Jalview
@jalview.org
Jalview is a free cross-platform program for multiple sequence alignment editing, visualisation and analysis. Use it to align, view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation. Jalview has built in DNA, RNA and protein sequence and structure visualisation and analysis capabilities, and provides a linked view of aligned DNA and Protein products. It uses Jmol to view 3D structures, and VARNA to display RNA secondary structure, and can also use Chimera, ChimeraX and Pymol for 3D structure visualisation. Experimental and predicted (eg alphafold and swiss-model) 3D structures for proteins can be automatically discovered via the 3D-Beacons network, and sequences and alignments retrieved from databases hosted at EMBL-EBI. The Jalview Desktop also provides a graphical interface to the alignment and analysis services provided by the JavA Bioinformatics Analysis Web Services framework.
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#0084A9
Deep Cerulean
0, 132, 169
193, 100, 33
100, 22, 0, 34
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Rajah
247, 198, 123
36, 89, 73
0, 20, 50, 3
#55190F
Redwood
85, 25, 15
9, 70, 20
0, 71, 82, 67
About Jalview
Jalview is an open-source bioinformatics project offering tools for editing, visualising and analysing multiple sequence alignments. Its software supports DNA, RNA and protein sequences, with features for exploring molecular structures, annotations, phylogenetic trees and principal components analysis plots. Users can also compare aligned DNA and protein sequences through linked views.
The Jalview Desktop application is available for most operating systems, with downloads, executable packages and source code provided. JalviewJS offers a web-based version with similar capabilities. For structural visualisation, Jalview can work with Jmol, VARNA, Chimera, ChimeraX and PyMOL. It can also discover experimental and predicted protein structures through the 3D-Beacons network and retrieve sequences and alignments from EMBL-EBI databases. The Desktop app provides access to alignment and analysis services through the Java Bioinformatics Analysis Web Services framework.
Jalview provides documentation, FAQs, a discussion forum, training courses, videos and hands-on exercises. Development is coordinated at the University of Dundee, and the project is released under the GPL. It is also recognised by ELIXIR as a biological information resource.
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