Fix TravisCI setup (removing last part of Jython hack)
Converting a tree into a librdf model and then serializing is slow, requires a lot of memory, and is not feasible for large trees. Refactoring CDAOIO.Writer to write triples directly to file instead of using librdf. This also makes the API more similar to other Bio.Phylo modules.
Default tree URI is blank, but still create a tree object.
Better tree URIs; avoid duplicating the tree ID.
Fixing some URI handling issues to make loading via librdf and isql identical.
Don't add a slash to tree_uri if it's blank
Use rdfs:label, not rdf:label.
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.