APE (Analysis of Phylogenetics and Evolution) is a package written in the R language for molecular evolution and phylogenetics. It provides utility functions for reading, writing, and manipulating phylogenetic trees, as well as advanced methods for phylogenetic and evolutionary analysis. APE leverages R's statistical and graphical capabilities and offers a flexible framework for developing and implementing new statistical methods. Key features include reading and writing phylogenetic trees, analyzing comparative data, estimating diversification rates, computing distances from genetic data, and generating publication-quality graphics. APE is freely available under the GNU General Public License and can be accessed through the official R package archive. The package supports various statistical analyses, such as phylogenetically independent contrasts, birth-death models, population genetics analysis, and non-parametric smoothing of evolutionary rates. It also facilitates the integration of external programs and supports the development of new methods.APE (Analysis of Phylogenetics and Evolution) is a package written in the R language for molecular evolution and phylogenetics. It provides utility functions for reading, writing, and manipulating phylogenetic trees, as well as advanced methods for phylogenetic and evolutionary analysis. APE leverages R's statistical and graphical capabilities and offers a flexible framework for developing and implementing new statistical methods. Key features include reading and writing phylogenetic trees, analyzing comparative data, estimating diversification rates, computing distances from genetic data, and generating publication-quality graphics. APE is freely available under the GNU General Public License and can be accessed through the official R package archive. The package supports various statistical analyses, such as phylogenetically independent contrasts, birth-death models, population genetics analysis, and non-parametric smoothing of evolutionary rates. It also facilitates the integration of external programs and supports the development of new methods.