#NEXUS begin paup; [-------- Settings for displaying, rooting, storing and saving trees ----------] set taxlabels = full tcompress torder = left autoclose outroot = monophyl maxtrees = 1000 increase = auto autoinc = 1000 rootmethod = outgroup; [-------------------- Set optimality criterion to distance --------------------] set criterion = distance; [---------------------------- Distance settings -------------------------------] dset negbrlen = setzero missdist = ignore dcollapse [*** Distance formula ***] distance = hky85 [total/mean/abs/p/jc/f81/tajnei/k2p/f84/hky85/k3p/ tamnei/gtr/custom/ml/logdet] [*** Substition rates ***] rates = equal [Equal rates] [rates = gamma shape = 0.5] [Gamma-distributed rates; alpha value needed!] [*** Proportion of invariant sites ***] pinvar = 0 [0.1, 0.2, ...] ; [-------------------------------- NJ settings ---------------------------------] defaults nj bionj breakties = random; [------------------------ Start writing to logfile ----------------------------] log start file = 'bionj_bootstrap.log' replace; [----------------------------- NJ bootstrapping -------------------------------] bootstrap search = nj grpfreq = no treefile = 'bionj_bootstrap.tre' brlens replace format = nexus [*** Number of replicates ***] nreps = 100 [1000, 10000, ...] ; [------------ Save the consensus tree with bootstrap support values -----------] savetrees file = 'bionj_bootstrap.con' savebootp = nodelabels from = 1 to = 1 format = altnexus brlens = no replace; [------------------------- Stop writing to logfile ----------------------------] log stop; end;