Sequence filename : /auto/dufayard/res/parc_wim/nucleic_M2933_99x1634_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 . 3 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... N_RGRFT: 39 N_GLOBL: 19 MAX_DIST: 19 . Log(lk) : * -> -8166.908936 . Log(lk) : -8166.908936 -> -8041.077652 17 swaps done . Log(lk) : -8041.077652 -> -8003.267252 15 swaps done . Log(lk) : -8003.267252 -> -7978.479263 12 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7698.604803 -> -7665.641466 11 swaps done . Log(lk) : -7665.641466 -> -7654.552811 11 swaps done . Log(lk) : -7654.552811 -> -7647.138105 10 swaps done . Log(lk) : -7647.138105 -> -7646.504843 7 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7642.324918 -> -7640.927098 5 swaps done . Log(lk) : -7640.927098 -> -7641.233081 6 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7640.927098 -> -7640.185398 6 swaps done . Log(lk) : -7640.185398 -> -7640.033785 3 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7640.010682 -> -7640.579180 4 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7640.010682 -> -7639.836752 4 swaps done . Log(lk) : -7639.836752 -> -7639.877678 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.836752 -> -7639.509931 3 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.509905 -> -7639.345396 3 swaps done . Log(lk) : -7639.345396 -> -7639.388298 1 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.345396 -> -7639.276578 1 swap done . Log(lk) : -7639.276578 -> -7639.231553 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.230997 -> -7639.207046 1 swap done . Log(lk) : -7639.207046 -> -7639.193813 0 swap done . Log(lk) : -7639.193813 -> -7639.185582 0 swap done . Log(lk) : -7639.185582 -> -7639.189710 0 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7639.185582 -> -7639.167427 0 swap done . Log(lk) : -7639.167427 -> -7639.157082 0 swap done . Log(lk) : -7639.157082 -> -7639.148598 0 swap done . Log(lk) : -7639.148598 -> -7639.141702 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods making move: 12 -> 49 (0.210241) making move: 13 -> 34 (0.667477) making move: 14 -> 25 (0.545782) making move: 18 -> 25 (0.011037) making move: 19 -> 30 (0.006674) making move: 25 -> 30 (0.000021) making move: 35 -> 32 (0.041503) making move: 36 -> 37 (0.004680) making move: 50 -> 11 (0.140847) making move: 51 -> 47 (0.016686) making move: 56 -> 61 (0.953603) making move: 58 -> 59 (0.393918) making move: 63 -> 56 (0.048778) making move: 65 -> 10 (3.785876) making move: 180 -> 181 (2.367972) making move: 182 -> 161 (0.097144) making move: 187 -> 181 (1.584212) Log (lk): -7622.881785 . Log(lk) : -7622.881785 -> -7622.666484 3 swaps done . Log(lk) : -7622.666484 -> -7622.606390 2 swaps done . Log(lk) : -7622.606390 -> -7622.559279 2 swaps done . Log(lk) : -7622.559279 -> -7622.526840 1 swap done . Log(lk) : -7622.526840 -> -7622.512408 1 swap done . Log(lk) : -7622.512408 -> -7622.508076 1 swap done . Log(lk) : -7622.508076 -> -7622.501397 2 swaps done . Log(lk) : -7622.501397 -> -7622.497958 0 swap done . Log(lk) : -7622.497958 -> -7622.491849 0 swap done . Log(lk) : -7622.491849 -> -7622.487668 1 swap done . Log(lk) : -7622.487668 -> -7622.480118 1 swap done . Log(lk) : -7622.480118 -> -7622.472627 0 swap done . Log(lk) : -7622.472627 -> -7622.460799 0 swap done . Log(lk) : -7622.460799 -> -7622.445868 0 swap done . Log(lk) : -7622.445868 -> -7622.424275 0 swap done . Log(lk) : -7622.424275 -> -7622.392833 0 swap done . Log(lk) : -7622.392833 -> -7622.360306 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods making move: 34 -> 36 (0.026488) Log (lk): -7622.263094 . Log(lk) : -7622.263094 -> -7622.251245 0 swap done . Log(lk) : -7622.251245 -> -7622.249857 0 swap done . Log(lk) : -7622.249857 -> -7622.249421 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 52 -> 48 (0.000121) Log (lk): -7622.248175 . Log(lk) : -7622.248175 -> -7622.247958 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 51 -> 47 (0.000108) Log (lk): -7622.247413 . Log(lk) : -7622.247413 -> -7622.247216 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 52 -> 48 (0.000106) Log (lk): -7622.246779 . Log(lk) : -7622.246779 -> -7622.246589 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 51 -> 47 (0.000107) Log (lk): -7622.246165 . Log(lk) : -7622.246165 -> -7622.245985 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 52 -> 48 (0.000148) Log (lk): -7622.245477 . Log(lk) : -7622.245477 -> -7622.245292 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 51 -> 47 (0.000178) Log (lk): -7622.244127 . Log(lk) : -7622.244127 -> -7622.243675 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 52 -> 48 (0.000650) Log (lk): -7622.242076 . Log(lk) : -7622.242076 -> -7622.241616 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 51 -> 47 (0.000673) Log (lk): -7622.238138 . Log(lk) : -7622.238138 -> -7622.237775 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 52 -> 48 (0.000087) Log (lk): -7622.237498 . Log(lk) : -7622.237498 -> -7622.237379 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 51 -> 47 (0.000085) Log (lk): -7622.237101 . Log(lk) : -7622.237101 -> -7622.237010 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 52 -> 48 (0.000084) Log (lk): -7622.236732 . Log(lk) : -7622.236732 -> -7622.236645 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 51 -> 47 (0.000080) Log (lk): -7622.236378 . Log(lk) : -7622.236378 -> -7622.236311 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 52 -> 48 (0.000016) Log (lk): -7622.236201 . Log(lk) : -7622.236201 -> -7622.236157 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 51 -> 47 (0.000019) Log (lk): -7622.236045 . Log(lk) : -7622.236045 -> -7622.236008 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 28 -> 30 (0.000046) Log (lk): -7622.235931 . Log(lk) : -7622.235931 -> -7622.235905 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 28 -> 30 (0.000048) Log (lk): -7622.235825 . Log(lk) : -7622.235825 -> -7622.235805 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 28 -> 30 (0.000050) Log (lk): -7622.235724 . Log(lk) : -7622.235724 -> -7622.235707 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 28 -> 30 (0.000051) Log (lk): -7622.235623 . Log(lk) : -7622.235623 -> -7622.235607 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 28 -> 30 (0.000053) Log (lk): -7622.235521 . Log(lk) : -7622.235521 -> -7622.235504 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 28 -> 30 (0.000055) Log (lk): -7622.235414 . Log(lk) : -7622.235414 -> -7622.235397 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 28 -> 30 (0.000057) Log (lk): -7622.235304 . Log(lk) : -7622.235304 -> -7622.235286 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 29 -> 17 (0.000059) Log (lk): -7622.235192 . Log(lk) : -7622.235192 -> -7622.235167 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 52 -> 48 (0.000013) Log (lk): -7622.235100 . Log(lk) : -7622.235100 -> -7622.235073 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 51 -> 47 (0.000013) Log (lk): -7622.235003 . Log(lk) : -7622.235003 -> -7622.234974 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 52 -> 48 (0.000013) Log (lk): -7622.234951 . Log(lk) : -7622.234951 -> -7622.234937 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization Log (lk): -7622.234937 nr_d_L: 1032934 nr_d_lk: 235924 nr_loc: 2600 nr_glb: 52 . Time used 0h24m39s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 1257.80user 0.00system 24:39.44elapsed 85%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps