Jalview is an free program for multiple sequence alignment editing, visualisation and analysis. Use it to 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. It uses Jmol to view 3D structures, and VARNA to display RNA secondary structure. The Jalview Desktop can also connect with databases and analysis services, and provides a graphical interface to the alignment and analysis services provided by the JavA Bioinformatics Analysis Web Services framework.