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

Author:
  • Thomas Pommier
  • Bjorn Canback
  • Per Lundberg
  • Ake Hagstrom
  • Anders Tunlid
Publishing year: 2009
Language: English
Pages: 736-742
Publication/Series: Bioinformatics
Volume: 25
Issue: 6
Document type: Journal article
Publisher: Oxford University Press

Abstract english

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.

Keywords

  • Bioinformatics and Systems Biology

Other

Published
  • Microbial Ecology
  • ISSN: 1367-4803
Anders Tunlid
E-mail: anders [dot] tunlid [at] biol [dot] lu [dot] se

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