Sequence filename : /auto/dufayard/res/parc_wim/nucleic_M2945_62x1271_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 . 4 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . Computing pairwise distances... . Building BIONJ tree... N_RGRFT: 24 N_GLOBL: 12 MAX_DIST: 12 . Log(lk) : * -> -38056.573302 . Log(lk) : -38056.573302 -> -37541.652822 6 swaps done . Log(lk) : -37541.652822 -> -37445.537531 6 swaps done . Log(lk) : -37445.537531 -> -37428.902820 2 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35302.283667 -> -35259.010964 2 swaps done . Log(lk) : -35259.010964 -> -35249.815750 1 swap done . Log(lk) : -35249.815750 -> -35244.291817 2 swaps done . Log(lk) : -35244.291817 -> -35238.660614 2 swaps done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35199.299023 -> -35188.005288 1 swap done . Log(lk) : -35188.005288 -> -35180.787888 0 swap done . Log(lk) : -35180.787888 -> -35175.387754 0 swap done . Log(lk) : -35175.387754 -> -35170.996382 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35166.382745 -> -35159.677862 0 swap done . Log(lk) : -35159.677862 -> -35153.579696 1 swap done . Log(lk) : -35153.579696 -> -35147.195697 1 swap done . Log(lk) : -35147.195697 -> -35142.903285 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35141.198992 -> -35137.172503 0 swap done . Log(lk) : -35137.172503 -> -35134.340340 0 swap done . Log(lk) : -35134.340340 -> -35132.295899 0 swap done . Log(lk) : -35132.295899 -> -35130.813312 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35129.532507 -> -35127.653037 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 30 -> 26 (1.573489) Log (lk): -35124.665687 . Log(lk) : -35124.665687 -> -35123.973876 1 swap done . Log(lk) : -35123.973876 -> -35123.636555 0 swap done . Log(lk) : -35123.636555 -> -35123.469369 0 swap done . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35121.996337 -> -35121.505240 0 swap done . Log(lk) : -35121.505240 -> -35121.210510 0 swap done . Log(lk) : -35121.210510 -> -35121.011424 0 swap done . Log(lk) : -35121.011424 -> -35120.874737 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization Log (lk): -35120.691205 . Last optimization step... . Log(lk) : * -> -35120.590701 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35120.590701 -> -35119.939451 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.939451 -> -35119.800986 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.800986 -> -35119.729645 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.729645 -> -35119.682951 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.682951 -> -35119.663996 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.663996 -> -35119.649034 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.649034 -> -35119.648417 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648417 -> -35119.648212 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648212 -> -35119.648194 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648194 -> -35119.648185 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648185 -> -35119.648176 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648176 -> -35119.648168 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648168 -> -35119.648160 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648160 -> -35119.648152 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648152 -> -35119.648144 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648144 -> -35119.648138 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648138 -> -35119.648131 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648131 -> -35119.648125 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648125 -> -35119.648118 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648118 -> -35119.648112 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648112 -> -35119.648106 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648106 -> -35119.648100 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648100 -> -35119.648095 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648095 -> -35119.648089 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648089 -> -35119.648084 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648084 -> -35119.648079 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648079 -> -35119.648074 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648074 -> -35119.648069 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648069 -> -35119.648065 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648065 -> -35119.648061 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648061 -> -35119.648056 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648056 -> -35119.648052 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648052 -> -35119.648048 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648048 -> -35119.648044 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648044 -> -35119.648040 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648040 -> -35119.648037 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648037 -> -35119.648033 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648033 -> -35119.648030 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648030 -> -35119.648026 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648026 -> -35119.648023 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648023 -> -35119.648020 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648020 -> -35119.648017 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648017 -> -35119.648014 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648014 -> -35119.648012 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648012 -> -35119.648009 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648009 -> -35119.648006 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648006 -> -35119.648004 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648004 -> -35119.648001 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.648001 -> -35119.647999 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.647999 -> -35119.647997 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.647997 -> -35119.647994 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.647994 -> -35119.647992 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.647992 -> -35119.647990 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.647990 -> -35119.647988 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.647988 -> -35119.647986 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.647986 -> -35119.647985 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.647985 -> -35119.647983 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.647983 -> -35119.647981 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.647981 -> -35119.647979 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.647979 -> -35119.647978 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.647978 -> -35119.647976 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.647976 -> -35119.647974 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.647974 -> -35119.647973 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.647973 -> -35119.647971 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.647971 -> -35119.647970 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.647970 -> -35119.647968 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.647968 -> -35119.647967 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.647967 -> -35119.647966 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.647966 -> -35119.647965 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.647965 -> -35119.647963 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.647963 -> -35119.647962 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.647962 -> -35119.647961 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.647961 -> -35119.647960 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.647960 -> -35119.647959 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.647959 -> -35119.647958 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... . Log(lk) : -35119.647958 -> -35119.647957 . Optimisation of the GTR parameters... . Optimisation of the gamma shape parameter... nr_d_L: 27280 nr_d_lk: 6492 nr_loc: 200 nr_glb: 13 . Time used 0h5m51s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 277.81user 0.00system 5:50.63elapsed 79%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps