begin paup;
log file=paup.log replace=yes;
set criterion=distance;
dset distance=F81 rates=gamma;
NJ;
lset nst=1 base=est rates=gamma shape=est;
lscores 1;

dset distance=ML;
lset nst=1 base=previous rates=gamma shape=previous;
NJ;
lset nst=1 base=est rates=gamma shape=est;
lscores 1;

dset distance=ML;
lset nst=1 base=previous rates=gamma shape=previous;
NJ;
lset nst=1 base=est rates=gamma shape=est;
lscores 1;

dset distance=ML;
lset nst=1 base=previous rates=gamma shape=previous;
NJ;

savetrees file=PaupNJ.tree replace=yes;

set criterion=likelihood;
lset nst=1 base=previous rates=gamma shape=previous;
set autoclose=yes;
hsearch start=1 swap=SPR Multrees=no;

describetrees /plot=phylogram;

savetrees file=PaupML.tree;

set criterion=distance;
dset distance=ML;
lset nst=1 base=previous rates=gamma shape=previous;
bootstrap Nreps=1000 search=NJ;

end;