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

@article{citeulike:4065464, 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: bcanback@acgt.se, tpommier@univ-montp2.fr Supplementary information: http:\\www.acgt.se\RAMI\SuppInfo 10.1093/bioinformatics/btp051}, author = {Pommier, Thomas and Canback, Bjorn and Lundberg, Per and Hagstrom, Ake and Tunlid, Anders}, citeulike-article-id = {4065464}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btp051}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/6/736}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19223450}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19223450}, doi = {10.1093/bioinformatics/btp051}, journal = {Bioinformatics}, keywords = {methods, phylodiversity}, month = {February}, pages = {btp051+}, posted-at = {2009-03-18 00:42:54}, priority = {2}, title = {RAMI, a tool for identification and characterization of phylogenetic clusters in microbial communities}, url = {http://dx.doi.org/10.1093/bioinformatics/btp051}, year = {2009} }

TY - JOUR ID - citeulike:4065464 L3 - citeulike-article-id:4065464 N2 - 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: bcanback@acgt.se, tpommier@univ-montp2.fr Supplementary information: http:\\www.acgt.se\RAMI\SuppInfo 10.1093/bioinformatics/btp051 JF - Bioinformatics TI - RAMI, a tool for identification and characterization of phylogenetic clusters in microbial communities SP - btp051 KW - methods KW - phylodiversity AU - Pommier, Thomas AU - Canback, Bjorn AU - Lundberg, Per AU - Hagstrom, Ake AU - Tunlid, Anders PY - 2009/02/17/ UR - http://dx.doi.org/10.1093/bioinformatics/btp051 ER -