Merge pull request #1 from spond/master

Updating to sergei's latest tweaks
Merge pull request #2 from spond/master

setup.py to include TNS
Update README.md
Update README.md
Adding filter option
Merge branch 'master' of github.com:spond/HIVClustering
Adding node filtering option '-k'
Expects a file with an id on each line
Purely white space fixes in _beastnetwork.py
updating documentation
updating documentation for filter
improving filtering description
Changing package_dir to `package_dir = {'': 'lib'}`
adding additional check to self.adjacency_list to see if empty
Adding Sergei's Q3 commits
Merge pull request #3 from stevenweaver/master

Sergei's Q3 fixes, Filter Option, and self.adjacency_list conditional fix.
Merge pull request #4 from veg/master

Merging veg back in