Jalview - A Sequence Alignment Editor and Viewer

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

If you use Jalview 2 in your work, please cite:
Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ (2009)
Jalview Version 2-a multiple sequence alignment editor and analysis
workbench. Bioinformatics 25: 1189-1191.

NOTE:
The 'source' is hosted at SourceForge by the SlackBuild maintainer.