adephylo: new tools for investigating the phylogenetic signal in biological traits

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Abstract
Summary:adephylo 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. 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 (≥2). Contact:t.jombart@imperial.ac.uk; dray@biomserv.univ-lyon1.fr Supplementary information: Supplementary data are available at Bioinformatics online.