Journal Article

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

Thomas Pommier, Björn Canbäck, Per Lundberg, Åke Hagström and Anders Tunlid

in Bioinformatics

Volume 25, issue 6, pages 736-742
Published in print March 2009 | ISSN: 1367-4803
Published online February 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp051

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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: tpommier@univ-montp2.fr; bcanback@acgt.se

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

Journal Article.  4648 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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