Paradis Emmanuel, Claude Julien, Strimmer Korbinian
Laboratoire de Paléontologie, Paléobiologie and Phylogénie, Institut des Sciences de l'Evolution, Université Montpellier II, F-34095 Montpellier cédex 05, France.
Bioinformatics. 2004 Jan 22;20(2):289-90. doi: 10.1093/bioinformatics/btg412.
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.
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.
系统发育与进化分析（Analysis of Phylogenetics and Evolution，APE）是一个用R语言编写的软件包，用于分子进化和系统发育研究。APE既提供了用于读取和写入数据以及操作系统发育树的实用函数，也提供了几种用于系统发育和进化分析的先进方法（例如比较和群体遗传方法）。APE利用了许多R语言的统计和图形函数，还为开发和实施进一步的统计方法以分析进化过程提供了一个灵活的框架。
该程序是免费的，可从官方R软件包存档库http://cran.r-project.org/src/contrib/PACKAGES.html#ape获取。APE遵循GNU通用公共许可证。
