Jalview

Jalview
Developer(s) Waterhouse A, Procter J, Barton G, Martin D.
(University of Dundee)
Original Version by Clamp M, Cuff J, Searle S, Barton G
Operating system UNIX, Linux, Mac, MS-Windows
Type Bioinformatics tool
Licence GPL
Website http://www.jalview.org

Jalview is a multiple sequence alignment editor and viewer written in the Java programming language. The programme was originally written by Michele Clamp whilst working in Geoff Barton's group at the EBI.[1]. Jalview 2, a re-engineered version produced by Andrew Waterhouse and Jim Procter whilst working in Geoff Barton's group at the University of Dundee, was released in 2005,[2] and its development is supported by the BBSRC.

It is used widely by a variety of web servers (e.g. the EBI ClustalW server and the Pfam protein domain database) but is available as a general purpose alignment editor.

Jalview has a wide range of functions in addition to multiple sequence alignment viewing and editing including calculating phylogenetic trees and viewing molecular structures. Many of these use external web services to import data.

References

  1. ^ Clamp M, Cuff J, Searle SM, Barton GJ (February 2004). "The Jalview Java alignment editor". Bioinformatics 20 (3): 426–7. doi:10.1093/bioinformatics/btg430. PMID 14960472. 
  2. ^ Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ (May 2009). "Jalview Version 2--a multiple sequence alignment editor and analysis workbench". Bioinformatics 25 (9): 1189–91. doi:10.1093/bioinformatics/btp033. PMC 2672624. PMID 19151095. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2672624.