How to do Multiple Sequence Alignment of proteins with biojava n to get the conserved regions!

John Kern: Strangely, this wiki help page contains a message from Senthil asking for help back in the summer of 2010. While appropriate for the mailing list, it seems strange here. Would it be help to replace it with the help page from http://wikimediafoundation.org/wiki/Main_Page Wikimedia?