first pass at entropy calculation bug fix
expanded doc string
added deprecation warning
added __str__ and fixed bug in test
added __contains__
added reversed
simplified documentation for SequenceCollection.degap()
fixed failing doc tests (had my test command wrong locally, but travis caught it)
Merge branch 'master' into issue-194
addresses comments from @ElDeveloper and @ElBrogrammer
added shownumpydoc directive
addressed two minor comments
addressed comment from @ElDeveloper
Merge pull request #220 from gregcaporaso/issue-194

addressing issues raised in #194
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