[EMBOSS] Nucleotide dotplots with EMBOSS

[Peter]

Hello EMBOSS team,

I've just been using dottup to produce dot plots comparing two
nucleotide sequences (two assemblies), where I have regions of very
high similarity but some inversions.
http://emboss.sourceforge.net/apps/release/6.2/emboss/apps/dottup.html

I've noticed that I can tell dotplot to reverse either of the
sequences, but I would actually like it to search both for forward
matches AND reverse matches to display on the same plot (ideally using
different colours). Is this possible already, or might it be a
reasonable feature request? Right now I can generate one plot with the
forward matches, and a second plot with the reverse matches - not
ideal.

Thanks,

Peter C.

P.S.
While I'm asking, I'd also like (colour) PDF output, since working
with PDF files is much easier on the Mac than postscript (which
thankfully is trivial to convert into PDF - so this isn't a big issue
for me).