Phylogenetic Data in R

Abstract

Summary: Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evol- ution 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 evolutionar y 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 fur ther statistical methods for the analysis of evolutionar y processes. Availability: The program is free and available from the offi- cial R package archive at http://cran.r-project.org/src/contrib/ PACKAGES.htmlape. APE is licensed under the GNU General Public License. Contact: paradisisem.univ-montp2.fr