Updating the documentation
Correct indentation level, 4 spaces instead of 8.
Use with statement to ease file handle management.
Remove unused variables (found with pylint).
Actually use BiopythonExperimentalWarning.
Remove unused imports.

Imports in tests that hint at untested functionality were left in place.
Fix for float('-inf') under Python 2.5 on Windows

See also commit 60f28efdfe19fdcb2bb3ca4dc2ca6a222be97394 where
this same fix was used in Bio/HMM/MarkovModel.py
There are now no Doc/*.txt files.

Updating the manifest to prevent this warning on install:
warning: no files found matching '*.txt' under directory 'Doc'
Remove unused variables.
Recognize MSAProbs CLUSTAL files.
Fix undeclared var in Bio._py3k
Scripts: Some more PEP8 whitespace cleanup.
BioSQL: Some more PEP8 whitespace cleanup.
Doc/examples: Some more PEP8 whitespace cleanup.
KDTree/Medline/NMR/NeuralNetwork: Some more PEP8 whitespace cleanup.
Fix failing doctest (dict order is platform dependent)

This was failing on Python 3.3 and Jython (possibly more).
Jython 2.5.2 doesn't like float('+inf')

This fixes a failing doctest in Doc/Tutorial.tex
Ignore BiopythonExperimentalWarning in test_Tutorial.py

(We're using this in SearchIO examples)