Good alignment program?

[Sathish, P.]

Hi:
I used to use Geneworks on Macintosh.  Unfortunately it takes time to
complete the alignment and requires lots of memory if you try aligning
long stretches of DNA,RNA or prtoteins.  A Power Macintosh is highly
recommended.
I now routinely use PileUp in GCG (in a Unix machine), as it is fast and
good.
Sometimes I use the netsite, http://www.ibc.wustl.edu/msa.html , to
perform small alignments.  It probably uses an alogorithm similar to
Clustalw.
To get neat publishable quality outputs of my alignment, I use the
netsite, http://ulrec3.unil.ch/software/BOX_form.html .  

Disclaimer:  I have no gain, monetary or otherwise, with any of the
products that I have mentioned above.  Just a user.

Hope this helps.
Warm regards,
sathish
-- 
P. Sathish Ph. D.
Post-Doctoral Researcher,
Department of Biochemistry,
Arrhenius Laboratories for Natural Sciences,
Stockholm University,
S 106 91 Stockholm,
Sweden.

Phone: +46 8 16 2464
Fax: +46 8 15 3679
E-mail: sathish at biokemi.su.se
WWW: http://130.237.179.82/sathish/sathish.html