Sequence filename : /auto/dufayard/res/parc_wim/nucleic_M2916_143x897_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 . 73 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... N_RGRFT: 56 N_GLOBL: 28 MAX_DIST: 28 . Log(lk) : * -> -3709.849302 . Log(lk) : -3709.849302 -> -3660.577122 24 swaps done . Log(lk) : -3660.577122 -> -3647.774202 17 swaps done . Log(lk) : -3647.774202 -> -3645.696644 15 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3519.480864 -> -3515.373969 13 swaps done . Log(lk) : -3515.373969 -> -3513.234302 8 swaps done . Log(lk) : -3513.234302 -> -3509.944024 6 swaps done . Log(lk) : -3509.944024 -> -3509.367388 3 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3507.458984 -> -3506.756143 6 swaps done . Log(lk) : -3506.756143 -> -3506.765480 5 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3506.756143 -> -3506.284394 5 swaps done . Log(lk) : -3506.284394 -> -3504.752962 5 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3504.722817 -> -3504.006217 3 swaps done . Log(lk) : -3504.006217 -> -3503.483364 3 swaps done . Log(lk) : -3503.483364 -> -3503.571430 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3503.483364 -> -3503.249309 2 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3503.249306 -> -3502.957606 1 swap done . Log(lk) : -3502.957606 -> -3503.719411 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3502.957606 -> -3502.839620 3 swaps done . Log(lk) : -3502.839620 -> -3502.781588 3 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3502.781584 -> -3502.887706 0 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3502.781584 -> -3502.771023 0 swap done . Log(lk) : -3502.771023 -> -3502.766934 1 swap done . Log(lk) : -3502.766934 -> -3502.883737 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3502.766934 -> -3502.760129 2 swaps done . Log(lk) : -3502.760129 -> -3502.762500 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3502.760129 -> -3502.753376 2 swaps done . Log(lk) : -3502.753376 -> -3502.752775 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods making move: 2 -> 247 (0.958112) making move: 24 -> 53 (0.088147) making move: 26 -> 36 (0.001068) making move: 27 -> 30 (0.004485) making move: 29 -> 30 (0.001687) making move: 34 -> 40 (0.201681) making move: 43 -> 39 (0.002610) making move: 47 -> 31 (0.000223) making move: 51 -> 15 (0.191403) making move: 94 -> 136 (0.327947) making move: 98 -> 131 (0.065148) making move: 102 -> 135 (0.043954) making move: 104 -> 135 (0.046191) making move: 106 -> 135 (0.041682) making move: 118 -> 101 (0.042894) making move: 132 -> 137 (2.474906) making move: 133 -> 101 (0.007370) making move: 135 -> 99 (0.117399) making move: 135 -> 105 (0.031783) making move: 136 -> 94 (0.157079) making move: 138 -> 99 (0.052420) making move: 141 -> 130 (9.666928) making move: 174 -> 198 (0.452821) making move: 178 -> 153 (0.509453) making move: 183 -> 152 (0.717565) making move: 220 -> 246 (0.055060) making move: 221 -> 224 (0.111882) making move: 221 -> 252 (0.212872) making move: 222 -> 246 (0.196149) making move: 223 -> 250 (0.091444) making move: 246 -> 222 (0.039590) making move: 248 -> 222 (0.004613) making move: 250 -> 246 (0.012931) Log (lk): -3480.858731 . Log(lk) : -3480.858731 -> -3480.704294 9 swaps done . Log(lk) : -3480.704294 -> -3480.662486 7 swaps done . Log(lk) : -3480.662486 -> -3480.774680 7 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3480.662486 -> -3480.478873 7 swaps done . Log(lk) : -3480.478873 -> -3480.410540 7 swaps done . Log(lk) : -3480.410540 -> -3480.507060 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3480.410540 -> -3480.400701 3 swaps done . Log(lk) : -3480.400701 -> -3480.386319 3 swaps done . Log(lk) : -3480.386319 -> -3480.513319 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3480.386319 -> -3480.379776 2 swaps done . Log(lk) : -3480.379776 -> -3480.389987 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3480.379776 -> -3480.373843 2 swaps done . Log(lk) : -3480.373843 -> -3480.381012 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3480.373843 -> -3480.373297 3 swaps done Trying SPR moves -calculating tree distances and estimating likelihoods making move: 168 -> 177 (2.898972) Log (lk): -3477.184162 . Log(lk) : -3477.184162 -> -3477.183523 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 82 -> 100 (0.000235) Log (lk): -3477.182892 . Log(lk) : -3477.182892 -> -3477.183059 2 swaps done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 99 -> 104 (0.000263) Log (lk): -3477.182490 . Log(lk) : -3477.182490 -> -3477.182789 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 198 -> 199 (0.000277) Log (lk): -3477.182192 . Log(lk) : -3477.182192 -> -3477.182495 3 swaps done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 125 -> 124 (0.000267) Log (lk): -3477.181912 . Log(lk) : -3477.181912 -> -3477.182273 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 102 -> 106 (0.000282) Log (lk): -3477.181660 . Log(lk) : -3477.181660 -> -3477.181926 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 91 -> 102 (0.000218) Log (lk): -3477.181397 . Log(lk) : -3477.181397 -> -3477.181540 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 104 -> 92 (0.000147) Log (lk): -3477.181112 . Log(lk) : -3477.181112 -> -3477.181168 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 92 -> 89 (0.000120) Log (lk): -3477.180822 . Log(lk) : -3477.180822 -> -3477.180767 2 swaps done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 91 -> 104 (0.000068) Log (lk): -3477.180569 . Log(lk) : -3477.180569 -> -3477.180512 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 135 -> 92 (0.000055) Log (lk): -3477.180329 . Log(lk) : -3477.180329 -> -3477.180271 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 81 -> 99 (0.000058) Log (lk): -3477.180088 . Log(lk) : -3477.180088 -> -3477.196656 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3477.180088 -> -3477.126804 2 swaps done . Log(lk) : -3477.126804 -> -3477.126353 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 242 -> 240 (0.007275) Log (lk): -3477.118938 . Log(lk) : -3477.118938 -> -3477.118627 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 238 -> 242 (0.000033) Log (lk): -3477.118589 . Log(lk) : -3477.118589 -> -3477.118477 2 swaps done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 82 -> 89 (0.000014) Log (lk): -3477.118457 . Log(lk) : -3477.118457 -> -3477.137403 1 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -3477.118457 -> -3477.118418 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization Log (lk): -3477.118418 nr_d_L: 1276818 nr_d_lk: 302367 nr_loc: 1500 nr_glb: 42 . Time used 0h15m39s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 805.61user 0.00system 15:39.78elapsed 85%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps