Sequence filename : /auto/dufayard/res/2.4.5/nucleic_M2901_56x1802_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 . 3 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... . Nbytes = 22952784 . Log(lk) : * -> -8426.882563 . Log(lk) : -8426.882563 -> -8341.156632 9 swaps done . Log(lk) : -8341.156632 -> -8298.710889 6 swaps done . Log(lk) : -8298.710889 -> -8290.645631 4 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7896.688866 -> -7890.239476 4 swaps done . Log(lk) : -7890.239476 -> -7888.406277 4 swaps done . Log(lk) : -7888.406277 -> -7884.776021 4 swaps done . Log(lk) : -7884.776021 -> -7884.276801 4 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7883.679727 -> -7876.188311 4 swaps done . Log(lk) : -7876.188311 -> -7874.334537 3 swaps done . Log(lk) : -7874.334537 -> -7873.251512 3 swaps done . Log(lk) : -7873.251512 -> -7872.815662 3 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7872.785558 -> -7872.382181 3 swaps done . Log(lk) : -7872.382181 -> -7871.718075 3 swaps done . Log(lk) : -7871.718075 -> -7871.846804 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7871.718075 -> -7870.990370 3 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.990345 -> -7870.682854 2 swaps done . Log(lk) : -7870.682854 -> -7870.562308 0 swap done . Log(lk) : -7870.562308 -> -7870.512071 0 swap done . Log(lk) : -7870.512071 -> -7870.475470 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.471893 -> -7870.439822 0 swap done . Log(lk) : -7870.439822 -> -7870.411391 0 swap done . Log(lk) : -7870.411391 -> -7870.384698 0 swap done . Last optimization step... . Log(lk) : * -> -7870.344354 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.344354 -> -7870.286675 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.286675 -> -7870.251275 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.251275 -> -7870.246775 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.246775 -> -7870.242289 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.242289 -> -7870.237745 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.237745 -> -7870.233201 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.233201 -> -7870.228598 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.228598 -> -7870.223990 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.223990 -> -7870.219316 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.219316 -> -7870.214642 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.214642 -> -7870.209902 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.209902 -> -7870.205162 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.205162 -> -7870.200355 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.200355 -> -7870.195547 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.195547 -> -7870.190670 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.190670 -> -7870.185986 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.185986 -> -7870.182602 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.182602 -> -7870.179683 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.179683 -> -7870.177282 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.177282 -> -7870.175307 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.175307 -> -7870.173634 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.173634 -> -7870.172163 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.172163 -> -7870.170700 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.170700 -> -7870.169237 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.169237 -> -7870.167774 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.167774 -> -7870.166310 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.166310 -> -7870.164847 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.164847 -> -7870.163383 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.163383 -> -7870.161920 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.161920 -> -7870.160456 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.160456 -> -7870.158993 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.158993 -> -7870.157529 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.157529 -> -7870.156065 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.156065 -> -7870.154601 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.154601 -> -7870.153137 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.153137 -> -7870.151673 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.151673 -> -7870.150208 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.150208 -> -7870.148743 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.148743 -> -7870.147278 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.147278 -> -7870.145813 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.145813 -> -7870.144348 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.144348 -> -7870.142882 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.142882 -> -7870.141416 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.141416 -> -7870.140325 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.140325 -> -7870.139315 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.139315 -> -7870.138302 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.138302 -> -7870.137290 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.137290 -> -7870.136279 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.136279 -> -7870.135270 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.135270 -> -7870.134262 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.134262 -> -7870.133256 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.133256 -> -7870.132251 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.132251 -> -7870.131247 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.131247 -> -7870.130245 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.130245 -> -7870.129244 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.129244 -> -7870.128245 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.128245 -> -7870.127247 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.127247 -> -7870.126252 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.126252 -> -7870.125259 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.125259 -> -7870.124267 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.124267 -> -7870.123277 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.123277 -> -7870.122288 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.122288 -> -7870.121300 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.121300 -> -7870.120314 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.120314 -> -7870.119329 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.119329 -> -7870.118323 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.118323 -> -7870.117447 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.117447 -> -7870.117428 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7870.117428 -> -7870.117428 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Final Log(lk) : -7870.117428 . Time used 0h4m5s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 238.42user 0.00system 4:05.02elapsed 97%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps