begin paup;
log file=Polpaup.log replace=yes;
set criterion=distance;
dset distance=GTR rates=gamma;
NJ;
lset nst=2 base=est tratio=est rates=gamma shape=est pinv=est;
lscores 1;

dset distance=ML;
lset nst=2 base=previous tratio= previous rates=gamma shape= previous pinv= previous;
NJ;
lset nst=2 base=est tratio=est rates=gamma shape=est pinv=est;
lscores 1;

dset distance=ML;
lset nst=2 base=previous tratio= previous rates=gamma shape= previous pinv= previous;
NJ;
lset nst=2 base=est tratio=est rates=gamma shape=est pinv=est;
lscores 1;

dset distance=ML;
lset nst=2 base=previous tratio= previous rates=gamma shape= previous pinv= previous;
NJ;

savetrees file=PaupNJ.tree replace=yes;

set criterion=likelihood;
lset nst=2 base=previous tratio= previous rates=gamma shape= previous pinv= previous;
set autoclose=yes;
hsearch start=1 swap=SPR Multrees=no;

describetrees /plot=phylogram;

savetrees file=PaupML.tree format=phylip;

set criterion=distance;
dset distance=ML;
lset nst=2 base=previous tratio= previous rates=gamma shape= previous pinv= previous;
bootstrap Nreps=1000 search=NJ;

end;