231 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190231 -> -5790.190225 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190225 -> -5790.190218 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190218 -> -5790.190212 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190212 -> -5790.190205 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190205 -> -5790.190199 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190199 -> -5790.190192 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190192 -> -5790.190185 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190185 -> -5790.190179 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190179 -> -5790.190172 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190172 -> -5790.190165 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190165 -> -5790.190158 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190158 -> -5790.190152 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190152 -> -5790.190145 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190145 -> -5790.190138 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190138 -> -5790.190131 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190131 -> -5790.190124 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190124 -> -5790.190117 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190117 -> -5790.190110 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190110 -> -5790.190103 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190103 -> -5790.190096 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190096 -> -5790.190089 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190089 -> -5790.190082 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190082 -> -5790.190075 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190075 -> -5790.190068 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190068 -> -5790.190060 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190060 -> -5790.190053 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190053 -> -5790.190046 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190046 -> -5790.190039 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190039 -> -5790.190031 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190031 -> -5790.190024 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190024 -> -5790.190016 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190016 -> -5790.190009 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190009 -> -5790.190001 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5790.190001 -> -5790.189994 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Final Log(lk) : -5790.189994 . Time used 0h6m7s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 365.57user 0.00system 6:06.16elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps