begin paup;
log file=paup.log replace=yes;
set criterion=distance;
dset distance=HKY rates=gamma;
NJ;
lset nst=2 base=est tratio=est rates=gamma Ncat=8 shape=est;
lscores 1;

dset distance=ML;
lset nst=2 base=previous tratio= previous rates=gamma Ncat=8 shape= previous;
NJ;
lset nst=2 base=est tratio=est rates=gamma Ncat=8 shape=est;
lscores 1;

dset distance=ML;
lset nst=2 base=previous tratio= previous rates=gamma Ncat=8 shape= previous;
NJ;
lset nst=2 base=est tratio=est rates=gamma Ncat=8 shape=est;
lscores 1;

dset distance=ML;
lset nst=2 base=previous tratio= previous rates=gamma Ncat=8 shape= previous;
NJ;

savetrees file=PaupNJ.tree replace=yes;

set criterion=likelihood;
lset nst=2 base=previous tratio= previous rates=gamma Ncat=8 shape= previous;
set autoclose=yes;
hsearch start=1 swap=NNI Multrees=no;

set criterion=likelihood;
lset nst=2 base=previous tratio= previous rates=gamma Ncat=8 shape= previous;
set autoclose=yes;
hsearch start=1 swap=TBR 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 Ncat=8 shape= previous;
bootstrap Nreps=1000 search=NJ;

end;