咖啡店 软件基因˚F爱米莉Ë旋涡的Çomputational一nalysis CAFE的目的是通过解释系统进化史并为进化推论提供统计基础的方式来分析基因家族大小的变化。 该程序使用生与死过程来模拟用户指定的系统发育树中的基因得失。 在此模型下生成的家庭规模分布可为评估观察到的分类单元之间家庭规模差异的重要性提供基础。 到 CAFE v4.2.1是CAFE应用程序常规发行版中的最新版本。 该手册和各种教程可以在网站（ ）上查看。 本文档介绍了如何下载和使用CAFE v4.2.1。 用 CAFE v4.2.1的必要输入是： 一个数据文件，包含系统发育树中包含的分类单元的基因家族大小 Newick格式的系统发育树，包括分支长度 根据以上输入，CAFE v4.2.1将计算： 整个树上或树中用户指定的分支子集上的生死参数λ的最大似然值λ（或单独的生死参数（分别为λ和μ）） 系统发育树中

TreeTime：最大似然定年和祖先序列推断 概述 TreeTime提供了用于祖先序列重建和分子钟系统发生学推论的例程，即一棵树，其中所有分支都按比例缩放，使得末端节点的位置对应于其采样时间，内部节点位于最可能的发散时间。 为了优化时间尺度系统发育的可能性，TreeTime使用一种迭代方法，该方法首先根据给定的树的分支长度来推断祖先序列，然后优化时间轴上不受约束的节点的位置，然后重复此循环。 唯一的拓扑优化是（可选）解析多面体的方式，这种方式与树上的采样时间约束最（近似）一致。 该软件包旨在用作命令行上的独立工具，或用作较大的系统发育分析工作流程中使用的库。 。 除了脚本TreeTime或经由命令行使用它，也有在一个小型Web服务器 。 看看我们的和。 特征 祖先序列重建（边缘和联合最大似然） 分子时钟树推论（边际和联合最大似然） GTR模型的推论 重生以最大化时间信号并优化根尖

The increasing availability of molecular and genetic databases coupled with the growing power of computers gives biologists opportunities to address new issues, such as the patterns of molecular evolution, and re-assess old ones, such as the role of adaptation in species diversification.In the second edition, the book continues to integrate a wide variety of data analysis methods into a single and flexible interface: the R language. This open source language is available for a wide range of computer systems and has been adopted as a computational environment by many authors of statistical software. Adopting R as a main tool for phylogenetic analyses will ease the workflow in biologists' data analyses, ensure greater scientific repeatability, and enhance the exchange of ideas and methodological developments. The second edition is completely updated, covering the full gamut of R packages for this area that have been introduced  to the market since its previous publication five years ago. There is also  a new chapter on the simulation of evolutionary data.  Graduate students and researchers in evolutionary biology can use this book as a reference for data analyses, whereas researchers in bioinformatics interested in evolutionary analyses will learn how to implement these methods in R. The book starts with a presentation of different R packages and gives a short introduction to R for phylogeneticists unfamiliar with this language. The basic phylogenetic topics are covered: manipulation of phylogenetic data, phylogeny estimation, tree drawing, phylogenetic comparative methods, and estimation of ancestral characters. The chapter on tree drawing uses R's powerful graphical environment. A section deals with the analysis of diversification with phylogenies, one of the author's favorite research topics. The last chapter is devoted to the development of phylogenetic methods with R and interfaces with other languages (C and C++). Some exercises conclude these chapters.

一本很好，很强大的，关于如何使用R进行进化树构建，模型选择，结果评估的书本