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Applied and Environmental Microbiology, April 2006, p. 2379-2384, Vol. 72, No. 4
0099-2240/06/$08.00+0     doi:10.1128/AEM.72.4.2379-2384.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Introducing TreeClimber, a Test To Compare Microbial Community Structures

Patrick D. Schloss and Jo Handelsman*

Department of Plant Pathology, University of Wisconsin—Madison, Madison, Wisconsin 53706

Received 22 October 2005/ Accepted 17 January 2006

The phylogenetic and ecological complexity of microbial communities necessitates the development of new methods to determine whether two or more communities have the same structure even though it is not possible to sample the communities exhaustively. To address this need, we adapted a method used in population genetics, the parsimony test, to determine the relatedness of communities. Here we describe our implementation of the parsimony test, TreeClimber, in which we reanalyzed six previously published studies and compared the results of the analysis to those obtained using {int}-LIBSHUFF.

* Corresponding author. Mailing address: Department of Plant Pathology, University of Wisconsin—Madison, Madison, WI 53706. Phone: (608) 263-8783. Fax: (608) 265-5289. E-mail: joh{at}plantpath.wisc.edu.

Applied and Environmental Microbiology, April 2006, p. 2379-2384, Vol. 72, No. 4
0099-2240/06/$08.00+0     doi:10.1128/AEM.72.4.2379-2384.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



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