title: RAMI: a tool for identification and characterization of phylogenetic clusters in microbial communities.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  RAMI is licensed under GNU GPL and can be run or downloaded from http://www.acgt.se/online.html.
  
  
  BACKGROUND
  http://www.acgt.se/RAMI/SuppInfo.
authors.affiliation: Department of Natural Science, Kalmar University, Kalmar, Sweden. tpommier@univ-montp2.fr
authors.forename: Thomas
authors.initials: T
authors.lastname: Pommier
authors.forename: Björn
authors.initials: B
authors.lastname: Canbäck
authors.forename: Per
authors.initials: P
authors.lastname: Lundberg
authors.forename: Ake
authors.initials: A
authors.lastname: Hagström
authors.forename: Anders
authors.initials: A
authors.lastname: Tunlid
mesh_terms: D001419:Bacteria / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry*; D004275:DNA, Ribosomal / Q000737:chemistry; D020407:Internet; D010802:Phylogeny; D012984:Software
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal