Fixed broken Bio.pairwise2

I fixed a major flaw in the pairwise2 implementation of Needleman-Wunch.

Here is a demonstration of the flaw: https://gist.github.com/4640508

This should definitely be merged.



This branch also removes a place where StockholmIO silently replaces "." gap characters with "-" gap characters, there are times when these are non synonymous.
You don't really have to merge this if you don't want to, of course you are the maintainer.