Tweak docstring formatting so 2to3 runs.

This fixes installation under Python 3 again, accidentally
broken during d93a9a04faac98627fd5ed3c0e1802eca5a7707f
Remove EOF whitespace and add a missing EOF newline.
Remove a useless semicolon.
Make comparisons to None, True and False conform to PEP8.
Avoid multiple statements on one line, fixes PEP8 E701 tree-wide.
Remove setuptools code (see mailing list)

The idea of using setuptools was to handle dependencies
automatically, particularly numpy. However, pip didn't
finish installing NumPy before Biopython. Using setuptools
had downsides too so we (Peter, Michiel and Brad) agreed
to remove it - see:

http://lists.open-bio.org/pipermail/biopython-dev/2013-July/010726.html
http://lists.open-bio.org/pipermail/biopython-dev/2013-July/010729.html
http://lists.open-bio.org/pipermail/biopython-dev/2013-July/010731.html
http://lists.open-bio.org/pipermail/biopython-dev/2013-July/010734.html
http://lists.open-bio.org/pipermail/biopython-dev/2013-July/010733.html
test_Fasttree_tool: Don't use out= option (-out flag) in commands

Older versions of FastTree don't have the -out option, but work with the wrapper
otherwise. This change lets the test pass on more platforms where the wrapper is
usable.

Also cleaned up some extraneous whitespace and PEP8 issues.
test_Prank_tool: removed uses of -noxml and -notree options

These options no longer exist in Prank. Instead, "no" is now the default, and
-showxml and -showtree are available options.
Update ClustalOmega wrapper for software version 1.2.0.
Added -showxml and -showtree options to Prank wrapper
Merge branch 'master', remote-tracking branch 'origin'
Downgrade non-null SFF padding error to a warning (issue #219).

Based on a patch from Martin Mokrejs, this allows the
Biopython SFF parser to be used on invalid SFF files
generated by sff-dump.2.1.7 though 2.1.9 when converting
from *.sra files (problem was due to reuse of an output
buffer, fixed in release 2.1.10).

Martin tested this on SRR088820.sff, ERR016587.sff, and
ERR016602.sff from the SRA.
Kwargs are passed as pyplot options

Getattr allows pyplot to have options dynamically passed to it.
Isinstance processes arguments passed into phylo draw in ways
appropriate to the data types used in them.
Added linecollection for clade lines option

An option is added that allows clade lines to be created with
matplotlib's linecollection objects.  The linecollection objects are
stored in tuples that are added to the pyplot plot.
Added changes based on feedback from @etal

Fixed spelling error, line size, and comment location.
Added exception catching for the format of user entered pyplot options key word
arguments.
Changed global to local object scope in the objects containing the plot line
collections.
Redundant error catching removed from  matplotlib.collections import.
Additional comment added to draw_clade_lines.
Removed test printing line and changed exception test try statement to have
better syntax.
Phylo.draw: edited docstring & made the printed error message a ValueError

Stripped some spurious whitespace.
Phylo.draw: rename local variables for PEP8 compliance

Removed unnecessary line continuations (end-of-line backslashes inside parens)
GenBank: Give better error output on invalid qualifiers

When encountering a multiline qualifier that doesn't contain an = sign
and doesn't correctly close the quotation marks, the error message
"TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'"
is less than helpful. Catch the None type and give a better error
message by raising a StopIteration.

Also add a unittest-based test case for this, as I couldn't figure out
how to properly test this with the old-style tests.

Signed-off-by: Kai Blin <kai.blin@biotech.uni-tuebingen.de>
Fix typo in class name (docstring change)

Documentation change only, no need for TravisCI tests [ci skip]
Updating CDAO library to remove dependency on librdf. Using RDFlib instead.