The Jalview Java alignment editor

Abstract

Summary: Multiple sequence alignment remains a crucial method for understanding the function of groups of related nucleic acid and protein sequences. However, it is known that automatic multiple sequence alignments can often be improved by manual editing. Therefore, tools are needed to view and edit multiple sequence alignments. Due to growth in the sequence databases, multiple sequence alignments can often be large and difficult to view efficiently. The Jalview Java alignment editor is presented here, which enables fast viewing and editing of large multiple sequence alignments. Availability: The Jar file and source code for Jalview is freely available via the World Wide Web at http://www.jalview.org. A Jalview mailing list is also available by e-mailing majordomo@sanger.ac.uk with subscribe Jalview in the body of the mail.