TogoWS no longer supports the EMBL database
Refactor long __init__ method to call two sub-methods

This change looks bigger than it really is due to the indentation
level changing; see diff view ignoring whitespace.
More explicit error message
Test brittle relative paths in Bio.SeqIO.index_db (issue #267)
Test some indexing relative path setups
Must close the SQLite handle prior to deleting
Fix incorrect HSPFragment property name (issue #364)
Change Newick tree parsing to handle numeric names

(cherry picked from commit 0002b528e4272a88839cb17c7e7711bc2183ef7f)
Signed-off-by: Eric Talevich <eric.talevich@gmail.com>
Don't install mysql-connector-python on TravisCI - issue #370

This is a short term solution to a known failure in the
unit tests (errors on Python 2.6, 2.7, 3.4, stalls on
Python 3.3 and PyPy) under TravisCI, presumably due to
an update to the version of mysql-connector-python.

e.g. TypeError: unhashable type: 'bytearray'
Support for fastsimcoal 2.51
Merge branch 'master' of github.com:biopython/biopython
fsc251 on unit test
PEP8 whitespace fixes.
Remove EOF whitespace (PEP8 W391).
Fix grammar in NEWS.
Fix EOL whitespace (PEP8 W291).
Thank Christian Brueffer for PEP8 cleanup, PR #377
Put docstring at start; reduce white spaces in example.

Needs further work to make it epydoc reStructuredText ready.
Fix RST indentation; PEP docstrings; Links for papers cited.

Getting a DOI for many of the papers was harder than usual,
perhaps a temp glitch on the publisher's website?
Fixes for PEP8 W2 whitespace warnings.