Sequence filename : /auto/dufayard/res/2.4.5/nucleic_M2587_117x1910_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 = 90315456 . Log(lk) : * -> -17463.878340 . Log(lk) : -17463.878340 -> -16960.581928 15 swaps done . Log(lk) : -16960.581928 -> -16829.085556 13 swaps done . Log(lk) : -16829.085556 -> -16783.099827 9 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16248.639442 -> -16186.445941 7 swaps done . Log(lk) : -16186.445941 -> -16161.277918 3 swaps done . Log(lk) : -16161.277918 -> -16146.890641 4 swaps done . Log(lk) : -16146.890641 -> -16131.173405 3 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16122.988601 -> -16109.106708 3 swaps done . Log(lk) : -16109.106708 -> -16101.519943 1 swap done . Log(lk) : -16101.519943 -> -16096.821231 1 swap done . Log(lk) : -16096.821231 -> -16093.835106 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16090.061695 -> -16085.676982 0 swap done . Log(lk) : -16085.676982 -> -16082.870612 0 swap done . Log(lk) : -16082.870612 -> -16081.027499 0 swap done . Log(lk) : -16081.027499 -> -16079.798851 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16078.355433 -> -16076.623873 0 swap done . Last optimization step... . Log(lk) : * -> -16074.640426 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16074.640426 -> -16072.878191 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16072.878191 -> -16071.797015 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16071.797015 -> -16071.057042 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16071.057042 -> -16070.614870 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16070.614870 -> -16070.320253 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16070.320253 -> -16070.142208 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16070.142208 -> -16070.022967 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16070.022967 -> -16069.950121 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.950121 -> -16069.901028 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.901028 -> -16069.870660 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.870660 -> -16069.850251 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.850251 -> -16069.837540 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.837540 -> -16069.828951 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.828951 -> -16069.823579 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.823579 -> -16069.819940 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.819940 -> -16069.817645 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.817645 -> -16069.816081 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.816081 -> -16069.815091 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.815091 -> -16069.814408 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.814408 -> -16069.813967 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.813967 -> -16069.813657 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.813657 -> -16069.813453 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.813453 -> -16069.813303 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.813303 -> -16069.813198 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.813198 -> -16069.813117 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.813117 -> -16069.813057 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.813057 -> -16069.813006 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.813006 -> -16069.812964 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812964 -> -16069.812927 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812927 -> -16069.812894 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812894 -> -16069.812864 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812864 -> -16069.812836 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812836 -> -16069.812809 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812809 -> -16069.812783 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812783 -> -16069.812759 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812759 -> -16069.812735 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812735 -> -16069.812712 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812712 -> -16069.812690 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812690 -> -16069.812669 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812669 -> -16069.812648 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812648 -> -16069.812628 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812628 -> -16069.812609 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812609 -> -16069.812590 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812590 -> -16069.812571 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812571 -> -16069.812553 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812553 -> -16069.812536 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812536 -> -16069.812519 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812519 -> -16069.812502 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812502 -> -16069.812486 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812486 -> -16069.812471 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812471 -> -16069.812456 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812456 -> -16069.812441 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812441 -> -16069.812427 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812427 -> -16069.812413 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812413 -> -16069.812400 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812400 -> -16069.812387 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812387 -> -16069.812374 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812374 -> -16069.812362 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812362 -> -16069.812350 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812350 -> -16069.812338 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812338 -> -16069.812327 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812327 -> -16069.812316 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812316 -> -16069.812305 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812305 -> -16069.812295 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812295 -> -16069.812285 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812285 -> -16069.812275 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812275 -> -16069.812266 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812266 -> -16069.812257 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812257 -> -16069.812248 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812248 -> -16069.812239 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812239 -> -16069.812231 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812231 -> -16069.812222 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812222 -> -16069.812214 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812214 -> -16069.812207 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812207 -> -16069.812199 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812199 -> -16069.812192 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812192 -> -16069.812185 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812185 -> -16069.812178 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812178 -> -16069.812171 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812171 -> -16069.812165 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812165 -> -16069.812158 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812158 -> -16069.812152 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812152 -> -16069.812146 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812146 -> -16069.812140 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812140 -> -16069.812135 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812135 -> -16069.812129 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812129 -> -16069.812124 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812124 -> -16069.812119 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812119 -> -16069.812114 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812114 -> -16069.812109 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812109 -> -16069.812104 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812104 -> -16069.812100 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812100 -> -16069.812095 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812095 -> -16069.812091 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812091 -> -16069.812087 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812087 -> -16069.812083 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812083 -> -16069.812079 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812079 -> -16069.812075 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16069.812075 -> -16069.812071 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Final Log(lk) : -16069.812071 . Time used 0h15m11s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 905.70user 0.00system 15:11.37elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps