title: Jalview Version 2--a multiple sequence alignment editor and analysis workbench.
abstract: 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.
  
  
  BACKGROUND
  The Jalview 2 Desktop application and JalviewLite applet are made freely available under the GPL, and can be downloaded from www.jalview.org.
authors.affiliation: School of Life Sciences Research, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
authors.forename: Andrew M
authors.initials: AM
authors.lastname: Waterhouse
authors.forename: James B
authors.initials: JB
authors.lastname: Procter
authors.forename: David M A
authors.initials: DM
authors.lastname: Martin
authors.forename: Michèle
authors.initials: M
authors.lastname: Clamp
authors.forename: Geoffrey J
authors.initials: GJ
authors.lastname: Barton
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D011506:Proteins