Sequence filename : /auto/dufayard/res/parc_wim/nucleic_M2588_68x1196_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 . 6 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... N_RGRFT: 26 N_GLOBL: 13 MAX_DIST: 13 . Log(lk) : * -> -13530.579172 . Log(lk) : -13530.579172 -> -13251.743581 11 swaps done . Log(lk) : -13251.743581 -> -13199.302586 7 swaps done . Log(lk) : -13199.302586 -> -13193.659035 4 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12154.409950 -> -12097.508657 5 swaps done . Log(lk) : -12097.508657 -> -12088.259717 5 swaps done . Log(lk) : -12088.259717 -> -12084.843689 3 swaps done . Log(lk) : -12084.843689 -> -12083.621915 2 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12059.620038 -> -12055.068228 0 swap done . Log(lk) : -12055.068228 -> -12053.615873 0 swap done . Log(lk) : -12053.615873 -> -12052.763664 0 swap done . Log(lk) : -12052.763664 -> -12052.473741 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12050.776820 -> -12049.990425 0 swap done . Log(lk) : -12049.990425 -> -12049.725652 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods making move: 28 -> 25 (0.144291) making move: 29 -> 27 (0.008206) making move: 64 -> 60 (0.301819) Log (lk): -12048.643576 . Log(lk) : -12048.643576 -> -12048.519799 1 swap done . Log(lk) : -12048.519799 -> -12048.479328 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12048.141556 -> -12048.042251 0 swap done . Log(lk) : -12048.042251 -> -12047.994479 0 swap done . Log(lk) : -12047.994479 -> -12047.966562 0 swap done . Log(lk) : -12047.966562 -> -12047.949450 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12047.914229 -> -12047.890702 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 54 -> 50 (0.004709) Log (lk): -12047.872389 . Log(lk) : -12047.872389 -> -12047.858847 1 swap done . Log(lk) : -12047.858847 -> -12047.856128 0 swap done . Log(lk) : -12047.856128 -> -12047.854697 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12047.845146 -> -12047.842161 0 swap done . Log(lk) : -12047.842161 -> -12047.840514 0 swap done . Log(lk) : -12047.840514 -> -12047.839410 0 swap done . Log(lk) : -12047.839410 -> -12047.838619 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 53 -> 55 (0.000172) Log (lk): -12047.838293 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12047.837376 -> -12047.836352 0 swap done . Log(lk) : -12047.836352 -> -12047.835706 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 37 -> 17 (0.000073) Log (lk): -12047.834622 . Log(lk) : -12047.834622 -> -12047.833999 2 swaps done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 53 -> 55 (0.000199) Log (lk): -12047.832763 . Log(lk) : -12047.832763 -> -12047.832205 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 53 -> 55 (0.000202) Log (lk): -12047.830938 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12047.830763 -> -12047.830265 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 37 -> 17 (0.000124) Log (lk): -12047.829819 . Log(lk) : -12047.829819 -> -12047.829275 2 swaps done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 53 -> 55 (0.000110) Log (lk): -12047.828375 . Log(lk) : -12047.828375 -> -12047.828033 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 37 -> 16 (0.000119) Log (lk): -12047.827678 . Log(lk) : -12047.827678 -> -12047.827521 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 37 -> 17 (0.000028) Log (lk): -12047.827493 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12047.827438 -> -12047.827284 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 37 -> 17 (0.000029) Log (lk): -12047.827255 . Log(lk) : -12047.827255 -> -12047.827108 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 37 -> 17 (0.000040) Log (lk): -12047.827069 . Log(lk) : -12047.827069 -> -12047.826930 2 swaps done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 53 -> 55 (0.000113) Log (lk): -12047.826470 . Log(lk) : -12047.826470 -> -12047.812168 1 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12047.811944 -> -12047.767634 0 swap done . Log(lk) : -12047.767634 -> -12047.733079 0 swap done . Log(lk) : -12047.733079 -> -12047.701318 0 swap done . Log(lk) : -12047.701318 -> -12047.691880 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12047.691864 -> -12047.689661 0 swap done . Log(lk) : -12047.689661 -> -12047.689120 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization Log (lk): -12047.689120 . Last optimization step... . Log(lk) : * -> -12047.689120 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12047.689120 -> -12047.689010 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12047.689010 -> -12047.688968 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12047.688968 -> -12047.688937 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12047.688937 -> -12047.688921 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12047.688921 -> -12047.688917 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12047.688917 -> -12047.688915 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -12047.688915 -> -12047.688914 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... nr_d_L: 180368 nr_d_lk: 55466 nr_loc: 1300 nr_glb: 25 . Time used 0h9m30s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 484.37user 0.00system 9:30.13elapsed 84%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps