# 编者信息 熊荣川 明湖实验室 xiongrongchuan@126.com http://blog.sciencenet.cn/u/Bearjazz The history of life unfolds within a phylogenetic context. Comparative phylogenetic methods are statistical approaches for analyzing historical patterns along phylogenetic trees. This task view describes R packages that implement a variety of different comparative phylogenetic methods. This is an active research area and much of the information is subject to change. One thing to note is that many important packages are not on CRAN: either they were formerly on CRAN and were later archived (for example, if they failed to incorporate necessary changes as R is updated) or they are developed elsewhere and have not been put on CRAN yet. Such packages may be found on GitHub, R-Forge, or authors' websites. 生命史是在系统发育的背景下展开的。比较系统发育方法是分析沿着系统发育树的历史模式的统计方法。这个任务视图描述了实现各种不同的比较系统发育方法的 R 包。这是一个活跃的研究领域，许多信息可能会发生变化。需要注意的一点是，许多重要的软件包不在 CRAN 上：要么它们以前在 CRAN 上，后来被归档（例如，如果在更新 R 时它们没有包含必要的更改），要么它们是在别处开发的，并且还没有放到 CRAN 上。这些软件包可以在 Github 、 R-Forge 或作者的网站上找到。 https://cran.r-project.org/web/views/Phylogenetics.html
# 编者信息 熊荣川 明湖实验室 xiongrongchuan@126.com http://blog.sciencenet.cn/u/Bearjazz Summary: phangorn is a package for phylogenetic reconstruction and analysis in the R language. Previously it was only possible to estimate phylogenetic trees with distance methods in R. phangorn, now offers the possibility of reconstructing phylogenies with distance based methods, maximum parsimony or maximum likelihood (ML) and performing Hadamard conjugation. Extending the general ML framework, this package provides the possibility of estimating mixture and partition models. Furthermore, phangorn offers several functions for comparing trees, phylogenetic models or splits, simulating character data and performing congruence analyses. 摘要： phangorn 是一个用 R 语言进行系统发育重建和分析的软件包。以前只能用距离法分析系统发生树。 Phangorn 现在可以用距离法、最大简约法和最大似然法重建系统发育关系，执行 Hadamard conjugation 。扩展了通用 ML 框架，该包提供了估计混合模型和分区模型的可能性。此外， Phangron 还提供了几种功能，用于比较系统发育树、系统发育模型或分支、模拟特征数据和进行一致性分析。 Schliep K P . phangorn: phylogenetic analysis in R . Bioinformatics, 2011, 27(4):: 592–593.
标签: 比较系统发育
