Sequence filename : /auto/dufayard/res/parc_wim/nucleic_M2711_123x1181_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 . 18 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... N_RGRFT: 48 N_GLOBL: 24 MAX_DIST: 24 . Log(lk) : * -> -11859.544565 . Log(lk) : -11859.544565 -> -11599.782061 14 swaps done . Log(lk) : -11599.782061 -> -11555.393169 10 swaps done . Log(lk) : -11555.393169 -> -11543.093504 8 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10736.333239 -> -10705.896294 6 swaps done . Log(lk) : -10705.896294 -> -10697.724607 4 swaps done . Log(lk) : -10697.724607 -> -10694.077890 5 swaps done . Log(lk) : -10694.077890 -> -10691.660959 3 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10683.279537 -> -10681.284786 3 swaps done . Log(lk) : -10681.284786 -> -10680.307118 1 swap done . Log(lk) : -10680.307118 -> -10679.846239 0 swap done . Log(lk) : -10679.846239 -> -10679.606633 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10679.485635 -> -10679.297638 1 swap done . Log(lk) : -10679.297638 -> -10679.173727 0 swap done . Log(lk) : -10679.173727 -> -10679.108569 1 swap done . Log(lk) : -10679.108569 -> -10678.828383 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10678.818536 -> -10678.775317 0 swap done . Log(lk) : -10678.775317 -> -10678.757237 0 swap done . Log(lk) : -10678.757237 -> -10678.748413 0 swap done . Log(lk) : -10678.748413 -> -10678.743616 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10678.742237 -> -10678.739045 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods making move: 13 -> 24 (0.000093) making move: 147 -> 165 (0.160959) making move: 148 -> 146 (3.306826) Log (lk): -10674.559765 . Log(lk) : -10674.559765 -> -10674.559022 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 22 -> 27 (0.000038) Log (lk): -10674.558980 . Log(lk) : -10674.558980 -> -10674.558661 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization Log (lk): -10674.558661 nr_d_L: 174168 nr_d_lk: 38153 nr_loc: 200 nr_glb: 25 . Time used 0h4m56s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 268.16user 0.00system 4:55.61elapsed 90%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps