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
Add an application wrapper and unit test for the MSAProbs alignment software.