Split getDNADistMatrix and getAADistMatrix?

[Jason Vander Heiden]

We could split out the redundant code in getDNADistMatrix() and getAADistMatrix() into helper functions, and move the the part that extends and existing matrix into a separate function too. I'm not sure whether it would be more user friendly to have separate functions or arguments to the same function that generate different behaviors. It's not called often, so performance isn't an issue

[Jason Vander Heiden]

Not worth it if we are just going to move this to C++ anyway.