Sequence filename : /auto/dufayard/res/2.4.5/nucleic_M2707_115x1677_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 . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... . Nbytes = 56512104 . Log(lk) : * -> -12008.179736 . Log(lk) : -12008.179736 -> -10879.209728 16 swaps done . Log(lk) : -10879.209728 -> -10591.013962 15 swaps done . Log(lk) : -10591.013962 -> -10719.583082 12 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -10591.013962 -> -10019.051302 12 swaps done . Log(lk) : -10019.051302 -> -9950.950292 12 swaps done . Log(lk) : -9950.950292 -> -10038.726747 8 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9950.950292 -> -9934.301983 8 swaps done . Log(lk) : -9934.301983 -> -9899.643763 9 swaps done . Log(lk) : -9899.643763 -> -9993.218967 9 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9899.643763 -> -9892.098787 9 swaps done . Log(lk) : -9892.098787 -> -9872.283283 9 swaps done . Log(lk) : -9872.283283 -> -9957.996342 7 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9872.283283 -> -9865.677238 7 swaps done . Log(lk) : -9865.677238 -> -9860.177388 5 swaps done . Log(lk) : -9860.177388 -> -9941.439467 6 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9860.177388 -> -9855.488696 6 swaps done . Log(lk) : -9855.488696 -> -9852.582903 5 swaps done . Log(lk) : -9852.582903 -> -9927.108239 5 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9852.582903 -> -9849.024171 5 swaps done . Log(lk) : -9849.024171 -> -9846.417730 3 swaps done . Log(lk) : -9846.417730 -> -9899.072510 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9846.417730 -> -9844.870117 3 swaps done . Log(lk) : -9844.870117 -> -9842.519106 3 swaps done . Log(lk) : -9842.519106 -> -9896.763660 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9842.519106 -> -9841.716543 3 swaps done . Log(lk) : -9841.716543 -> -9839.088500 3 swaps done . Log(lk) : -9839.088500 -> -9884.742567 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9839.088500 -> -9836.349546 3 swaps done . Log(lk) : -9836.349546 -> -9835.155969 3 swaps done . Log(lk) : -9835.155969 -> -9880.432020 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9835.155969 -> -9827.238885 3 swaps done . Log(lk) : -9827.238885 -> -9819.794909 3 swaps done . Log(lk) : -9819.794909 -> -9818.037991 2 swaps done . Log(lk) : -9818.037991 -> -9817.512930 3 swaps done . Log(lk) : -9817.512930 -> -9827.467735 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9817.512930 -> -9816.517326 3 swaps done . Log(lk) : -9816.517326 -> -9813.840192 3 swaps done . Log(lk) : -9813.840192 -> -9820.004289 2 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9813.840192 -> -9811.863373 2 swaps done . Log(lk) : -9811.863373 -> -9811.173870 2 swaps done . Log(lk) : -9811.173870 -> -9818.909997 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9811.173870 -> -9810.551835 3 swaps done . Log(lk) : -9810.551835 -> -9809.051293 3 swaps done . Log(lk) : -9809.051293 -> -9813.904856 0 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9809.051293 -> -9806.788263 0 swap done . Log(lk) : -9806.788263 -> -9805.807147 0 swap done . Log(lk) : -9805.807147 -> -9809.676662 1 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9805.807147 -> -9804.392232 1 swap done . Log(lk) : -9804.392232 -> -9803.941656 1 swap done . Log(lk) : -9803.941656 -> -9806.686925 0 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9803.941656 -> -9802.928224 0 swap done . Log(lk) : -9802.928224 -> -9802.809845 0 swap done . Log(lk) : -9802.809845 -> -9804.865473 0 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9802.809845 -> -9802.059982 0 swap done . Log(lk) : -9802.059982 -> -9802.024848 0 swap done . Log(lk) : -9802.024848 -> -9803.264384 0 swap done . Moving backward (topology + branch lengths) . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9802.024848 -> -9801.481861 0 swap done . Log(lk) : -9801.481861 -> -9801.450113 0 swap done . Last optimization step... . Log(lk) : * -> -9801.049488 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9801.049488 -> -9800.820427 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.820427 -> -9800.734330 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.734330 -> -9800.691150 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.691150 -> -9800.669586 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.669586 -> -9800.657852 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.657852 -> -9800.651603 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.651603 -> -9800.647599 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.647599 -> -9800.644851 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.644851 -> -9800.642587 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.642587 -> -9800.640573 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.640573 -> -9800.638599 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.638599 -> -9800.636253 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.636253 -> -9800.633213 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.633213 -> -9800.630039 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.630039 -> -9800.625924 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625924 -> -9800.625597 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625597 -> -9800.625587 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625587 -> -9800.625581 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625581 -> -9800.625578 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625578 -> -9800.625576 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625576 -> -9800.625574 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625574 -> -9800.625573 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625573 -> -9800.625572 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625572 -> -9800.625571 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625571 -> -9800.625570 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625570 -> -9800.625569 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625569 -> -9800.625568 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625568 -> -9800.625567 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625567 -> -9800.625566 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625566 -> -9800.625565 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625565 -> -9800.625564 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625564 -> -9800.625563 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625563 -> -9800.625562 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625562 -> -9800.625561 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625561 -> -9800.625559 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625559 -> -9800.625558 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625558 -> -9800.625557 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625557 -> -9800.625556 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625556 -> -9800.625554 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625554 -> -9800.625553 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625553 -> -9800.625552 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625552 -> -9800.625550 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625550 -> -9800.625549 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625549 -> -9800.625548 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625548 -> -9800.625546 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625546 -> -9800.625545 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625545 -> -9800.625543 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625543 -> -9800.625542 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625542 -> -9800.625540 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625540 -> -9800.625539 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625539 -> -9800.625537 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625537 -> -9800.625535 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625535 -> -9800.625534 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625534 -> -9800.625532 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625532 -> -9800.625530 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625530 -> -9800.625528 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625528 -> -9800.625527 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625527 -> -9800.625525 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625525 -> -9800.625523 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625523 -> -9800.625521 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625521 -> -9800.625519 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625519 -> -9800.625517 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625517 -> -9800.625515 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625515 -> -9800.625513 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625513 -> -9800.625511 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625511 -> -9800.625509 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625509 -> -9800.625506 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625506 -> -9800.625504 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625504 -> -9800.625502 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625502 -> -9800.625499 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625499 -> -9800.625497 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625497 -> -9800.625495 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625495 -> -9800.625492 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625492 -> -9800.625489 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625489 -> -9800.625487 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625487 -> -9800.625484 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625484 -> -9800.625481 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625481 -> -9800.625479 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625479 -> -9800.625476 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625476 -> -9800.625473 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625473 -> -9800.625470 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625470 -> -9800.625467 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625467 -> -9800.625464 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625464 -> -9800.625461 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625461 -> -9800.625458 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625458 -> -9800.625454 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625454 -> -9800.625451 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625451 -> -9800.625448 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625448 -> -9800.625444 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625444 -> -9800.625441 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625441 -> -9800.625437 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625437 -> -9800.625434 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625434 -> -9800.625430 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625430 -> -9800.625426 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625426 -> -9800.625422 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625422 -> -9800.625418 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625418 -> -9800.625414 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625414 -> -9800.625410 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Log(lk) : -9800.625410 -> -9800.625406 . Optimisation of the GTR parameters... . WARNING : BFGS failed ! . Optimising one-by-one... . Optimisation of the gamma shape parameter... . Final Log(lk) : -9800.625406 . Time used 0h22m44s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 1358.08user 0.00system 22:44.54elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps