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

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Author

Summary, in 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.

Publishing year

2009

Language

English

Pages

736-742

Publication/Series

Bioinformatics

Volume

25

Issue

6

Document type

Journal article

Publisher

Oxford University Press

Topic

  • Bioinformatics and Systems Biology

Status

Published

Research group

  • Microbial Ecology
  • Theoretical Population Ecology and Evolution Group

ISBN/ISSN/Other

  • ISSN: 1367-4803