Sequence filename : /auto/dufayard/res/2.4.5/nucleic_M2862_54x1011_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 = 20216280 . Log(lk) : * -> -18475.363763 . Log(lk) : -18475.363763 -> -18121.125351 5 swaps done . Log(lk) : -18121.125351 -> -18095.707293 4 swaps done . Log(lk) : -18095.707293 -> -18086.809374 3 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16391.893980 -> -16347.581331 3 swaps done . Log(lk) : -16347.581331 -> -16342.926351 1 swap done . Log(lk) : -16342.926351 -> -16341.283524 0 swap done . Log(lk) : -16341.283524 -> -16340.523117 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16288.789919 -> -16278.806802 1 swap done . Log(lk) : -16278.806802 -> -16274.761799 0 swap done . Log(lk) : -16274.761799 -> -16272.815143 0 swap done . Log(lk) : -16272.815143 -> -16271.800737 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16265.332260 -> -16262.190033 0 swap done . Log(lk) : -16262.190033 -> -16260.788734 0 swap done . Log(lk) : -16260.788734 -> -16260.086093 0 swap done . Last optimization step... . Log(lk) : * -> -16259.570025 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16259.570025 -> -16257.393317 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16257.393317 -> -16256.390970 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16256.390970 -> -16255.949982 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.949982 -> -16255.744622 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.744622 -> -16255.654625 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.654625 -> -16255.613987 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.613987 -> -16255.596536 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.596536 -> -16255.588546 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.588546 -> -16255.585024 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.585024 -> -16255.583427 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.583427 -> -16255.582671 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.582671 -> -16255.582270 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.582270 -> -16255.582024 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.582024 -> -16255.581842 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.581842 -> -16255.581672 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.581672 -> -16255.581539 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.581539 -> -16255.581406 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.581406 -> -16255.581273 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.581273 -> -16255.581139 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.581139 -> -16255.580999 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.580999 -> -16255.580853 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.580853 -> -16255.580704 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.580704 -> -16255.580551 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.580551 -> -16255.580392 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.580392 -> -16255.580227 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.580227 -> -16255.580058 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.580058 -> -16255.579882 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.579882 -> -16255.579700 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.579700 -> -16255.579511 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.579511 -> -16255.579315 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.579315 -> -16255.579112 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.579112 -> -16255.578901 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.578901 -> -16255.578682 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.578682 -> -16255.578456 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.578456 -> -16255.578221 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.578221 -> -16255.577977 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.577977 -> -16255.577724 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.577724 -> -16255.577461 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.577461 -> -16255.577189 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.577189 -> -16255.576906 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.576906 -> -16255.576613 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.576613 -> -16255.576309 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.576309 -> -16255.575993 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.575993 -> -16255.575666 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.575666 -> -16255.575326 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.575326 -> -16255.574973 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.574973 -> -16255.574607 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.574607 -> -16255.574228 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.574228 -> -16255.573834 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.573834 -> -16255.573426 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.573426 -> -16255.573002 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.573002 -> -16255.572562 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.572562 -> -16255.572106 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.572106 -> -16255.571632 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.571632 -> -16255.571141 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.571141 -> -16255.570631 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.570631 -> -16255.570103 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.570103 -> -16255.569554 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.569554 -> -16255.568985 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.568985 -> -16255.567864 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.567864 -> -16255.563688 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.563688 -> -16255.562904 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.562904 -> -16255.562902 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -16255.562902 -> -16255.562902 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Final Log(lk) : -16255.562902 . Time used 0h1m54s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 112.55user 0.00system 1:53.83elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps