Remove unused imports and rearrange import order in Bio.SeqUtils
In seq1(), compare the uppercase versions of the three letter codes.

Otherwise this function is hard to use, as users have to bring their
sequences into the Xxx spelling format.
Travis should be providing NumPy on Python 3.2 now (or soon)
TravisCI should support Python 3.3 now.

They're also dropping Python 3.1 but that wasn't officiall
supported and we were not using it anyway.
Generalise TravisCI Python 3 support
Even float('inf') fails on Windows Python 2.5
Refactor utility functions in Bio.SearchIO

Some general-usage functions are now in Bio._utils
Refactor Bio.Phylo._sugar into Bio._utils
Refactor doctests in various submodules to use Bio._utils.run_doctest
Fix mass spectrometry method parsing.
Fix typos.
PEP8 whitespace cleanup.
Fix parsing of the mass spectrometry position elements.

The previous code resulted in a generator-type object as argument for int(),
leading to an exception.
Uniprot XML file that contains entries for all comment element types.

The base file is from accession O44185 with comment elements from the
following accessions added: Q00955, Q8W1X2, Q9BZZ5, P28335, Q01718,
P11911, Q06811, P55902, P42212, O14543, P40939, A6NMY6.
Add a more comprehensive regression test, especially to test comment elements.
Updating the documentation. Also need to find some solution for calculating the correlation
More typo and duplicate word fixes.
Avoid float array in Tutorial doctests
Implementing and documenting information content
Merge branch 'master' of github.com:biopython/biopython