{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,14]],"date-time":"2026-04-14T00:10:01Z","timestamp":1776125401325,"version":"3.50.1"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"15","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: \u00a0adephylo is a package for the R software dedicated to the analysis of comparative evolutionary data. Phylogenetic comparative methods initially aimed at accounting for or removing the effects of phylogenetic signal in the analysis of biological traits. However, recent approaches have shown that considerable information can be gathered from the study of the phylogenetic signal. In particular, close examination of phylogenetic structures can unveil interesting evolutionary patterns. For this purpose, we developed the package adephylo that provides tools for quantifying and describing the phylogenetic structures of biological traits. adephylo implements tests of phylogenetic signal, phylogenetic distances and proximities, and novel methods for describing further univariate and multivariate phylogenetic structures. These tools open up new perspectives in the analysis of evolutionary comparative data.<\/jats:p><jats:p>Availability: The stable version is available from CRAN: http:\/cran.r-project.org\/web\/packages\/adephylo\/. The development version is hosted by R-Forge: http:\/\/r-forge.r-project.org\/projects\/adephylo\/. Both versions can be installed directly from R. adephylo is distributed under the GNU General Public Licence (\u22652).<\/jats:p><jats:p>Contact: \u00a0t.jombart@imperial.ac.uk; dray@biomserv.univ-lyon1.fr<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq292","type":"journal-article","created":{"date-parts":[[2010,6,5]],"date-time":"2010-06-05T02:21:06Z","timestamp":1275704466000},"page":"1907-1909","source":"Crossref","is-referenced-by-count":390,"title":["<i>adephylo<\/i>: new tools for investigating the phylogenetic signal in biological traits"],"prefix":"10.1093","volume":"26","author":[{"given":"Thibaut","family":"Jombart","sequence":"first","affiliation":[{"name":"1 Department of Infectious Disease Epidemiology, Imperial College - Faculty of Medicine, MRC Centre for Outbreak Analysis and Modelling, St Marys Campus, Norfolk Place, London W2 1PG, UK and 2Universit\u00e9 de Lyon, F-69000, Lyon; Universit\u00e9 Lyon 1; CNRS, UMR5558, Laboratoire de Biom\u00e9trie et Biologie Evolutive, F-69622, Villeurbanne, France"}]},{"given":"Fran\u00e7ois","family":"Balloux","sequence":"additional","affiliation":[{"name":"1 Department of Infectious Disease Epidemiology, Imperial College - Faculty of Medicine, MRC Centre for Outbreak Analysis and Modelling, St Marys Campus, Norfolk Place, London W2 1PG, UK and 2Universit\u00e9 de Lyon, F-69000, Lyon; Universit\u00e9 Lyon 1; CNRS, UMR5558, Laboratoire de Biom\u00e9trie et Biologie Evolutive, F-69622, Villeurbanne, France"}]},{"given":"St\u00e9phane","family":"Dray","sequence":"additional","affiliation":[{"name":"1 Department of Infectious Disease Epidemiology, Imperial College - Faculty of Medicine, MRC Centre for Outbreak Analysis and Modelling, St Marys Campus, Norfolk Place, London W2 1PG, UK and 2Universit\u00e9 de Lyon, F-69000, Lyon; Universit\u00e9 Lyon 1; CNRS, UMR5558, Laboratoire de Biom\u00e9trie et Biologie Evolutive, F-69622, Villeurbanne, France"}]}],"member":"286","published-online":{"date-parts":[[2010,6,4]]},"reference":[{"key":"2023012508010975100_B1","first-page":"895","article-title":"A method for testing the assumption of phylogenetic independence in comparative data","volume":"1","author":"Abouheif","year":"1999","journal-title":"Evol. 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