In ``Bio/Sequencing/Applications/__init__.py`` you need to do Python 3 friendly local imports (see the master branch and https://github.com/biopython/biopython/commit/eddb1a93f6bc03897ed69302c0d009e24a0ee1bb for reference). e.g.

    from ._Novoalign import NovoalignCommandline

Not the old style:

    from _Novoalign import NovoalignCommandline

This is one of the reasons TravisCI is currently failing on Python 3.