Ran 2to3 over all source files. Installs locally on Python 2.7 and 3.4 and passes unit tests. However, examples don’t yet work on Python 3.4.
Fixed bug that meant the sum of the overlap scores was incorrect for paired-end reads aligned to the OT-strand.
Local compatibility on Python 2.7 and Python 3.4.

Will try Travis builds on Python 2.6, 2.7, 3.2, 3.3 and 3.4