MALIGNED: a multiple sequence alignment editor.

A multiple sequence alignment editor is described which runs on a VAX/VMS system and can exchange data with a number of other programs, including those of the Genetics Computer Group (GCG). Up to 199 sequences can be aligned. The quality of the alignment can be easily judged during its development because the display attributes to each character are determined by the way it matches the other sequences. Four methods are available for calculating the highlighting to emphasize different aspects of the relationships of the sequences and up to four styles of highlighting can be used at the same time. Laser printer output is suitable for publication without modification.