You may wish to look at IUBio archive, which holds software in
various areas of molecular biology, for Macintosh, Wintel and other systems.
See ftp://iubio.bio.indiana.edu/, or use http:// or gopher:// to this
server. Via http or gopher, you can search the abstracts or readme
files of software for key phrases like sequence analysis.
One possible program for sequence analysis is SeqPup, found
in the /molbio/seqpup/ subfolder on IUBio archive.
-- d.gilbert--biocomputing--indiana u--bloomington--gilbertd at bio.indiana.edu