Sequence filename : /auto/dufayard/res/parc_wim/nucleic_M2707_115x1677_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: 45 N_GLOBL: 22 MAX_DIST: 22 . Log(lk) : * -> -11971.369870 . Log(lk) : -11971.369870 -> -10908.433911 18 swaps done . Log(lk) : -10908.433911 -> -10598.538501 16 swaps done . Log(lk) : -10598.538501 -> -10726.420366 11 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10598.538501 -> -10028.286923 11 swaps done . Log(lk) : -10028.286923 -> -9959.784594 11 swaps done . Log(lk) : -9959.784594 -> -10033.527569 9 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9959.784594 -> -9933.124508 9 swaps done . Log(lk) : -9933.124508 -> -9902.474220 8 swaps done . Log(lk) : -9902.474220 -> -9995.909363 9 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9902.474220 -> -9898.447806 9 swaps done . Log(lk) : -9898.447806 -> -9876.347580 7 swaps done . Log(lk) : -9876.347580 -> -9965.573202 8 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9876.347580 -> -9870.672761 8 swaps done . Log(lk) : -9870.672761 -> -9866.367646 6 swaps done . Log(lk) : -9866.367646 -> -9942.689753 6 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9866.367646 -> -9862.689145 6 swaps done . Log(lk) : -9862.689145 -> -9860.785347 4 swaps done . Log(lk) : -9860.785347 -> -9923.392777 5 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9860.785347 -> -9856.267546 5 swaps done . Log(lk) : -9856.267546 -> -9855.855157 4 swaps done . Log(lk) : -9855.855157 -> -9926.514290 6 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9855.855157 -> -9851.319225 6 swaps done . Log(lk) : -9851.319225 -> -9846.133621 3 swaps done . Log(lk) : -9846.133621 -> -9892.787439 5 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9846.133621 -> -9843.717839 5 swaps done . Log(lk) : -9843.717839 -> -9841.983060 3 swaps done . Log(lk) : -9841.983060 -> -9885.680678 4 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9841.983060 -> -9839.338327 4 swaps done . Log(lk) : -9839.338327 -> -9837.667696 3 swaps done . Log(lk) : -9837.667696 -> -9869.157678 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9837.667696 -> -9835.490205 3 swaps done . Log(lk) : -9835.490205 -> -9833.945864 2 swaps done . Log(lk) : -9833.945864 -> -9860.189479 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9833.945864 -> -9832.175311 3 swaps done . Log(lk) : -9832.175311 -> -9830.646811 3 swaps done . Log(lk) : -9830.646811 -> -9851.966850 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9830.646811 -> -9829.285869 3 swaps done . Log(lk) : -9829.285869 -> -9827.594522 2 swaps done . Log(lk) : -9827.594522 -> -9844.775759 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9827.594522 -> -9821.323344 2 swaps done . Log(lk) : -9821.323344 -> -9819.125578 2 swaps done . Log(lk) : -9819.125578 -> -9818.413693 1 swap done . Log(lk) : -9818.413693 -> -9817.948758 0 swap done . Log(lk) : -9817.948758 -> -9818.015459 1 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9817.948758 -> -9816.941562 1 swap done . Log(lk) : -9816.941562 -> -9816.074957 1 swap done . Log(lk) : -9816.074957 -> -9814.827131 1 swap done . Log(lk) : -9814.827131 -> -9814.416483 0 swap done . Log(lk) : -9814.416483 -> -9814.731525 1 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9814.416483 -> -9813.565804 1 swap done . Log(lk) : -9813.565804 -> -9813.135526 1 swap done . Log(lk) : -9813.135526 -> -9812.879522 0 swap done . Log(lk) : -9812.879522 -> -9812.726388 0 swap done . Log(lk) : -9812.726388 -> -9812.724814 0 swap done . Log(lk) : -9812.724814 -> -9812.694854 0 swap done . Log(lk) : -9812.694854 -> -9812.912255 0 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9812.694854 -> -9812.061689 0 swap done . Log(lk) : -9812.061689 -> -9811.896643 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 163 -> 158 (0.291917) Log (lk): -9811.233789 . Log(lk) : -9811.233789 -> -9811.166035 2 swaps done . Log(lk) : -9811.166035 -> -9811.178308 0 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9811.166035 -> -9810.992481 0 swap done . Log(lk) : -9810.992481 -> -9810.915694 0 swap done . Log(lk) : -9810.915694 -> -9810.883281 0 swap done . Log(lk) : -9810.883281 -> -9810.874243 0 swap done . Log(lk) : -9810.874243 -> -9810.865816 1 swap done . Log(lk) : -9810.865816 -> -9810.852240 0 swap done . Log(lk) : -9810.852240 -> -9810.848998 0 swap done . Log(lk) : -9810.848998 -> -9810.855204 0 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9810.848998 -> -9810.803398 0 swap done . Log(lk) : -9810.803398 -> -9810.779925 0 swap done . Log(lk) : -9810.779925 -> -9810.735990 0 swap done . Log(lk) : -9810.735990 -> -9810.723404 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 163 -> 158 (0.004892) Log (lk): -9810.717994 . Log(lk) : -9810.717994 -> -9810.714199 1 swap done . Log(lk) : -9810.714199 -> -9810.712231 0 swap done . Log(lk) : -9810.712231 -> -9810.711141 0 swap done . Log(lk) : -9810.711141 -> -9810.710531 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 163 -> 158 (0.000031) Log (lk): -9810.710500 . Log(lk) : -9810.710500 -> -9810.710086 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization Log (lk): -9810.710083 . Last optimization step... . Log(lk) : * -> -9810.710083 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9810.710083 -> -9810.685576 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9810.685576 -> -9810.675360 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9810.675360 -> -9810.667639 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9810.667639 -> -9810.663785 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9810.663785 -> -9810.659548 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9810.659548 -> -9810.656454 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9810.656454 -> -9810.656231 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9810.656231 -> -9810.656120 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9810.656120 -> -9810.656089 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9810.656089 -> -9810.656081 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9810.656081 -> -9810.656072 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9810.656072 -> -9810.656066 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9810.656066 -> -9810.656061 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9810.656061 -> -9810.656058 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9810.656058 -> -9810.656053 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9810.656053 -> -9810.656049 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9810.656049 -> -9810.656046 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9810.656046 -> -9810.656043 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9810.656043 -> -9810.656041 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9810.656041 -> -9810.656038 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9810.656038 -> -9810.656036 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9810.656036 -> -9810.656034 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9810.656034 -> -9810.656033 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9810.656033 -> -9810.656032 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... nr_d_L: 190960 nr_d_lk: 45557 nr_loc: 400 nr_glb: 25 . Time used 0h12m36s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 650.39user 0.00system 12:36.35elapsed 85%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps