Both MUSTANG and MATT are good choices:
http://www.cs.mu.oz.au/~arun/mustang/
http://groups.csail.mit.edu/cb/matt/
On Jan 12, 2010, at 7:17 AM, Ronnie Berntsson wrote:
> Dear all,
>
> A bit off the topic question perhaps.
> I am trying to find a program which can do multiple structural sequence alignments. What I would like is a program which can take as input PDB codes (or files), and which will output a multiple sequence alignment in FASTA format with the full sequences of the supplied proteins intact. Preferably said server/program should be able to handle at least 20 input pdbs at once.
> I've been looking around, but have so far failed to find a program which does this. If anyone knows of a program or server which could handle this, I would be very grateful.
>
> Cheers,
> Ronnie Berntsson
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