Sequence filename : /auto/dufayard/res/parc_wim/nucleic_M2708_78x1107_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 . 15 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... N_RGRFT: 30 N_GLOBL: 15 MAX_DIST: 15 . Log(lk) : * -> -7100.033577 . Log(lk) : -7100.033577 -> -6927.999129 10 swaps done . Log(lk) : -6927.999129 -> -6872.741802 9 swaps done . Log(lk) : -6872.741802 -> -6841.539466 9 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6623.802412 -> -6581.128960 5 swaps done . Log(lk) : -6581.128960 -> -6574.183135 4 swaps done . Log(lk) : -6574.183135 -> -6569.647594 3 swaps done . Log(lk) : -6569.647594 -> -6584.612805 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6569.647594 -> -6562.128528 3 swaps done . Log(lk) : -6562.128528 -> -6560.117798 2 swaps done . Log(lk) : -6560.117798 -> -6579.091444 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6560.117798 -> -6552.203864 3 swaps done . Log(lk) : -6552.203864 -> -6553.710730 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6552.203864 -> -6546.082269 2 swaps done . Log(lk) : -6546.082269 -> -6548.013719 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6546.082269 -> -6545.283578 3 swaps done . Log(lk) : -6545.283578 -> -6544.461982 2 swaps done . Log(lk) : -6544.461982 -> -6548.831845 1 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6544.461982 -> -6540.198883 1 swap done . Log(lk) : -6540.198883 -> -6538.907791 1 swap done . Log(lk) : -6538.907791 -> -6538.547905 0 swap done . Log(lk) : -6538.547905 -> -6538.461090 1 swap done . Log(lk) : -6538.461090 -> -6537.468700 1 swap done . Log(lk) : -6537.468700 -> -6537.019994 0 swap done . Log(lk) : -6537.019994 -> -6536.927666 0 swap done . Log(lk) : -6536.927666 -> -6536.909686 0 swap done . Log(lk) : -6536.909686 -> -6536.917166 0 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -6536.909686 -> -6536.478285 0 swap done . Log(lk) : -6536.478285 -> -6536.373526 0 swap done . Log(lk) : -6536.373526 -> -6536.336982 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations making move: 16 -> 31 (0.016347) Log (lk): -6536.227821 . Log(lk) : -6536.227821 -> -6536.204155 0 swap done . Log(lk) : -6536.204155 -> -6536.187462 1 swap done . Log(lk) : -6536.187462 -> -6536.173109 0 swap done . Log(lk) : -6536.173109 -> -6536.159390 0 swap done . Log(lk) : -6536.159390 -> -6536.146509 0 swap done . Log(lk) : -6536.146509 -> -6536.133803 0 swap done . Log(lk) : -6536.133803 -> -6536.121812 0 swap done . Log(lk) : -6536.121812 -> -6536.109939 1 swap done . Log(lk) : -6536.109939 -> -6536.098765 0 swap done . Log(lk) : -6536.098765 -> -6536.087759 0 swap done . Log(lk) : -6536.087759 -> -6536.077531 0 swap done . Log(lk) : -6536.077531 -> -6536.067547 0 swap done . Log(lk) : -6536.067547 -> -6536.058463 0 swap done . Log(lk) : -6536.058463 -> -6536.049773 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 78 -> 85 (0.041273) Log (lk): -6535.983264 . Log(lk) : -6535.983264 -> -6535.972123 0 swap done . Log(lk) : -6535.972123 -> -6535.962783 0 swap done . Log(lk) : -6535.962783 -> -6535.954214 0 swap done . Log(lk) : -6535.954214 -> -6535.940996 1 swap done . Log(lk) : -6535.940996 -> -6535.891105 0 swap done . Log(lk) : -6535.891105 -> -6535.877969 0 swap done . Log(lk) : -6535.877969 -> -6535.869618 0 swap done . Log(lk) : -6535.869618 -> -6535.862614 0 swap done . Log(lk) : -6535.862614 -> -6535.856211 0 swap done . Log(lk) : -6535.856211 -> -6535.850000 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 84 -> 85 (0.016450) Log (lk): -6535.817640 . Log(lk) : -6535.817640 -> -6535.810849 0 swap done . Log(lk) : -6535.810849 -> -6535.805852 0 swap done . Log(lk) : -6535.805852 -> -6535.801197 0 swap done . Log(lk) : -6535.801197 -> -6535.796588 0 swap done . Log(lk) : -6535.796588 -> -6535.792084 0 swap done . Log(lk) : -6535.792084 -> -6535.787604 2 swaps done . Log(lk) : -6535.787604 -> -6535.783213 0 swap done . Log(lk) : -6535.783213 -> -6535.778843 0 swap done . Log(lk) : -6535.778843 -> -6535.774556 0 swap done . Log(lk) : -6535.774556 -> -6535.770292 0 swap done . Log(lk) : -6535.770292 -> -6535.766101 0 swap done . Log(lk) : -6535.766101 -> -6535.761938 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 84 -> 78 (0.008448) Log (lk): -6535.743851 . Log(lk) : -6535.743851 -> -6535.738815 0 swap done . Log(lk) : -6535.738815 -> -6535.734736 0 swap done . Log(lk) : -6535.734736 -> -6535.730877 0 swap done . Log(lk) : -6535.730877 -> -6535.727061 0 swap done . Log(lk) : -6535.727061 -> -6535.723353 0 swap done . Log(lk) : -6535.723353 -> -6535.719662 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 85 -> 84 (0.008228) Log (lk): -6535.702012 . Log(lk) : -6535.702012 -> -6535.697641 0 swap done . Log(lk) : -6535.697641 -> -6535.694022 0 swap done . Log(lk) : -6535.694022 -> -6535.690609 0 swap done . Log(lk) : -6535.690609 -> -6535.687247 0 swap done . Log(lk) : -6535.687247 -> -6535.683976 0 swap done . Log(lk) : -6535.683976 -> -6535.680726 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 78 -> 85 (0.006276) Log (lk): -6535.666841 . Log(lk) : -6535.666841 -> -6535.663162 0 swap done . Log(lk) : -6535.663162 -> -6535.660054 0 swap done . Log(lk) : -6535.660054 -> -6535.657079 0 swap done . Log(lk) : -6535.657079 -> -6535.654133 0 swap done . Log(lk) : -6535.654133 -> -6535.651259 0 swap done . Log(lk) : -6535.651259 -> -6535.648399 1 swap done . Log(lk) : -6535.648399 -> -6535.645603 0 swap done . Log(lk) : -6535.645603 -> -6535.642819 0 swap done . Log(lk) : -6535.642819 -> -6535.640095 0 swap done . Log(lk) : -6535.640095 -> -6535.637384 0 swap done . Log(lk) : -6535.637384 -> -6535.634735 0 swap done . Log(lk) : -6535.634735 -> -6535.632100 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 84 -> 78 (0.006055) Log (lk): -6535.619308 . Log(lk) : -6535.619308 -> -6535.616087 0 swap done . Log(lk) : -6535.616087 -> -6535.613480 0 swap done . Log(lk) : -6535.613480 -> -6535.611021 0 swap done . Log(lk) : -6535.611021 -> -6535.608604 0 swap done . Log(lk) : -6535.608604 -> -6535.606248 0 swap done . Log(lk) : -6535.606248 -> -6535.603912 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 85 -> 84 (0.004177) Log (lk): -6535.597948 . Log(lk) : -6535.597948 -> -6535.596845 0 swap done . Log(lk) : -6535.596845 -> -6535.595933 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 78 -> 85 (0.001546) Log (lk): -6535.592531 . Log(lk) : -6535.592531 -> -6535.591535 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 84 -> 85 (0.000743) Log (lk): -6535.589290 . Log(lk) : -6535.589290 -> -6535.588259 0 swap done . Log(lk) : -6535.588259 -> -6535.587429 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 78 -> 84 (0.001483) Log (lk): -6535.584477 . Log(lk) : -6535.584477 -> -6535.583588 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 85 -> 84 (0.000555) Log (lk): -6535.581558 . Log(lk) : -6535.581558 -> -6535.580663 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 78 -> 85 (0.000443) Log (lk): -6535.578725 . Log(lk) : -6535.578725 -> -6535.577907 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 84 -> 85 (0.000459) Log (lk): -6535.575965 . Log(lk) : -6535.575965 -> -6535.575150 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 78 -> 84 (0.000374) Log (lk): -6535.573129 . Log(lk) : -6535.573129 -> -6535.572396 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 85 -> 84 (0.000359) Log (lk): -6535.570788 . Log(lk) : -6535.570788 -> -6535.570600 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization Log (lk): -6535.570840 nr_d_L: 386536 nr_d_lk: 86290 nr_loc: 1610 nr_glb: 30 . Time used 0h12m25s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 662.41user 0.00system 12:24.83elapsed 88%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps