Jalview

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	2.11[1] / 4 July 2019
Written in	Java
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. The program was originally written by Michele Clamp whilst working in Geoff Barton's group at the University of Oxford and European Bioinformatics Institute (EBI).[2] Jalview 2, a re-engineered version produced by Andrew Waterhouse and Jim Procter whilst working in Geoff Barton's group at the School of Life Sciences, University of Dundee, was released in 2005,[3] and its development is supported by the Biotechnology and Biological Sciences Research Council (BBSRC) and Wellcome Trust.

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

Jalview has a wide range of functions in addition to multiple sequence alignment generation, viewing and editing, including calculating phylogenetic trees and viewing molecular structures. Recent versions of Jalview include features for the analysis of genetic variation from public databases or local Variant Call Format (VCF) files. Jalview connects to many external web services to import data and perform calculations.

References

"Release History".
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.
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.

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[1] "Release History".

[pmid14960472-2] 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.

[pmid19151095-3] 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 2672624. PMID 19151095.