Fixing a bug of SeqIO.PdbIO in parsing pdb-atom

Fixing a problem that SeqIO.PdbIO outputs erroneous amino acid sequence
if the ATOM record has more than one missing segments.
Phylo: reimplement BranchColo.to_hex() to use string format codes, not math

Thanks to joelb123 who reported the potential for weird results:
https://github.com/biopython/biopython/issues/214
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