Alignments of protein and nucleic acid sequences are a central aid to understanding biological systems. Although several effective tools now exist for the rapid automatic alignment of large numbers of sequences (e.g. see: [Higgins \& Sharp, 1989][Vingron \& Argos, 1989][Feng \& Doolittle, 1987][Barton \& Sternberg, 1987], the preparation of publication quality figures of such alignments with annotations is often extremely difficult.
Artwork using pen/ink/dry lettering can allow labelling and boxing,
however, this involves a great deal of labour and a fair degree of
skill to produce visually pleasing results (e.g. the large 128
sequence globin alignment in [Barton \& Sternberg, 1987]). With the advent of powerful
word-processing and graphics packages for personal computers, many
laboratories `tidy up' their alignments by judicious mouse-work.
Although good results may be obtained by this route, the process in
common with conventional artwork is rather inflexible. A particular
problem is that having chosen a number of characters per line and
character pointsize, it is difficult subsequently to modify the
figure. It is also laborious to add new sequences to an existing
figure. In addition, one is normally limited to the use of one of a
few fixed-width fonts (e.g. Courier) rather than the full range of
fonts available to the word-processor. The table drawing facilities
of various packages can overcome the problems of proportional fonts.
For example, the Unix `troff' macros `tbl' were used to prepare the
alignments in [Barton \& Sternberg, 1990], though subsequently re-typed by the J.
Mol. Biol.! [Lamport, 1986] tables were used for the 88
sequence annexin alignment in [Barton et al., 1991] and the 67 sequence
SH2 domain alignment in [Russell et al., 1992]; both figures were extremely
time consuming to prepare, but rather easier to update than a
conventionally word-processed alignment.
The ALSCRIPT program described in this article was developed specifically to allow the easy formatting and graphical display of large multiple sequence alignments. Although written originally for the author's use the interface is relatively friendly, and should be easy to learn by anyone familiar with plotting graphs.