Sequence filename : /auto/dufayard/res/parc_wim/nucleic_M2901_56x1802_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: 21 N_GLOBL: 10 MAX_DIST: 10 . Log(lk) : * -> -8424.114026 . Log(lk) : -8424.114026 -> -8351.483844 7 swaps done . Log(lk) : -8351.483844 -> -8301.465627 7 swaps done . Log(lk) : -8301.465627 -> -8288.101555 5 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7895.608927 -> -7887.738026 3 swaps done . Log(lk) : -7887.738026 -> -7886.556239 2 swaps done . Log(lk) : -7886.556239 -> -7884.563315 3 swaps done . Log(lk) : -7884.563315 -> -7883.488640 3 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7882.966903 -> -7877.172658 3 swaps done . Log(lk) : -7877.172658 -> -7870.868502 3 swaps done . Log(lk) : -7870.868502 -> -7868.516011 3 swaps done . Log(lk) : -7868.516011 -> -7868.390226 2 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7868.342683 -> -7868.086953 2 swaps done . Log(lk) : -7868.086953 -> -7868.315343 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7868.086953 -> -7867.650306 3 swaps done . Log(lk) : -7867.650306 -> -7867.745692 1 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7867.650306 -> -7867.524754 1 swap done . Log(lk) : -7867.524754 -> -7867.783316 1 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -7867.524754 -> -7867.477267 1 swap done . Log(lk) : -7867.477267 -> -7867.449662 0 swap done . Log(lk) : -7867.449662 -> -7867.444042 0 swap done . Log(lk) : -7867.444042 -> -7867.441178 0 swap done . Log(lk) : -7867.441178 -> -7867.439137 0 swap done . Log(lk) : -7867.439137 -> -7867.437444 0 swap done . Log(lk) : -7867.437444 -> -7867.435946 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods making move: 29 -> 58 (0.753226) making move: 43 -> 53 (2.098251) making move: 44 -> 97 (14.246253) making move: 45 -> 58 (4.331672) making move: 58 -> 34 (1.083957) making move: 71 -> 79 (1.545066) making move: 81 -> 70 (0.849371) making move: 89 -> 74 (4.654672) making move: 94 -> 95 (0.561174) making move: 96 -> 91 (0.205357) making move: 105 -> 95 (0.282112) Log (lk): -7827.474004 . Log(lk) : -7827.474004 -> -7827.297008 1 swap done . Log(lk) : -7827.297008 -> -7827.223134 0 swap done . Log(lk) : -7827.223134 -> -7827.169693 0 swap done . Log(lk) : -7827.169693 -> -7827.124587 0 swap done . Log(lk) : -7827.124587 -> -7827.077072 0 swap done . Log(lk) : -7827.077072 -> -7827.023455 0 swap done . Log(lk) : -7827.023455 -> -7826.974478 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations making move: 30 -> 32 (0.181097) Log (lk): -7826.663596 . Log(lk) : -7826.663596 -> -7826.613508 0 swap done . Log(lk) : -7826.613508 -> -7826.578193 0 swap done . Log(lk) : -7826.578193 -> -7826.537080 0 swap done . Log(lk) : -7826.537080 -> -7826.527432 0 swap done . Log(lk) : -7826.527432 -> -7826.525143 0 swap done . Log(lk) : -7826.525143 -> -7826.524552 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations making move: 62 -> 38 (0.019990) Log (lk): -7826.462299 . Log(lk) : -7826.462299 -> -7826.461107 0 swap done . Log(lk) : -7826.461107 -> -7826.460868 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 64 -> 63 (0.061374) Log (lk): -7826.399390 . Log(lk) : -7826.399390 -> -7826.397300 1 swap done . Log(lk) : -7826.397300 -> -7826.397087 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization Log (lk): -7826.396906 nr_d_L: 41408 nr_d_lk: 13049 nr_loc: 209 nr_glb: 14 . Time used 0h2m3s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 117.45user 0.00system 2:03.18elapsed 95%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps