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Bioinformatics Advance Access published online on February 17, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp051
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

RAMI, a tool for identification and characterization of phylogenetic clusters in microbial communities

Thomas Pommier 1,2,*, Björn Canbäck 3, Per Lundberg 4, Åke Hagström 1 and Anders Tunlid 5

1Department of Natural Science, Kalmar University, Kalmar, Sweden, 2Present address: UMR 5119, Ecosystèmes Lagunaires, CNRS, Ifremer, UM2, IRD. Université Montpellier II, Montpellier, France, 3Björn Canbäck Bioinformatics, Vindögatan 66, SE-257 33 Rydebäck, Sweden, 4Department of Theoretical Ecology, Lund University, Lund, Sweden and 5Department of Microbial Ecology, Lund University, Lund, Sweden

*To whom correspondence should be addressed. Thomas Pommier, E-mail: bcanback{at}acgt.se, tpommier{at}univ-montp2.fr


  Abstract

Motivation: The most common approach to estimate microbial diversity is based on the analysis of DNA sequences of specific target genes including ribosomal genes. Commonly, the sequences are grouped into operational taxonomic units based on genetic distance (sequence similarity) instead of genetic change (patristic distance). This method may fail to adequately identify clusters of evolutionary related sequences and it provides no information on the phylogenetic structure of the community. An ease-of-use web application for this purpose has been missing.

Results: We have developed RAMI which clusters related nodes in a phylogenetic tree based on the patristic distance. RAMI also produces indices of cluster properties and other indices used in population and community studies on-the-fly.

Availability: RAMI is licensed under GNU GPL and can be run or downloaded from http:\\www.acgt.se\online.html.

Contact: bcanback{at}acgt.se, tpommier{at}univ-montp2.fr

Supplementary information: http:\\www.acgt.se\RAMI\SuppInfo

Associate Editor: Martin Bishop

Received on September 6, 2008; revised on January 22, 2009; accepted on January 22, 2009

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