Sequence filename : /auto/dufayard/res/parc_wim/nucleic_M2913_81x897_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 . 84 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... N_RGRFT: 31 N_GLOBL: 15 MAX_DIST: 15 . Log(lk) : * -> -2592.095007 . Log(lk) : -2592.095007 -> -2560.856384 12 swaps done . Log(lk) : -2560.856384 -> -2549.703750 12 swaps done . Log(lk) : -2549.703750 -> -2550.420484 8 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2549.703750 -> -2453.759788 8 swaps done . Log(lk) : -2453.759788 -> -2451.637871 9 swaps done . Log(lk) : -2451.637871 -> -2448.741998 6 swaps done . Log(lk) : -2448.741998 -> -2446.904681 6 swaps done . Log(lk) : -2446.904681 -> -2451.131439 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2446.904681 -> -2445.639995 3 swaps done . Log(lk) : -2445.639995 -> -2449.824351 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2445.639995 -> -2443.997531 3 swaps done . Log(lk) : -2443.997531 -> -2443.785732 3 swaps done . Log(lk) : -2443.785732 -> -2443.913657 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2443.785732 -> -2443.636736 3 swaps done . Log(lk) : -2443.636736 -> -2443.663946 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2443.636736 -> -2443.532839 3 swaps done . Log(lk) : -2443.532839 -> -2443.403644 3 swaps done . Log(lk) : -2443.403644 -> -2440.016269 2 swaps done . Log(lk) : -2440.016269 -> -2438.403757 2 swaps done . Log(lk) : -2438.403757 -> -2438.408824 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2438.403757 -> -2438.077962 2 swaps done . Log(lk) : -2438.077962 -> -2437.817204 1 swap done . Log(lk) : -2437.817204 -> -2437.758210 1 swap done . Log(lk) : -2437.758210 -> -2437.712612 0 swap done . Log(lk) : -2437.712612 -> -2437.671391 0 swap done . Log(lk) : -2437.671391 -> -2437.659995 0 swap done . Log(lk) : -2437.659995 -> -2437.655803 0 swap done . Log(lk) : -2437.655803 -> -2437.655569 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods making move: 23 -> 54 (0.241604) making move: 23 -> 30 (0.109202) making move: 30 -> 29 (0.040385) making move: 46 -> 39 (0.247956) making move: 55 -> 22 (0.140272) making move: 56 -> 54 (0.021357) making move: 60 -> 86 (0.560905) making move: 64 -> 14 (0.162310) making move: 65 -> 22 (0.076621) making move: 78 -> 80 (0.020666) making move: 83 -> 93 (0.017248) making move: 86 -> 63 (0.010156) making move: 93 -> 63 (0.051272) making move: 112 -> 103 (7.005050) making move: 113 -> 80 (0.000690) making move: 117 -> 11 (0.004150) making move: 153 -> 143 (0.181924) Log (lk): -2425.571777 . Log(lk) : -2425.571777 -> -2425.445711 3 swaps done . Log(lk) : -2425.445711 -> -2425.413779 2 swaps done . Log(lk) : -2425.413779 -> -2425.402519 1 swap done . Log(lk) : -2425.402519 -> -2425.425608 1 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2425.402519 -> -2425.262222 1 swap done . Log(lk) : -2425.262222 -> -2425.264363 1 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2425.262222 -> -2425.254432 1 swap done . Log(lk) : -2425.254432 -> -2425.259936 1 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2425.254432 -> -2425.251970 1 swap done . Log(lk) : -2425.251970 -> -2425.252665 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods making move: 2 -> 114 (0.869049) making move: 7 -> 151 (0.021837) making move: 7 -> 138 (0.000742) making move: 9 -> 154 (0.029859) making move: 64 -> 81 (0.051578) making move: 82 -> 66 (0.010601) making move: 114 -> 11 (0.012052) making move: 114 -> 130 (0.035743) making move: 117 -> 118 (0.003802) making move: 138 -> 10 (0.050145) making move: 141 -> 5 (0.017957) Log (lk): -2422.472565 . Log(lk) : -2422.472565 -> -2422.524510 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2422.472565 -> -2422.441172 3 swaps done . Log(lk) : -2422.441172 -> -2422.456506 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2422.441172 -> -2422.434755 3 swaps done . Log(lk) : -2422.434755 -> -2422.428234 2 swaps done . Log(lk) : -2422.428234 -> -2422.427188 1 swap done . Log(lk) : -2422.427188 -> -2422.433118 0 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2422.427188 -> -2422.423107 0 swap done . Log(lk) : -2422.423107 -> -2422.423175 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods making move: 117 -> 66 (0.068719) making move: 135 -> 79 (0.024432) Log (lk): -2422.266184 . Log(lk) : -2422.266184 -> -2422.454955 1 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2422.266184 -> -2422.263366 1 swap done . Log(lk) : -2422.263366 -> -2422.258718 1 swap done . Log(lk) : -2422.258718 -> -2422.256979 0 swap done . Log(lk) : -2422.256979 -> -2422.256497 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations making move: 130 -> 132 (0.006815) Log (lk): -2422.242351 . Log(lk) : -2422.242351 -> -2422.238553 0 swap done . Log(lk) : -2422.238553 -> -2422.235166 0 swap done . Log(lk) : -2422.235166 -> -2422.233746 0 swap done . Log(lk) : -2422.233746 -> -2422.233006 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 23 -> 51 (0.000127) Log (lk): -2422.232863 . Log(lk) : -2422.232863 -> -2422.232812 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 23 -> 47 (0.000011) Log (lk): -2422.232793 . Log(lk) : -2422.232793 -> -2422.232770 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 23 -> 47 (0.000011) Log (lk): -2422.232751 . Log(lk) : -2422.232751 -> -2422.232735 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 23 -> 47 (0.000011) Log (lk): -2422.232715 . Log(lk) : -2422.232715 -> -2422.232700 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 23 -> 47 (0.000012) Log (lk): -2422.232679 . Log(lk) : -2422.232679 -> -2422.232664 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 23 -> 47 (0.000011) Log (lk): -2422.232644 . Log(lk) : -2422.232644 -> -2422.232629 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 23 -> 47 (0.000012) Log (lk): -2422.232613 . Log(lk) : -2422.232613 -> -2422.232601 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 78 -> 81 (0.000097) Log (lk): -2422.232504 . Log(lk) : -2422.232504 -> -2422.232439 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 117 -> 81 (0.000143) Log (lk): -2422.232297 . Log(lk) : -2422.232297 -> -2422.417038 1 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2422.232297 -> -2422.232257 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 78 -> 81 (0.000127) Log (lk): -2422.232112 . Log(lk) : -2422.232112 -> -2422.232074 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization Log (lk): -2422.232069 . Last optimization step... . Log(lk) : * -> -2422.232069 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2422.232069 -> -2422.231971 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2422.231971 -> -2422.231968 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2422.231968 -> -2422.231966 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2422.231966 -> -2422.231964 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2422.231964 -> -2422.231962 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2422.231962 -> -2422.231960 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2422.231960 -> -2422.231958 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2422.231958 -> -2422.231957 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2422.231957 -> -2422.231956 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2422.231956 -> -2422.231954 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2422.231954 -> -2422.231953 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2422.231953 -> -2422.231952 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2422.231952 -> -2422.231951 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -2422.231951 -> -2422.231950 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... nr_d_L: 275208 nr_d_lk: 85327 nr_loc: 1127 nr_glb: 49 . Time used 0h3m37s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 215.36user 0.00system 3:36.97elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps