To the group,
I am using G. Barton's ALSCRIPT/AMAS family of programs to annotate my
alignments. As you may know, the "default" behaviour of these
programs (if you use them in a very rudimentary way, as I do!)
is to shade the entire "column" at a given position when conservation
is found at that position. Thus, even gaps, the " " character, are
shaded, or colored. My question : does anyone know a trick to
tell ALSCRIPT to make these blank positions in the alignment white?
I've tried various permutations of the MASK commands but can't seem
to get the desired result.
Thank you for your attention to this matter,
Brian I. Osborne bosborne at nature.berkeley.edu
Plant Gene Expression Center TEL 510 559 5924
800 Buchanan St. FAX 510 559 5678
Albany CA 94710 USA