APE is an R package for phylogenetic and evolutionary analysis. It provides functions for reading, writing, and manipulating phylogenetic trees, as well as advanced methods for phylogenetic and evolutionary analysis. APE uses R's statistical and graphical functions and offers a flexible framework for developing new statistical methods. It is available free of charge from the R package archive and is licensed under the GNU General Public License. APE focuses on statistical analyses using phylogenetic and genealogical trees. It includes functions for reading and writing trees, comparative data analysis, diversification analysis, distance computation, and other tools. It also produces complex population genetics plots, such as the generalized skyline plot. APE is command-line driven, with functions called by the user. The package is easy to extend and can be used to develop new methods. It can also call external programs like PHYLIP through shell commands. APE is useful for evolutionary analysis, including phylogenetic tree manipulation, comparative methods, and population genetics. It is also useful for data analysis and can be extended to include other functionalities. APE is a powerful tool for phylogenetic and evolutionary analysis, and is widely used in bioinformatics.APE is an R package for phylogenetic and evolutionary analysis. It provides functions for reading, writing, and manipulating phylogenetic trees, as well as advanced methods for phylogenetic and evolutionary analysis. APE uses R's statistical and graphical functions and offers a flexible framework for developing new statistical methods. It is available free of charge from the R package archive and is licensed under the GNU General Public License. APE focuses on statistical analyses using phylogenetic and genealogical trees. It includes functions for reading and writing trees, comparative data analysis, diversification analysis, distance computation, and other tools. It also produces complex population genetics plots, such as the generalized skyline plot. APE is command-line driven, with functions called by the user. The package is easy to extend and can be used to develop new methods. It can also call external programs like PHYLIP through shell commands. APE is useful for evolutionary analysis, including phylogenetic tree manipulation, comparative methods, and population genetics. It is also useful for data analysis and can be extended to include other functionalities. APE is a powerful tool for phylogenetic and evolutionary analysis, and is widely used in bioinformatics.