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

Pommier, Thomas ; Canback, Bjorn ; Lundberg, Per LU ; Hagstrom, Ake and Tunlid, Anders LU (2009) In Bioinformatics 25(6). p.736-742
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... (More)
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. (Less)
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author
; ; ; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Bioinformatics
volume
25
issue
6
pages
736 - 742
publisher
Oxford University Press
external identifiers
  • wos:000264189600006
  • scopus:62549131197
ISSN
1367-4803
DOI
10.1093/bioinformatics/btp051
language
English
LU publication?
yes
id
9f217021-8436-4ff7-aeb0-737bdf576a33 (old id 1405019)
date added to LUP
2016-04-01 12:07:21
date last changed
2024-03-26 01:30:56
@article{9f217021-8436-4ff7-aeb0-737bdf576a33,
  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.}},
  author       = {{Pommier, Thomas and Canback, Bjorn and Lundberg, Per and Hagstrom, Ake and Tunlid, Anders}},
  issn         = {{1367-4803}},
  language     = {{eng}},
  number       = {{6}},
  pages        = {{736--742}},
  publisher    = {{Oxford University Press}},
  series       = {{Bioinformatics}},
  title        = {{RAMI: a tool for identification and characterization of phylogenetic clusters in microbial communities}},
  url          = {{http://dx.doi.org/10.1093/bioinformatics/btp051}},
  doi          = {{10.1093/bioinformatics/btp051}},
  volume       = {{25}},
  year         = {{2009}},
}