UniFrac Analysis

Well, just a note of some interesting articles regarding new statistical techniques to analyze sequence libraries in a manner akin to analyzing DGGE profiles:

Lozupone, C. and R. Knight. 2005. UniFrac: a New Phylogenetic Method for Comparing Microbial Communities. AEM: 71: 8228-35.

And an application of UniFrac:
Ley, R.E. et al. 2005. Obesity alters gut microbial ecology. PNAS. 102:11070-11075.

To use UniFrac, you will need to download and operate "Python" software.
You will also need to download a special "Numeric" module. Make sure you download the Numeric, not the NumPy, module.
Then you will need to download the .zip file of the unifrac program (http://bayes.colorado.edu/unifrac.zip).

The UniFrac program is not trivial to use if you haven't had any experience with Python or similar languages. I've emailed Dr. Lozupone and she has indicated that eventually a web-based UniFrac program will be available. However, not yet.

You will need phylogenetic trees in Newick tree format as the input data file for this program.