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;