Department of Infectious Disease Epidemiology, Imperial College-Faculty of Medicine, MRC Centre for Outbreak Analysis and Modelling, St Marys Campus, Norfolk Place, London, UK.
Bioinformatics. 2010 Aug 1;26(15):1907-9. doi: 10.1093/bioinformatics/btq292. Epub 2010 Jun 4.
adephylo is a package for the R software dedicated to the analysis of comparative evolutionary data. Phylogenetic comparative methods initially aimed at accounting for or removing the effects of phylogenetic signal in the analysis of biological traits. However, recent approaches have shown that considerable information can be gathered from the study of the phylogenetic signal. In particular, close examination of phylogenetic structures can unveil interesting evolutionary patterns. For this purpose, we developed the package adephylo that provides tools for quantifying and describing the phylogenetic structures of biological traits. adephylo implements tests of phylogenetic signal, phylogenetic distances and proximities, and novel methods for describing further univariate and multivariate phylogenetic structures. These tools open up new perspectives in the analysis of evolutionary comparative data.
The stable version is available from CRAN: http:/cran.r-project.org/web/packages/adephylo/. The development version is hosted by R-Forge: http://r-forge.r-project.org/projects/adephylo/. Both versions can be installed directly from R. adephylo is distributed under the GNU General Public Licence (> or =2).
adephylo 是一个专门用于分析比较进化数据的 R 软件包。进化比较方法最初旨在分析生物特征时解释或去除系统发育信号的影响。然而，最近的方法表明，从研究系统发育信号中可以收集到相当多的信息。特别是，对系统发育结构的仔细检查可以揭示有趣的进化模式。为此，我们开发了 adephylo 包，提供了用于量化和描述生物特征的系统发育结构的工具。adephylo 实现了对系统发育信号、系统发育距离和相似度的检验，以及描述进一步的单变量和多变量系统发育结构的新方法。这些工具为进化比较数据的分析开辟了新的视角。
稳定版本可从 CRAN 获得：http://cran.r-project.org/web/packages/adephylo/。开发版本托管在 R-Forge 上：http://r-forge.r-project.org/projects/adephylo/。这两个版本都可以直接从 R 中安装。adephylo 根据 GNU 通用公共许可证（>=2）分发。
