Sequence filename : /auto/dufayard/res/parc_wim/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... N_RGRFT: 27 N_GLOBL: 13 MAX_DIST: 13 . Log(lk) : * -> -6104.441894 . Log(lk) : -6104.441894 -> -6049.115789 9 swaps done . Log(lk) : -6049.115789 -> -6038.778239 6 swaps done . Log(lk) : -6038.778239 -> -6036.534993 3 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5796.647487 -> -5793.240076 3 swaps done . Log(lk) : -5793.240076 -> -5792.554505 1 swap done . Log(lk) : -5792.554505 -> -5792.371467 0 swap done . Log(lk) : -5792.371467 -> -5792.303391 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5791.840945 -> -5791.786568 0 swap done . Log(lk) : -5791.786568 -> -5791.764346 0 swap done . Log(lk) : -5791.764346 -> -5791.754663 0 swap done . Log(lk) : -5791.754663 -> -5791.750343 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods making move: 82 -> 130 (2.536996) making move: 133 -> 136 (0.676630) Log (lk): -5786.439005 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5786.405996 -> -5786.105124 1 swap done . Log(lk) : -5786.105124 -> -5785.941990 0 swap done . Log(lk) : -5785.941990 -> -5785.831991 0 swap done . Log(lk) : -5785.831991 -> -5785.742540 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5785.742183 -> -5785.701417 0 swap done . Log(lk) : -5785.701417 -> -5785.691594 0 swap done . Log(lk) : -5785.691594 -> -5785.689511 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations making move: 33 -> 19 (0.098932) Log (lk): -5785.538970 . Log(lk) : -5785.538970 -> -5785.510527 2 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5785.506348 -> -5785.491791 0 swap done . Log(lk) : -5785.491791 -> -5785.484849 0 swap done . Log(lk) : -5785.484849 -> -5785.478732 0 swap done . Log(lk) : -5785.478732 -> -5785.473128 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5785.472619 -> -5785.468002 0 swap done . Log(lk) : -5785.468002 -> -5785.460068 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations making move: 13 -> 12 (0.002184) Log (lk): -5785.452373 . Log(lk) : -5785.452373 -> -5785.447871 1 swap done . Log(lk) : -5785.447871 -> -5785.444806 1 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5785.444760 -> -5785.441910 0 swap done . Log(lk) : -5785.441910 -> -5785.439150 0 swap done . Log(lk) : -5785.439150 -> -5785.436469 0 swap done . Log(lk) : -5785.436469 -> -5785.435008 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5785.434885 -> -5785.434638 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 58 -> 57 (0.003865) Log (lk): -5785.425572 . Log(lk) : -5785.425572 -> -5785.415743 1 swap done . Log(lk) : -5785.415743 -> -5785.385168 1 swap done . Log(lk) : -5785.385168 -> -5785.307105 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5785.307081 -> -5784.544312 1 swap done . Log(lk) : -5784.544312 -> -5783.886879 1 swap done . Log(lk) : -5783.886879 -> -5783.780670 1 swap done . Log(lk) : -5783.780670 -> -5783.776199 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -5783.770547 -> -5783.769133 0 swap done . Log(lk) : -5783.769133 -> -5783.768522 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization Log (lk): -5783.767951 nr_d_L: 78624 nr_d_lk: 20816 nr_loc: 272 nr_glb: 14 . Time used 0h2m42s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 128.67user 0.00system 2:41.86elapsed 79%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps