[BioPython] Clustalw multiple alignment

[Andrew Dalke]

Brad:
> Martel has the following requirements:

> PyXML

> I don't know right now if python2.0 will have enough XML integrated to
> allow Martel to work with it alone.

It should.  I read through some of the python-dev mailing list archives
last night, and it will have SAX support.  That's all Martel really needs.
Though that will make things dependent on Python 2.0 instead of 1.5.2.

> mxTextTools

I've been concerned about that dependency.  Don't know if we should
include mxTextTools in a distribution, or have people download it
seperately.  The latter is easier for us, but harder for others.  Another
option is mxTextTools includes a pur Python implementation, which I
haven't yet tested.  We might include that in a distribution as a fallback,
although as Jeff points out that means people might start using it and
complain about the speed.

BTW, for Martel my plan is to make a "0.3" version Real Soon Now.  This
will be the last major version, excepting bug fixes, to use the existing
XML SIG library.  Then I switch over to the 2.0 beta series for testing.
I'm liking a lot of things in 2.0.

I've also got a beta for the next mxTextTools, which has some changes to
simplify Martel generation code, so I'll likely start work to support that,
though with backwards compatible support for older mxTextTools
installations.

                    Andrew