export alignment as plain or simply formatted text

Jalview feature request submitted by:
From: "Rudi Grams" <rgrams@gmx.net>
To: <help@jalview.org>
Subject: JalView -plain text export
Date: Fri, 18 May 2007 14:34:40 +0700
It would be very helpful if Jalview can export alignments as plain text
with options to:

1 show all amino acid residues of all sequences
2 only residues different to a reference sequence
2.1 with the suboption to distinguish between similar/non-similar residues

Normally this is done by dots for identical and upper/lowercase
characters for similar/non-similar.

Such feature would make it much easier to include alignments in
publications which do not accept coloured figures but insist on some
kind of differentiation between identical/similar/non-similar. EMBOSS
showalign can do this but it does not provide separate numbering for
each sequence.

Many thanks,

Rudi