begin paup;
log file=Polpaup.log replace=yes;
set criterion=distance;
dset distance=GTR rates=gamma;
NJ;
lset NST=6 base=est Rmatrix=estimate rclass=(abaaea) rates=gamma Ncat=8 shape=estimate;
lscores 1;

dset distance=ML;
lset NST=6 base=previous Rmatrix=previous rates=gamma Ncat=8 shape=previous;
NJ;
lset NST=6 base=est Rmatrix=estimate rclass=(abaaea) rates=gamma Ncat=8 shape=estimate;
lscores 1;

dset distance=ML;
lset NST=6 base=previous Rmatrix=previous rates=gamma Ncat=8 shape=previous;
NJ;
lset NST=6 base=est Rmatrix=estimate rclass=(abaaea) rates=gamma Ncat=8 shape=estimate;
lscores 1;

dset distance=ML;
lset NST=6 base=previous Rmatrix=previous rates=gamma Ncat=8 shape=previous;
NJ;

savetrees file=PaupNJ.tree replace=yes;

set criterion=likelihood;
lset NST=6 base=previous Rmatrix=previous rates=gamma Ncat=8 shape=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=6 Rmatrix=previous rates=gamma Ncat=8 shape=previous;
bootstrap Nreps=1000 search=NJ;

end;