Jalview

From Wikipedia, the free encyclopedia
Jump to: navigation, search
Jalview
Developer(s) Andrew Waterhouse, James Procter, David Martin and Geoffrey Barton at the University of Dundee.
Original version by Michele Clamp, James Cuff, Stephen Searle, Geoffrey Barton.
Stable release
2.9.0b2[1] / 16 October 2015; 11 months ago (2015-10-16)
Operating system UNIX, Linux, Mac OS X, Microsoft Windows
Type Bioinformatics tool
Licence GPL
Website http://www.jalview.org

Jalview is a piece of bioinformatics software that is used to look at and edit multiple sequence alignments. It is written in the Java programming language. The programme was originally written by Michele Clamp whilst working in Geoff Barton's group at the EBI.[2] 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,[3] 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[edit]

  1. ^ "Release History". 
  2. ^ 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. 
  3. ^ 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 2672624free to read. PMID 19151095.