Well so far folks have mentioned Macaw, Pileup, Pima, Clustalv, and Essee (ese
e). Treealign is another to add to this group of multiple aligners. Treealign
was written by Jotun Hein. It does multiple alignmnts and creates phylogenetic
trees at the same time. Treealign was written in C and runs on just about any
thing with a C compiler - BUT is probably not appropriate for PCs as it needs a
lot of memory. As per all such programs - garbage in += garbage out.
A method you may want to try is a combination of automatic and manual aligners.
Run your sequences through one of the above programs and they may show you some
"motifs" to look for and give you a general idea of things and then you can ad
just the alignment manually. As your at the PSC I know you have access to a VA
X so you might want to consider getting MALIGNED for manual alignment.
Maligned is a GREAT program for manual alignment written by Steve Clark.
Maligned has a variety of shading options based on the percent identities
present at each position in the alignment so that as you add gaps to a
sequence(s) you can easily see how it affects the alignment. Once you have
done all the aligning and are satisfied with the shading you can print the
output on a HP laser printer (or compatibles), a dot matrix printer, or a
Postscript printer. Maligned can also produce a spreadsheet with statistical
information about every position in the alignment which is easy to dump into
a spreadsheet package (Lotus...) and graph and/or manipulate to your hearts
content. Maligned is WELL documented and user friendly. I can't give it
justice in this little blurb - if there is interest I'll post a better
description. If you haven't noticed - I like it :-) The one catch is that
Maligned is for VAX/VMS only.
Treealign is available from ftp.bio.indiana.edu and ftp.bchs.uh.edu.
(may be available from embl and nic.funet.fi - I haven't checked)
Maligned is available from ftp.bio.indiana.edu, ftp.bchs.uh.edu, nic.funet.fi,
and netserv at embl-heidelberg.de. Kudos to Don Gilbert, Dan Davison, Rob Harper
, and Rainer Fuchs for running those sites.
Best of Luck,
Dan Jacobson
danj at jhuhyg.sph.jhu.edu
