[BioPython] new version of AlignInfo: Now you can choose to have gap consensus

[Brad Chapman]

Hi Sebastian;

> Here is a new version of AlignInfo. It's based on Biophyton 1.1. I
> changed the function dumb_align, now it looks like this:

I think I understand why you want gaps, but I think the right thing
to do in this case would be to have a separate function (called
gap_consensus or something) which implements this functionality
instead of changing dumb_consensus. 

This way the behavior of the current function is unmodified (to
maintain consistency) and we can have your new functionality. If you
could make a diff of AlignInfo.py with the added function and send
it to me, I'd be happy to add it to CVS.

Also, I remember a while back during my written exams reading a mail
from you about some documentation problems about ClustalW. If you
could send a patch for that too I could get both things taken care
of at the same time. 

Thanks!
Brad