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.