PAUP batch file

[Perform a branch and bound analysis and save the trees to files]
#NEXUS
begin paup;
log file=bandbanalysis.txt;
basef;
set criterion=parsimony;
bandb;
des /plot=phylo;
savetrees /brlens file=bandbp.tre;
cont /save file=bandbc.tre;
log stop;
end;
 
[Another example batch file with a bootstrap analysis]
#NEXUS
begin paup;
log file=paup_hs_bs_log.txt;
dset /distance=total;
showdist;
basef;
set criterion=parsimony;
set maxtrees=1000;
hs /addseq=rand nreps=25;
outgroup 1;
des /root=outgroup outroot=monophyl;
cont /maj;
set maxtrees=10000;
bo nreps=1000 /addseq=rand nreps=10;
savetrees maxdeci=0 from=1 to=1 saveboot=both file=primate-bo.tre;
log stop;