Cool, and I agree with @antgonza that we should coordinate (pun intended?) file formats and Python objects to store the results, so that visualization can be done in Emperor.

This is related to an open QIIME issue where NMDS coordinate files don't work with make_2d_plots.py, make_3d_plots.py, or Emperor:

https://github.com/qiime/qiime/issues/1341

I think it's time for a ```Coordinates``` class in bipy. This class would be a data container with serialization methods, similar to ```DistanceMatrix```. What do you guys think?