Looking for a multi-sequence alignment program

[Francois Jeanmougin]

In article <3282FA20.1774 at bbsrc.ac.uk>,
	Andy Phillips <andy.phillips at bbsrc.ac.uk> writes:
[...]
>The only hassle is getting the files into the right format for Clustal. 
>I use the GCG program TOPIR to convert a file of sequence names in GCG 
>format into a single PIR file. I feel there must be an alternative to 
>this that doesn't require access to GCG, and doesn't involve assembling 
>the PIR file with a text editor. Any suggestions?

	First, ClustalW runs on UNIXs, VMS, DOS, MAC (enough?), so I don't 
think you are using a DOS version of GCG ;-), you will increase clustalw
perfs by installing a new version on the same system.
	Second, Clustalw could read several formats (like fasta format...),
so it depends of what is your sequences format first. Installing Readseq
from Don Gilbert is a good solution:
ftp://ftp.bio.indiana.edu/molbio/readseq

	Plans on clustalw are (as far as I know): X interface, including
readseq...Just waiting for a grant for Julie (anyone has one???).

							Francois.
Remember ClustalW 1.6 on-line help:
http://www-igbmc.u-strasbg.fr/BioInfo/ClustalW/clustalwOLH.html
http://www.u.arizona.edu/~schluter/ClustalW/index.html
-- 
Francois Jeanmougin
Service de bioinformatique / bioinformatics service
IGBMC BP 163 67404 Illkirch France
tel :(France) 03 88 65 32 71 / (international) (+33) 3 88 65 32 71
e-mail : jeanmougin at igbmc.u-strasbg.fr
"les poissons sans fish, les pieds sans foot" (STTELLLA)