Do any open-source tools exist for visualizing multiple sequence alignments in a web browser? I am looking for a way to integrate alignment viewing capabilities into an existing web application. I don't just want a "dumb" block of text, but rather something that would be contextually aware of the alignment and possibly allow annotation, small segment viewing (as opposed to full alignment), and other features. I only want to be able to view existing alignments, not actually generate alignments from separate sequences.
JBrowse looks very promising. I'll give it a shot, thanks!