[BioPython] script for clustal alignment format

[Andrew Dalke]

Jeff:
>Andrew, how do you feel about bundling mxTT with Martel/Biopython?

Not a problem.  The other option is to provide an alternate location for
downloading mxTT.

> Do you know how stable mxTT is?

Quite.  I hasn't changed in about a year.  I've talked with Marc-Andre a
bit about a possible 2.0 - a 2.0 since he's concerned about keeping things
stable for existing 1.x users.

>Also, when should we add Martel to the Biopython distribution?  I'm
>planning on making one more release soon, and we could work on integration
>after that.

I take it we've decided that Martel is usable and has the needed
performance?
I don't think there's been real solid testing and characterization by anyone
other than me, although looking at the list traffic there have been a couple
of people who've tried it out.

There haven't been any problems reported to me, so I'm guessing people are
not running into problems, implying that the code is reasonably useful in
its current state.  I am hoping to get some more feedback.

I still have the nagging feeling that Martel doesn't support some class of
file formats (tree-based phylogeny ones?).  But that hasn't yet happened, so
I shouldn't be too concerned, and I've ideas for other ways to handle those.

Development-wise, the API still needs to be converted to SAX 2.0 and support
added for namespaces.  There also needs to be a way to convert the callback
form into an iterator one.  The code isn't too complicated, but as you
all can tell I haven't been able to work much on the project :(  Maybe
two more weeks?  Three?

                    Andrew