Sequence filename : /auto/dufayard/res/parc_wim/nucleic_M2564_142x1130_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: 56 N_GLOBL: 28 MAX_DIST: 28 . Log(lk) : * -> -22421.306241 . Log(lk) : -22421.306241 -> -21969.365539 14 swaps done . Log(lk) : -21969.365539 -> -21905.602260 12 swaps done . Log(lk) : -21905.602260 -> -21881.696577 9 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -20548.346070 -> -20497.585887 6 swaps done . Log(lk) : -20497.585887 -> -20482.873993 6 swaps done . Log(lk) : -20482.873993 -> -20472.588788 4 swaps done . Log(lk) : -20472.588788 -> -20467.313853 4 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -20459.304139 -> -20457.030535 1 swap done . Log(lk) : -20457.030535 -> -20456.045506 1 swap done . Log(lk) : -20456.045506 -> -20450.614234 2 swaps done . Log(lk) : -20450.614234 -> -20442.934208 2 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -20442.766141 -> -20441.606180 0 swap done . Log(lk) : -20441.606180 -> -20441.318070 0 swap done . Log(lk) : -20441.318070 -> -20441.209215 0 swap done . Log(lk) : -20441.209215 -> -20441.011577 1 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -20441.002246 -> -20440.241437 0 swap done . Log(lk) : -20440.241437 -> -20440.139210 0 swap done . Log(lk) : -20440.139210 -> -20440.104618 0 swap done . Log(lk) : -20440.104618 -> -20440.088364 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -20440.084203 -> -20440.074433 0 swap done . Log(lk) : -20440.074433 -> -20440.069411 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods making move: 13 -> 46 (0.585331) making move: 28 -> 45 (0.021749) making move: 46 -> 11 (2.287404) making move: 48 -> 77 (2.890250) making move: 73 -> 15 (1.547247) making move: 255 -> 265 (1.567015) making move: 258 -> 261 (2.541261) Log (lk): -20419.252171 . Log(lk) : -20419.252171 -> -20417.322732 2 swaps done . Log(lk) : -20417.322732 -> -20415.967267 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -20415.953926 -> -20415.747491 0 swap done . Log(lk) : -20415.747491 -> -20415.717657 0 swap done . Log(lk) : -20415.717657 -> -20415.712847 0 swap done . Log(lk) : -20415.712847 -> -20415.711914 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods making move: 13 -> 46 (0.694266) Log (lk): -20412.902742 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -20412.890417 -> -20412.821215 0 swap done . Log(lk) : -20412.821215 -> -20412.807077 0 swap done . Log(lk) : -20412.807077 -> -20412.801602 0 swap done . Log(lk) : -20412.801602 -> -20412.799016 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -20412.798797 -> -20412.797360 0 swap done . Log(lk) : -20412.797360 -> -20412.796595 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations making move: 40 -> 56 (0.242211) Log (lk): -20411.468694 . Log(lk) : -20411.468694 -> -20411.943994 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -20411.468694 -> -20411.442044 2 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -20411.442027 -> -20411.426133 1 swap done . Log(lk) : -20411.426133 -> -20411.330064 0 swap done . Log(lk) : -20411.330064 -> -20411.276396 0 swap done . Log(lk) : -20411.276396 -> -20411.240290 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -20411.240110 -> -20411.220062 0 swap done . Log(lk) : -20411.220062 -> -20411.210481 0 swap done . Log(lk) : -20411.210481 -> -20411.206334 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations making move: 220 -> 275 (0.034954) Log (lk): -20408.817271 . Log(lk) : -20408.817271 -> -20411.544217 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -20408.817271 -> -20408.786684 3 swaps done . Log(lk) : -20408.786684 -> -20408.298473 3 swaps done . Log(lk) : -20408.298473 -> -20407.575065 2 swaps done . Log(lk) : -20407.575065 -> -20407.374998 0 swap done . Log(lk) : -20407.374998 -> -20407.276420 0 swap done . Log(lk) : -20407.276420 -> -20407.238649 0 swap done . Log(lk) : -20407.238649 -> -20407.226984 0 swap done . Log(lk) : -20407.226984 -> -20407.223602 0 swap done . Log(lk) : -20407.223602 -> -20407.222651 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations making move: 62 -> 65 (1.291806) Log (lk): -20405.511039 . Log(lk) : -20405.511039 -> -20405.425091 0 swap done . Log(lk) : -20405.425091 -> -20405.419523 0 swap done . Log(lk) : -20405.419523 -> -20405.418557 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations making move: 47 -> 10 (0.440787) Log (lk): -20404.654739 . Log(lk) : -20404.654739 -> -20404.599436 1 swap done . Log(lk) : -20404.599436 -> -20404.597055 0 swap done . Log(lk) : -20404.597055 -> -20404.596180 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization Log (lk): -20404.596208 nr_d_L: 544832 nr_d_lk: 120301 nr_loc: 365 nr_glb: 28 . Time used 0h18m53s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 1005.22user 0.00system 18:52.58elapsed 88%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps