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Bioinformatics Advance Access originally published online on January 16, 2009
Bioinformatics 2009 25(9):1189-1191; doi:10.1093/bioinformatics/btp033
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Jalview Version 2—a multiple sequence alignment editor and analysis workbench

Andrew M. Waterhouse 1,{dagger},{ddagger}, James B. Procter 1,{dagger}, David M. A. Martin 1, Michèle Clamp 2 and Geoffrey J. Barton 1,*

1School of Life Sciences Research, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK and 2Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA

*To whom correspondence should be addressed.


  Abstract

Summary: Jalview Version 2 is a system for interactive WYSIWYG editing, analysis and annotation of multiple sequence alignments. Core features include keyboard and mouse-based editing, multiple views and alignment overviews, and linked structure display with Jmol. Jalview 2 is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server.

Availability: The Jalview 2 Desktop application and JalviewLite applet are made freely available under the GPL, and can be downloaded from www.jalview.org

Contact: g.j.barton@dundee.ac.uk

{dagger}The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

{ddagger}Present address: Genome Exploration Research Group, RIKEN Omics Science Center and the Functional RNA Research Program, Frontier Research System, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho Tsurumi-ku Yokohama, Kanagawa 230-0045, Japan.

Associate Editor: Jonathan Wren

Received on November 24, 2008; revised on November 24, 2008; accepted on January 8, 2009

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