Sure there are some possibilities of drawing nice boxes around your
sequence homologies using a spreadsheet or a word-processor.
The main disadvantage however is that you have to do it by hand which
is a very tedious work (i know that by experience).
So i think any program facilitating this would be of great help for
many of us.
If there are programs out there, no matter what OS they are for, please
make them available!
I myself have written a quick&dirty program in VAX-Pascal that takes
PRETTY-output files from GCG-LINEUP (CLUSTAL files to come soon)
and shades them in colors or gray-scales according to identity or
amino acid similarity. Output is suitable either for LJ250 color printer
or as a UIS file for later conversion with DEC's RENDER-program supplied
with VWS. The latter format can be converted into almost anything important
on VAXes, including POSTSCRIPT.
If anyone is interested in this, please write. My address is