{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T13:35:52Z","timestamp":1761917752506},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2784,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Availability: RAMI is licensed under GNU GPL and can be run or downloaded from http:\/\/www.acgt.se\/online.html.<\/jats:p>\n               <jats:p>Contact: \u00a0tpommier@univ-montp2.fr; bcanback@acgt.se<\/jats:p>\n               <jats:p>Supplementary information: \u00a0http:\/\/www.acgt.se\/RAMI\/SuppInfo<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp051","type":"journal-article","created":{"date-parts":[[2009,2,18]],"date-time":"2009-02-18T03:25:13Z","timestamp":1234927513000},"page":"736-742","source":"Crossref","is-referenced-by-count":55,"title":["RAMI: a tool for identification and characterization of phylogenetic clusters in microbial communities"],"prefix":"10.1093","volume":"25","author":[{"given":"Thomas","family":"Pommier","sequence":"first","affiliation":[{"name":"1 Department of Natural Science, Kalmar University, Kalmar, 2Bj\u00f6rn Canb\u00e4ck Bioinformatics, Vind\u00f6gatan 66, SE-257 33 Rydeb\u00e4ck, 3Department of Theoretical Ecology and 4Department of Microbial Ecology, Lund University, Lund, Sweden"}]},{"given":"Bj\u00f6rn","family":"Canb\u00e4ck","sequence":"additional","affiliation":[{"name":"1 Department of Natural Science, Kalmar University, Kalmar, 2Bj\u00f6rn Canb\u00e4ck Bioinformatics, Vind\u00f6gatan 66, SE-257 33 Rydeb\u00e4ck, 3Department of Theoretical Ecology and 4Department of Microbial Ecology, Lund University, Lund, Sweden"}]},{"given":"Per","family":"Lundberg","sequence":"additional","affiliation":[{"name":"1 Department of Natural Science, Kalmar University, Kalmar, 2Bj\u00f6rn Canb\u00e4ck Bioinformatics, Vind\u00f6gatan 66, SE-257 33 Rydeb\u00e4ck, 3Department of Theoretical Ecology and 4Department of Microbial Ecology, Lund University, Lund, Sweden"}]},{"given":"\u00c5ke","family":"Hagstr\u00f6m","sequence":"additional","affiliation":[{"name":"1 Department of Natural Science, Kalmar University, Kalmar, 2Bj\u00f6rn Canb\u00e4ck Bioinformatics, Vind\u00f6gatan 66, SE-257 33 Rydeb\u00e4ck, 3Department of Theoretical Ecology and 4Department of Microbial Ecology, Lund University, Lund, Sweden"}]},{"given":"Anders","family":"Tunlid","sequence":"additional","affiliation":[{"name":"1 Department of Natural Science, Kalmar University, Kalmar, 2Bj\u00f6rn Canb\u00e4ck Bioinformatics, Vind\u00f6gatan 66, SE-257 33 Rydeb\u00e4ck, 3Department of Theoretical Ecology and 4Department of Microbial Ecology, Lund University, Lund, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2009,2,17]]},"reference":[{"key":"2023051209125724200_B1","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1038\/nature02649","article-title":"Fine-scale phylogenetic architecture of a complex bacterial community","volume":"430","author":"Acinas","year":"2004","journal-title":"Nature"},{"key":"2023051209125724200_B2","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1016\/S1369-5274(03)00055-9","article-title":"New approaches to analyzing microbial biodiversity data","volume":"6","author":"Bohannan","year":"2003","journal-title":"Curr. 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