Partial commit
Add NucleotideSequence.nondegenerates()

Also added @total_ordering and __lt__ to allow native sorting of BiologicalSequences.

Still needs more testing and docstrings.
Remove native sequence sorting.

It works to specify `key` in `sorted` calls, no need to add complexity to the existing sequence classes at this point.
Remove unused import
Add more tests, docstrings, gap character support
Performance improvements for ~2x speedup.

Is now slightly faster than version in PyCogent.
Use generator comprehension, add comment about try/except

Thanks for the suggestions @wasade!
Remove documentation warning from tree.py

Fixes #223

Thanks doc-whisperer @ElBrogrammer
Merge pull request #227 from ElDeveloper/user-warning

Remove documentation warning from tree.py
add @wasade's suggested comment to try/except
add comment about other performance-optimized code
union non-expandable chars outside loop

Thanks @wasade!
Merge pull request #224 from ElBrogrammer/expand-degens

Add method to expand degeneracies
testing out RTD
Add missing import and change constructor
Merge branch 'master' of git://github.com/biocore/scikit-bio into port-rfam
STY: Make code adhere to the project standards
MAINT: Remove irrelevant Exceptions
TST: Add tests for clustal

These tests were directly ported from the test suite in cogent. Some
clean-up took place but there was nothing major, most of it was PEP-8
related.
TST: Add tests for the Rfam related code