Cope with missing date lines in SwissProt files (reported by Jan T Kim)
Add missing bookdoc_130101.dtd (reported by Jared Sampson, RedMine Bug 3422)
Update bug tracker URL (reported by Jared Sampson, RedMine Bug 3422)
Change to set_structure. Allows writing of individual (S)MCRAs
Added unit tests for PDBIO
Boolean flag in write_end converted to T/F
Fasttree wrapper 1.0

This wrapper can be used in similar ways to the Phyml and Raxml wrappers.
It has been tested with several command line arguments.

Basic usage:
_Fasttree.FastTreeCommandline(fasttree_exe, output_input='<OutputFile> <InputFile>')
Added Fasttree wrapper access
Added filename=True, PEP8, and -help changes

Based on feedback I added filename=True in some places, in -output_input
it was unable to be added due to an issue further described in the github
comments.  I converted the docstrings to PEP8 and removed the -help option.
Fixed input/output and -help

Created separate -input and -output arguments.  Added filename=True to
them.  Added -help and -expert with one line docstrings for them.  
Fixed "2nd" switch to have the name "Second" also to avoid an error.
Updated 'second', 'input', and 'output' to 'out'

Made changes based on feedback
Removed extra comment at 'nome'
Minimal test unit for fasttree

Based on Tests/test_Clustalw_tool.py and the Phylo cookbook.
Removed 'is_required' from 'out'

Setting that parameter is optional
Travis: Added fasttree to apt-get install line

Allows installation of fasttree
Added type safety using 'checker_function'

Added type safety for data such as ints, filenames, and floats or decimals.
Changed float and decimal type safety

The is_decimal function is now used and allows the data type to be
any number including but not limited to float or decimal.
Fasttree: extracted checker functions; removed extra whitespace
Fasttree: check that 'pseudo' is numeric, for our wrapper

FastTree accepts '-pseudo' as a switch, too, but since we've specified it as an
option with an argument, "pseudo=True" will serialize as '-pseudo True' which
is not valid for FastTree. So, the user must do "pseudo=1" instead.
Added Nate to NEWS and CONTRIB