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{{Infobox Software
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|website=http://www.jalview.org
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'''Jalview''' is a [[multiple sequence alignment]] editor & viewer written in the [[Java (programming language)|Java programming language]]. It is used widely in a variety of web pages (e.g. the [[European Bioinformatics Institute|EBI]] [[ClustalW]] server and the [[Pfam]] protein domain database) but is available as a general purpose alignment editor.<br>
'''Jalview''' is a [[multiple sequence alignment]] editor and viewer written in the [[Java (programming language)|Java programming language]]. The programme was originally written by Michele Clamp in [[Geoff Barton]]'s group.<ref name="pmid14960472">{{cite journal |author=Clamp M, Cuff J, Searle SM, Barton GJ |title=The Jalview Java alignment editor |journal=Bioinformatics |volume=20 |issue=3 |pages=426–7 |year=2004 |month=February |pmid=14960472 |doi=10.1093/bioinformatics/btg430 |url=}}</ref><ref name="pmid19151095">{{cite journal |author=Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ |title=Jalview Version 2--a multiple sequence alignment editor and analysis workbench |journal=Bioinformatics |volume=25 |issue=9 |pages=1189–91 |year=2009 |month=May |pmid=19151095 |pmc=2672624 |doi=10.1093/bioinformatics/btp033 |url=}}</ref>


It is used widely by a variety of web servers (e.g. the [[European Bioinformatics Institute|EBI]] [[ClustalW]] server and the [[Pfam]] protein domain database) but is available as a general purpose alignment editor.<br>
Use Jalview for:
*Viewing
Jalview has a wide range of functions in addition to multiple sequence alignment viewing and editing including calculating [[phylogenetic tree]]s and viewing molecular structures. Many of these use external [[web services]] to import data.
**Reads and writes alignments in a variety of formats (Fasta, PFAM, MSF, Clustal, BLC, PIR)

***Save alignments and associated trees in Jalview XML format.
==References==
*Editing
{{Reflist}}
**Gaps can be inserted/deleted using the mouse or keyboard.
**Group editing (insertion deletion of gaps in groups of sequences).
**Removal of gapped columns.
*Analysis
**Align sequences using Web Services (Clustal, Muscle...)
**Amino acid conservation analysis similar to that of AMAS.
**Alignment sorting options (by name, tree order, percent identity, group).
**[[UPGMA]] and NJ trees calculated and drawn based on percent identity distances.
**Sequence clustering using principal component analysis.
**Removal of redundant sequences.
**Smith Waterman pairwise alignment of selected sequences.
*Annotation
**Use web based secondary structure prediction programs (JNet).
*Annotation
**User predefined or custom colour schemes to colour alignments or groups.
**Sequence feature retrieval and display on the alignment.
*Publishing
**Print your alignment with colours and annotations.
**Create HTML pages.
**Output alignment as portable network graphics image (PNG).
**Output alignment as encapsulated postscript file (EPS).


[[Category:Bioinformatics software]]
[[Category:Bioinformatics software]]
[[Category:Computational phylogenetics]]
[[Category:Computational phylogenetics]]

{{Bioinformatics-stub}}

Revision as of 12:21, 14 June 2011

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 systemUNIX, Linux, Mac, MS-Windows
TypeBioinformatics tool
LicenceLGPL
Websitehttp://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 in Geoff Barton's group.[1][2]

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 (2004). "The Jalview Java alignment editor". Bioinformatics. 20 (3): 426–7. doi:10.1093/bioinformatics/btg430. PMID 14960472. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  2. ^ Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ (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. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
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