[BioPython] script for clustal alignment format

[Brad Chapman]

[mxTT and biopython -- Andrew proposes an alternative download site]
Jeff:
> My preference, though, would be to go ahead and bundle
> it (if possible etc etc), since it's small, and we could merge the
> installations.  I suspect that the parsers are/will be Biopython's most
> used code, so this would make things easier for a lot of users.

+1 for including mxTT with Biopython. I think it wouldn't be a problem 
to modify the setup.py so that it checks for mxTT (ie. by trying to
import it) and if it is not present, goes ahead and installs it.

[including Martel with Biopython]
> There's already code in Biopython that requires Martel (Brad's ClustalW
> stuff), and I'm reasonably convinced that it can do the stuff already done
> with the parsers, with at least comparable or better execution speed.

Agreed. My vote is to include both Martel and mxTT in the next
distribution, so people will want to use my Clustalw parser
:-). Seriously, I think the sooner we get it integrated, the sooner we 
can use it for other things, like a Genbank parser (keeping the hints
coming!).

As Jeff says, we don't have to switch everything over to it (I
don't want to try and change the BLAST parser over!), but it
gives an alternative option for making new parsers, and will also get
Martel some extra exposure/testing, so that Andrew will be more likely 
to become famous for it :-)

Brad