I quick one, with neither pretty of prettybox, I can shade aa in a msf file. I
can get boxes and so on, but what I want sre different shades of gray for area
with different degree of sequence conservation. Depneding on used matrix, what
is a homology in one case would not be in another.
I tried boxshade, but it seems not to be able to do what I want
Eagerly awating suggestions...