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RAMI: a tool for id...
RAMI: a tool for identification and characterization of phylogenetic clusters in microbial communities
- Article/chapterEnglish2009
Publisher, publication year, extent ...
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2009-02-17
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Oxford University Press (OUP),2009
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LIBRIS-ID:oai:lup.lub.lu.se:9f217021-8436-4ff7-aeb0-737bdf576a33
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https://lup.lub.lu.se/record/1405019URI
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https://doi.org/10.1093/bioinformatics/btp051DOI
Supplementary language notes
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Language:English
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Summary in:English
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Subject category:art swepub-publicationtype
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Subject category:ref swepub-contenttype
Notes
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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.
Subject headings and genre
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Canback, Bjorn
(author)
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Lundberg, PerLund University,Lunds universitet,Evolutionär ekologi,Biologiska institutionen,Naturvetenskapliga fakulteten,Evolutionary ecology,Department of Biology,Faculty of Science(Swepub:lu)teor-plu
(author)
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Hagstrom, Ake
(author)
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Tunlid, AndersLund University,Lunds universitet,MEMEG,Biologiska institutionen,Naturvetenskapliga fakulteten,Department of Biology,Faculty of Science(Swepub:lu)mbek-atu
(author)
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Evolutionär ekologiBiologiska institutionen
(creator_code:org_t)
Related titles
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In:Bioinformatics: Oxford University Press (OUP)25:6, s. 736-7421367-48031460-2059
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