Jalview (http://www.jalview.org) is a free, open source, multiple sequence alignment software for editing, annotating and analysing proteins, RNA and DNA data. It is integrated workbench with tools for structure prediction, phylogenetic tree visualization and consensus and conservation analysis. Jalview was developed in the School of Life Sciences at the University of Dundee.
Jalview features include:
• integrated multiple window interface
• sequence visualization, editing and annotation
• multiple sequence alignment
• consensus, conservation and clustering analysis
• Secondary structure prediction plus protein disorder prediction
• functional site analysis
• phylogenetic trees and principle component analysis
• 3D structure visualization with Jmol
• accessing data from databases repositories (eg Pfam, Rfam, PDB, UniProt and ENA)
• figure generation
There are two types of Jalview program:
• Jalview Desktop is a stand alone application which will run on Mac, MS Windows, Linux and any other platform that supports Java
• JalviewLite applet is a web-based application without the desktop’s webservices and figure generation capabilities
The Barton Group at University of Dundee (http://www.compbio.dundee.ac.uk) coordinates the development of Jalview, with the support of the BBSRC and Wellcome Trust. All the various people, groups and organizations that have supported and contributed to Jalview are listed on the Jalview website (http://www.jalview.org/community).
For more information about our resources please visit:
http://www.compbio.dundee.ac.uk; http://www.compbio.dundee.ac.uk/jpred; http://www.dundee.ac.uk; http://www.lifesci.dundee.ac.uk; http://www.compbio.dundee.ac.uk/jabaws
Jalview Online Training YouTube Channel is a free bioinformatics educational course suitable for Undergraduate and PhD students. Playlists include (a) Getting Started; (b) Selecting and Editing Sequences; (c) Colour, Appearance and Figure Generation; (d) Jalview Dundee. This online educational material was produced by Dr Suzanne Duce, School of Life Sciences, University of Dundee.
