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 [email protected] with subscribe Jalview in the body of the mail.

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Author notes

1The Wellcome Trust Sanger Institute and 2The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK, 3School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, UK and 4The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK