Looking for a multi-sequence alignment program

Andy Phillips andy.phillips at bbsrc.ac.uk
Fri Nov 8 06:14:36 EST 1996


Alex Chang wrote:
> 
> This may be a FAQ.
> 
> My friend is looking for a multi-sequence alignment program, preferably a
> MS-Window based program.
> 
> Thanks
> 
> Alex Chang
> Pathology
> University of British Columbia
> achang at hivnet.ubc.ca

I use ClustalW (a DOS program) to generate the inital lineup, and then Genedoc to 
edit and print it. There are links to both of these (and other alignment programs) in 
the Software section of my Really Quite Useful MolBio Page:

http://www.lars.bbsrc.ac.uk/plantsci/molbiol/molbiol.html

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?

Andy

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