Skip Navigation


Bioinformatics Advance Access originally published online on February 17, 2009
Bioinformatics 2009 25(6):736-742; doi:10.1093/bioinformatics/btp051
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow Supplementary Data
Right arrow Supplementary Data
Right arrowOA All Versions of this Article:
25/6/736    most recent
btp051v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by Pommier, T.
Right arrow Articles by Tunlid, A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Pommier, T.
Right arrow Articles by Tunlid, A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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

Thomas Pommier 1,*,{dagger}, Björn Canbäck 2,*, Per Lundberg 3, Åke Hagström 1 and Anders Tunlid 4

1Department of Natural Science, Kalmar University, Kalmar, 2Björn Canbäck Bioinformatics, Vindögatan 66, SE-257 33 Rydebäck, 3Department of Theoretical Ecology and 4Department of Microbial Ecology, Lund University, Lund, Sweden

*To whom correspondence should be addressed.


  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{at}univ-montp2.fr; bcanback{at}acgt.se

Supplementary information: http://www.acgt.se/RAMI/SuppInfo

{dagger}Present address: UMR 5119 Ecosystèmes Lagunaires CNRS Ifremer UM2 IRD. Université Montpellier II Montpellier France.

Associate Editor: Martin Bishop

Received on September 6, 2008; revised on January 22, 2009; accepted on January 22, 2009

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.