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  • Pommier, Thomas, et al. (author)
  • RAMI: a tool for identification and characterization of phylogenetic clusters in microbial communities
  • 2009
  • In: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1460-2059. ; 25:6, s. 736-742
  • Journal article (peer-reviewed)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.
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Type of publication
journal article (1)
Type of content
peer-reviewed (1)
Author/Editor
Tunlid, Anders (1)
Lundberg, Per (1)
Pommier, Thomas (1)
Hagstrom, Ake (1)
Canback, Bjorn (1)
University
Lund University (1)
Language
English (1)
Research subject (UKÄ/SCB)
Natural sciences (1)
Year
2009 (1)

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