MISC: General clean-up to clustal.py and tests

A variety of changes took place in this commit:

    - Private functions i. e. the ones that are only intended to be used
      within this module were changed to be prefixed by an underscore,
      the test suite was changed accordingly (thanks @gregcaporaso).
    - Remove unnecessary white-spaces and add an underscore to catch the
      return value of a cast-to-int operation. **
    - Change parse_clustal to yield joined sequences instead of lists of
      sequences, additionally update the documentation to reflect these
      changes. **

** Thanks @wasade.