NewickIO: parse branch lengths in scientific notation (Issue #220)

Included a unit test for it, too.

Thanks to mathli for reporting this bug and offering a fix.
Prank wrapper: added versions to option docs for -(show|no)(xml|tree) change

Their wiki says the change occurred at version 120626:
http://code.google.com/p/prank-msa/wiki/NewFeatures?tm=6
test_Prank_tool: handle Prank's new stdout logging style

Old Prank output:

PRANK: converting 'Quality/example.fasta' to 'temp with space.fas'

New Prank output:

-----------------
 PRANK v.130820:
-----------------

Input for the analysis
 - converting 'Quality/example.fasta' to 'temp with space.fas'
test_Prank_tool: find ".best.nex" output file from the latest Prank

In yet another twist, the latest version of Prank names its output files
"*.best.nex", "*.best.fas", etc. instead of the established "*.2.nex" which the
unittest expected. The unittest now checks for both extensions.
Move one-to-three protein letter maps into Bio.Data.IUPACData
SeqUtils.seq3 now creates a copy of the imported IUPACData dict

This is to prevent a bug where the IUPACData dict is imported in some other
modules, and the key-value pairs have unexpected values due to seq3's update.
Move Bio.SCOP.three_to_one_dict to Bio.Data.SCOPData
Add deprecation warning in place of old SCOP's 3-to-1 dict
IUPACData: fixed small typo protein_letters_31to1 -> protein_letters_3to1
Fix PDBIO blank occupancy handling

* Used @peterjc's suggested format string modification
* Added unit test for blank occupancy writing
Add DSSP unit test.

* Tweak DSSP method to avoid tmp file
* Test parsing of pregenerated DSSP file
* Test generation of DSSP file from PDB file

Conflicts:
	Tests/test_PDB.py
Using test_XXX_tool.py for unit tests dependent on a binary
Move dependency free DSSP testing into test_PDB.py
Tutorial/Phylo: mention CDAO support, FastTree wrapper

Suggest DendroPy, PyCogent as other good Python libraries for phylogenetics.
NEWS: mention that there were bug fixes, test improvements since beta.
DSSP test: support more versions.
Fix DSSP changes under Python 2.5 (with statement)
Turn PDB numpy import error into MissingPythonDependencyError

This is an ImportError subclass, so shouldn't break anything.
It has the benefit of making things cleaner in the unit tests,
e.g. test_DSSP_tool.py
Python 3 fix for test_DSSP_tool.py
Fix copy & paste error in last commit.