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Open Access Open Badges Research article

Variance adjusted weighted UniFrac: a powerful beta diversity measure for comparing communities based on phylogeny

Qin Chang1, Yihui Luan1* and Fengzhu Sun23*

Author Affiliations

1 School of Mathematics, Shandong University, Jinan, Shandong 250100, PR China

2 TNLIST/Department of Automation, Tsinghua University, Beijing 100084, PR China

3 Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089-2910, USA

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BMC Bioinformatics 2011, 12:118  doi:10.1186/1471-2105-12-118

Published: 25 April 2011



Beta diversity, which involves the assessment of differences between communities, is an important problem in ecological studies. Many statistical methods have been developed to quantify beta diversity, and among them, UniFrac and weighted-UniFrac (W-UniFrac) are widely used. The W-UniFrac is a weighted sum of branch lengths in a phylogenetic tree of the sequences from the communities. However, W-UniFrac does not consider the variation of the weights under random sampling resulting in less power detecting the differences between communities.


We develop a new statistic termed variance adjusted weighted UniFrac (VAW-UniFrac) to compare two communities based on the phylogenetic relationships of the individuals. The VAW-UniFrac is used to test if the two communities are different. To test the power of VAW-UniFrac, we first ran a series of simulations which revealed that it always outperforms W-UniFrac, as well as UniFrac when the individuals are not uniformly distributed. Next, all three methods were applied to analyze three large 16S rRNA sequence collections, including human skin bacteria, mouse gut microbial communities, microbial communities from hypersaline soil and sediments, and a tropical forest census data. Both simulations and applications to real data show that VAW-UniFrac can satisfactorily measure differences between communities, considering not only the species composition but also abundance information.


VAW-UniFrac can recover biological insights that cannot be revealed by other beta diversity measures, and it provides a novel alternative for comparing communities.