[BioPython] Clustalw multiple alignment

[Jeffrey Chang]

> Will do. I will write up some tests and docs, and get it in there. Right
> now it would be under Bio.Align -> does this sound good to people, or are
> there other suggestions?

Put the clustalw stuff in Bio.ClustalW.  We'll reserve Bio.Align (or
something like it) for generalized alignment code.

> I've been using it with 2.0b1 for a while now, without any problems
> (although Andrew's reverse() function did pick up a bug in the beta
> version!). So in general, I think the code is pretty happy with 2.0.

That's great news!  Maybe it's time for me to upgrade.

> So, right now only prodoc and gobase are failing, which I think
> (hopefully) is the expected failure rate right now.

Yep, that's been happening for a while.  We should aim to fix that before
the next release, though...

Jeff