Begin paup; set autoclose=yes warntree=no warnreset=no; log start file=paup_batch.log replace; execute young/young.nxs; cstatus; set criterion=distance; dset distance=jc; nj treefile=young.paup.nj breakties=random replace; UPGMA treefile=young.paup.upgma breakties=random replace; bootstrap search=nj treefile=young.paup.bnj nreps=1000 replace; set criterion=parsimony; set maxtrees=1000 increase=no; pset collapse=no; hsearch addseq=random nreps=10 nchuck=1000 chuckscore=1 swap=nni; savetrees file=young.paup.p; end;