mostly address the additions for 0.1.0

**NOT READY FOR MERGE** Too tired to keep going tonight, but it's getting close and I want the tests to run overnight.

This addresses the issues in #25 that are important for skbio 0.1.0, including adding a ``ProteinSequence`` object, adding a ``NucleotideSequence.translate`` method, and various other clean-ups and method additions. 

Still a few things to do:
 - [ ] look for obvious performance bottlenecks
 - [ ] doc strings for new ``NucleotideSequence`` methods