{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,14]],"date-time":"2026-01-14T20:39:12Z","timestamp":1768423152462,"version":"3.49.0"},"reference-count":16,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2007,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Accurate taxonomy is best maintained if species are arranged as hierarchical groups in phylogenetic trees. This is especially important as trees grow larger as a consequence of a rapidly expanding sequence database. Hierarchical group names are typically manually assigned in trees, an approach that becomes unfeasible for very large topologies.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We have developed an automated iterative procedure for delineating stable (monophyletic) hierarchical groups to large (or small) trees and naming those groups according to a set of sequentially applied rules. In addition, we have created an associated ungrouping tool for removing existing groups that do not meet user-defined criteria (such as monophyly). The procedure is implemented in a program called GRUNT (GRouping, Ungrouping, Naming Tool) and has been applied to the current release of the Greengenes (Hugenholtz) 16S rRNA gene taxonomy comprising more than 130,000 taxa.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>GRUNT will facilitate researchers requiring comprehensive hierarchical grouping of large tree topologies in, for example, database curation, microarray design and pangenome assignments. The application is available at the greengenes website [1].<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-8-402","type":"journal-article","created":{"date-parts":[[2007,10,18]],"date-time":"2007-10-18T18:14:18Z","timestamp":1192731258000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool"],"prefix":"10.1186","volume":"8","author":[{"given":"Daniel","family":"Dalevi","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Todd Z","family":"DeSantis","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jakob","family":"Fredslund","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gary L","family":"Andersen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Victor M","family":"Markowitz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Philip","family":"Hugenholtz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2007,10,18]]},"reference":[{"key":"1774_CR1","unstructured":"GRUNT page at the Greengenes website[http:\/\/greengenes.lbl.gov\/GRUNT]"},{"issue":"4","key":"1774_CR2","doi-asserted-by":"publisher","first-page":"554","DOI":"10.1002\/elps.1150190416","volume":"19","author":"W Ludwig","year":"1998","unstructured":"Ludwig W, et al.: Bacterial phylogeny based on comparative sequence analysis. 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Bioinformatics 2003, 19(12):1572\u20134. 10.1093\/bioinformatics\/btg180","journal-title":"Bioinformatics"},{"issue":"21","key":"1774_CR7","doi-asserted-by":"publisher","first-page":"2688","DOI":"10.1093\/bioinformatics\/btl446","volume":"22","author":"A Stamatakis","year":"2006","unstructured":"Stamatakis A: RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22(21):2688\u201390. 10.1093\/bioinformatics\/btl446","journal-title":"Bioinformatics"},{"key":"1774_CR8","volume-title":"Genetic algorithm approaches for the phylogenetic analysis of large biologiical sequence datasets under the maximum likelihood criterion","author":"D Zwickl","year":"2006","unstructured":"Zwickl D: Genetic algorithm approaches for the phylogenetic analysis of large biologiical sequence datasets under the maximum likelihood criterion. University of Texas Austin; 2006."},{"key":"1774_CR9","unstructured":"The Newick tree format[http:\/\/evolution.genetics.washington.edu\/phylip\/newicktree.html]"},{"key":"1774_CR10","unstructured":"Gexcellent. [http:\/\/cgi-www.daimi.au.dk\/cgi-chili\/gexcellent\/front.py]"},{"key":"1774_CR11","volume-title":"Nucleic Acid Res","author":"E Pruesse","year":"2007","unstructured":"Pruesse E, Quast C, Knittel K, Fuchs B, Ludwig W, Peplies J, Gl\u00f6ckner FO: SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acid Res 2007, in press."},{"issue":"1","key":"1774_CR12","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1073\/pnas.0608255104","volume":"104","author":"EL Brodie","year":"2007","unstructured":"Brodie EL, et al.: Urban aerosols harbor diverse and dynamic bacterial populations. 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