[BioPython] Clustalw multiple alignment

[Brad Chapman]

Jeff wrote:
>  Scripting code that provides interfaces to programs are certainly
>  needed within biopython!  Should we include this package in the
distribution?

Well, I definately have no objections to that :-). If other people would
find this useful I would be very happy to include it.

>  This seems to have a lot of requirements that currently aren't in the
>  Biopython spec (Python 1.6+, XML, Martel), but perhaps that means it's
>  time to update the requirements list.

Yeah, this was one of the major things holding me back from suggesting
this. I really enjoyed using Martel and I think it might be worthwhile to
get this to be more closely integrated with Biopython, if people are for
this. Right now Martel has the following requirements:

1. The PyXML package -> I don't know right now if python2.0 will have
enough XML integrated to allow Martel to work with it alone. I follow the
XML-SIG, and it seems like the XML support will be much improved in the
next beta release, so it may be possible to access this than. On the
other hand, it also looks like they aren't much interested in supporting
1.5.2 (having Unicode support in 2.0 is a big reason to move the XML work
to use that) in future releases, so this will probably push Biopython to
require 2.0 if we stick with this.

2. mxTextTools (http://starship.python.net/~lemburg/mxTextTools.html)

I don't mind these requirements (obviously :-), but I don't know how
other people feel about this. 

But, if no one has any contrary opinions, I would be happy to include the
clustal stuff I wrote. 

Brad