You may want to look at seqapp at ftp.bio.indiana.edu:/molbio/seqapp.
In article <199403171627.AA24423 at wugate.wustl.edu> brett at BORCIM.WUSTL.EDU writes:
> 1 Mac or VMS based
seqapp is a mac app
> 2 handle large numbers of sequences
I've fed it multi-megabyte files of hundreds of sequences
of around 3500bp each w/ no problem.
> 3 handle internal overlaps properly
you'll have to decide -- it relies the CAP software of
Xiaoqiu Huang for automatic contig alignments, or clustalV
by Des Higgins for multisequence alignments, plus you can
do hand alignments fairly easily.
> 4 generate a consensus
of a simple sort
> 5 oh yeah, must be cheap too!
in 6 months or so, I hope to have the cross-platform version
up to speed for these things also.
-- d.gilbert--biocomputing--indiana u--bloomington--gilbertd at bio.indiana.edu