Summary: Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well as several advanced methods for phylogenetic and evolutionary analysis (e.g. comparative and population genetic methods). APE takes advantage of the many R functions for statistics and graphics, and also provides a flexible framework for developing and implementing further statistical methods for the analysis of evolutionary processes.

Availability: The program is free and available from the official R package archive at http://cran.r-project.org/src/contrib/PACKAGES.html#ape. APE is licensed under the GNU General Public License.

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Author notes

1Laboratoire de Paléontologie, Paléobiologie and Phylogénie, Institut des Sciences de l'Évolution, Université Montpellier II, F-34095 Montpellier cédex 05, France and 2Department of Statistics, University of Munich, Ludwigstrasse 33, D-80539 Munich, Germany