Jalview is a free program developed for the interactive editing, analysis and visualization of multiple sequence alignments. It can also work with sequence annotation, secondary structure information, phylogenetic trees and 3D molecular structures.

JalviewLite and Jalview Desktop

JalviewLite allows sequence alignments to be visualized in a web page, along with annotation, phylogenetic trees, and associated 3D structures. It has built in support for a wide range of alignment file formats, GFF files, and Jalview's own sequence and alignment annotation format. It allows editing, and can also show the consensus sequence, sequence logo and amino acid conservation for your alignment. analysis, tree and principal component analysis calculations.

The other flavour of Jalview is the Jalview Desktop:

The Jalview Desktop is an application you can launch from the web or install locally. It's designed for the kind of in-depth sequence analysis necessary when exploring new protein or RNA sequence families to understand how their sequence relates to structure and function.
The Desktop can access sequence, alignment, 3D structure and annotation databases, and web services for multiple alignment, protein disorder and secondary structure prediction and functional analysis.

Some of the most important things about the Jalview desktop are that you can save all your work as a Jalview Project, and create multiple visualizations of the same alignment, making it easy to create figures describing your findings that can be exported as an image, an HTML document or an encapsulated Postscript file.

Jalview is Open Source Bioinformatics Software

Jalview is developed in Java, and the source has always been freely available. In 2010, we launched Jalview's own git repository, which lets bioinformatics developers from around the world contribute to Jalview. To find out more, head on over to Jalview Development.