Jalview

About

Jalview is a free, open source, cross-platform program for multiple sequence alignment editing, visualisation, and analysis. Users can align, view, and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots, and explore molecular structures and annotation. It provides built-in DNA, RNA, and protein sequence and structure visualisation and analysis, along with a linked view of aligned DNA and protein products. For 3D structures it uses Jmol, and it can use VARNA for RNA secondary structure and Chimera, ChimeraX, and PyMOL for 3D visualisation. Experimental and predicted protein structures can be discovered automatically via the 3D-Beacons network, and sequences and alignments can be retrieved from databases hosted at EMBL-EBI. The Jalview Desktop also offers a graphical interface to the alignment and analysis services of the JABAWS web services framework.