Principal Investigator:

Rob Knight -

Department of Chemistry and Biochemistry
Campus Box 215
University of Colorado at Boulder
Boulder, CO 80309

Contact Us:

Requests, suggestions, or technical issues -
Analysis related questions -


Micah Hamady -
Catherine Lozupone -

We welcome your feedback/sponsorship. Please send your comments/suggestions to

Cite Us:

Lozupone, Hamady & Knight, "UniFrac - An Online Tool for Comparing Microbial Community Diversity in a Phylogenetic Context.", BMC Bioinformatics 2006, 7:371 - PubMed

Lozupone, Hamady, Kelley & Knight, "Quantitative and qualitative (beta) diversity measures lead to different insights into factors that structure microbial communities." Appl Environ Microbiol. 2007 Jan 12 - PubMed

Lozupone C, Knight R. "UniFrac: a new phylogenetic method for comparing microbial communities." Appl Environ Microbiol. 2005 Dec;71(12):8228-35. - PubMed


Click here to download source code.

Other Software: (You do not need to re-register)

DivergentSet uses a phyogenetic tree to guide the construction of divergent sets of sequences, and, even on a single CPU, is up to two orders of magnitude faster than the naive method of using a full distance matrix. The DivergentSet software makes it easier to perform a wide range of bioinformatics analyses, including finding significant motifs and covariations.

MotifCluster allows you to analyze motifs in a set of protein sequences, relating them to the alignment, phylogeny, and (where available) the 3D structures. It is useful for detecting remote homologies between protein families, for understanding which proteins are most likely to share functions, and for identifying residue changes that might be important for the evolution of new enzyme activities.

Go back to online UniFrac.