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UniFrac – An online tool for comparing microbial community diversity in a phylogenetic context

Catherine Lozupone1, Micah Hamady2 and Rob Knight3*

Author affiliations

1 Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA

2 Department of Computer Science, University of Colorado, Boulder, CO 80309, USA

3 Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA

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Citation and License

BMC Bioinformatics 2006, 7:371  doi:10.1186/1471-2105-7-371

Published: 7 August 2006



Moving beyond pairwise significance tests to compare many microbial communities simultaneously is critical for understanding large-scale trends in microbial ecology and community assembly. Techniques that allow microbial communities to be compared in a phylogenetic context are rapidly gaining acceptance, but the widespread application of these techniques has been hindered by the difficulty of performing the analyses.


We introduce UniFrac, a web application available at webcite, that allows several phylogenetic tests for differences among communities to be easily applied and interpreted. We demonstrate the use of UniFrac to cluster multiple environments, and to test which environments are significantly different. We show that analysis of previously published sequences from the Columbia river, its estuary, and the adjacent coastal ocean using the UniFrac interface provided insights that were not apparent from the initial data analysis, which used other commonly employed techniques to compare the communities.


UniFrac provides easy access to powerful multivariate techniques for comparing microbial communities in a phylogenetic context. We thus expect that it will provide a completely new picture of many microbial interactions and processes in both environmental and medical contexts.