Style change, avoid unnecessary dictionary .keys() method call

Based on a GitHub comment by @namn refering to Guido's email:
https://mail.python.org/pipermail/python-dev/2014-April/134187.html
Check for unicode byte order marks (BOMs) in Newick trees under Python 2

Cherry-picked from pull request #241 / #310
Thank Nigel for Newick unicode BOM fix
Split unit test method into three smaller tests
Mark Tests/SubsMat/acc_rep_mat.pik as binary to solve Pickle problem

If the pickle file has DOS/Windows newlines which can happen under
Windows depending on how git was configured, the C based pickle code
in Python 3.4 fails to to load it with this exception:

_pickle.UnpicklingError: the STRING opcode argument must be quoted

See test_SubsMat.py and this thread on the mailing list for background:
http://lists.open-bio.org/pipermail/biopython-dev/2014-April/011274.html
Tweak doctest for int vs long issue on 64 bit Windows

Rather than (7, 52), Manlio Calvi reports getting (7L, 52L)
with 64 bit Python 2.7 under Windows 7, see mailing list:
http://lists.open-bio.org/pipermail/biopython-dev/2014-April/011276.html