begin paup;
log file=paup.log replace=yes;
set criterion=distance;
dset distance=HKY rates=gamma;
NJ;
lset nst=6 base=est Rmatrix=est rclass=(a b c d b e) rates=gamma Ncat=8 shape=est pinv=est;
lscores 1;

dset distance=ML;
lset NST=6 base=previous Rmatrix=previous rclass=(a b c d b e) rates=gamma Ncat=8 shape=previous pinv=previous;
NJ;
lset NST=6 base=est Rmatrix=estimate rclass=(a b c d b e) rates=gamma Ncat=8 shape=estimate pinv=est;
lscores 1;

dset distance=ML;
lset NST=6 base=previous Rmatrix=previous rclass=(a b c d b e) rates=gamma Ncat=8 shape=previous pinv=previous;
NJ;
lset NST=6 base=est Rmatrix=estimate rclass=(a b c d b e) rates=gamma Ncat=8 shape=estimate pinv=est;
lscores 1;

dset distance=ML;
lset NST=6 base=previous Rmatrix=previous rclass=(a b c d b e) rates=gamma Ncat=8 shape=previous pinv=previous;
NJ;

savetrees file=PaupNJ.tree replace=yes;

set criterion=likelihood;
lset NST=6 base=previous Rmatrix=previous rclass=(a b c d b e) rates=gamma Ncat=8 shape=previous pinv=previous;
set autoclose=yes;
hsearch start=1 swap=NNI Multrees=yes;

set criterion=likelihood;
lset NST=6 base=previous Rmatrix=previous rclass=(a b c d b e) rates=gamma Ncat=8 shape=previous pinv=previous;
set autoclose=yes;
hsearch start=1 swap=TBR Multrees=yes;

savetrees file=PaupML.tree format=nexus;

set criterion=distance;
dset distance=ML;
lset NST=6 base=previous Rmatrix=previous rclass=(a b c d b e) rates=gamma Ncat=8 shape=previous pinv=previous;
bootstrap Nreps=1000 search=NJ;

end;