Portal de Periódicos da CAPES

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

2009; Oxford University Press; Volume: 25; Issue: 6 Linguagem: Inglês

10.1093/bioinformatics/btp051

1367-4811

Thomas Pommier, Björn Canbäck, Per Lundberg, Åke Hagström, Anders Tunlid,

Microbial Community Ecology and Physiology

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. Availability: RAMI is licensed under GNU GPL and can be run or downloaded from http://www.acgt.se/online.html. Contact: tpommier@univ-montp2.fr; bcanback@acgt.se Supplementary information: http://www.acgt.se/RAMI/SuppInfo