Fix #168, Fix #1506
Adding scripts/trajectory_analysis.py
fixing errors
initial change to support pep8 biom
version 10:08am
JOSH: de-camelcase 10:30
alpha diversity
JOSH: more de-camelcase 11:13
JOSH: Change DenseTable to Table
beta div
Merge branch 'biom_pep8' of https://github.com/antgonza/qiime into biom_pep8
shared phylotypes
JOSH: Put tabs back
TST/API: Fix broken tests and deprecated API usage

Some of the code was making calls to methods that no longer exist and/or
accessing private member variables.
TST: Fix broken tests

Doing a conversion on an object that was being directly fed into
pycogent's dist_chisq was raising an exception regarding the data type,
converting this back to a dense numpy array fixes the problem.
Merge branch 'biom_pep8' of https://github.com/antgonza/qiime into biom_pep8
core microbiome
JOSH: even more camelcase
Merge branch 'biom_pep8' of github.com:antgonza/qiime into biom_pep8
Merge branch 'biom_pep8' of https://github.com/antgonza/qiime into biom_pep8