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Jalview icon

Jalview

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...

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  • Linux
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What is Jalview?

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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