Sequence filename : /auto/dufayard/res/2.4.5/nucleic_M2623_139x1044_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 = 86501800 . Log(lk) : * -> -50696.348726 . Log(lk) : -50696.348726 -> -49450.756803 15 swaps done . Log(lk) : -49450.756803 -> -49236.604235 10 swaps done . Log(lk) : -49236.604235 -> -49172.017791 8 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46610.191524 -> -46454.813131 10 swaps done . Log(lk) : -46454.813131 -> -46363.228595 7 swaps done . Log(lk) : -46363.228595 -> -46316.662438 6 swaps done . Log(lk) : -46316.662438 -> -46290.674003 6 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46242.506252 -> -46228.557181 8 swaps done . Log(lk) : -46228.557181 -> -46214.853220 5 swaps done . Log(lk) : -46214.853220 -> -46210.844392 5 swaps done . Log(lk) : -46210.844392 -> -46189.279655 4 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46186.226673 -> -46175.855927 4 swaps done . Log(lk) : -46175.855927 -> -46169.370521 3 swaps done . Log(lk) : -46169.370521 -> -46166.451087 3 swaps done . Log(lk) : -46166.451087 -> -46164.980006 3 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46164.733307 -> -46163.002491 4 swaps done . Log(lk) : -46163.002491 -> -46159.714143 5 swaps done . Log(lk) : -46159.714143 -> -46157.248455 3 swaps done . Log(lk) : -46157.248455 -> -46156.578803 3 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46156.537120 -> -46155.833343 2 swaps done . Log(lk) : -46155.833343 -> -46156.118214 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46155.833343 -> -46154.710851 2 swaps done . Log(lk) : -46154.710851 -> -46154.876738 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46154.710851 -> -46154.474030 2 swaps done . Log(lk) : -46154.474030 -> -46155.249715 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46154.474030 -> -46154.164326 2 swaps done . Log(lk) : -46154.164326 -> -46153.924637 1 swap done . Log(lk) : -46153.924637 -> -46153.844930 0 swap done . Log(lk) : -46153.844930 -> -46153.801047 0 swap done . Log(lk) : -46153.801047 -> -46153.774155 0 swap done . Log(lk) : -46153.774155 -> -46153.753884 0 swap done . Log(lk) : -46153.753884 -> -46153.738341 0 swap done . Log(lk) : -46153.738341 -> -46153.728276 0 swap done . Last optimization step... . Log(lk) : * -> -46153.715441 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.715441 -> -46153.695980 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.695980 -> -46153.682965 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.682965 -> -46153.671984 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.671984 -> -46153.663494 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.663494 -> -46153.656342 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.656342 -> -46153.649707 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.649707 -> -46153.643654 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.643654 -> -46153.637936 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.637936 -> -46153.632612 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.632612 -> -46153.627561 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.627561 -> -46153.622800 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.622800 -> -46153.618268 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.618268 -> -46153.613963 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.613963 -> -46153.609851 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.609851 -> -46153.605920 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.605920 -> -46153.602185 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.602185 -> -46153.599172 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.599172 -> -46153.596510 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.596510 -> -46153.594002 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.594002 -> -46153.591617 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.591617 -> -46153.589347 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.589347 -> -46153.587185 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.587185 -> -46153.585120 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.585120 -> -46153.583151 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.583151 -> -46153.581267 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.581267 -> -46153.579466 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.579466 -> -46153.577740 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.577740 -> -46153.576088 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.576088 -> -46153.574503 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.574503 -> -46153.572983 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.572983 -> -46153.571523 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.571523 -> -46153.570121 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.570121 -> -46153.568772 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.568772 -> -46153.567476 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.567476 -> -46153.566228 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.566228 -> -46153.565027 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.565027 -> -46153.563869 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.563869 -> -46153.562753 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.562753 -> -46153.562208 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -46153.562208 -> -46153.562208 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Final Log(lk) : -46153.562208 . Time used 0h8m32s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 510.89user 0.00system 8:32.89elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps