Utility   functions: These packages include functions for   manipulating trees or associated data. ape has   functions for randomly resolving polytomies, creating branch lengths, getting   information about tree size or other properties, pulling in data from   GenBank, and many more. phylobase has   functions for traversing a tree (i.e., getting all descendants from a   particular node specified by just two of its descendants).geiger can   prune trees and data to an overlapping set of taxa. tidytree can   convert a tree object in to a tidy data frame and has other tidy approaches   to manipulate tree data. evobiR can   do fuzzy matching of names (to allow some differences). rphast implements   an R interface to the PHAST, which can be used for many types of analysis in   comparative and evolutionary genomics, such as estimating models of evolution   from sequence data, scoring alignments for conservation or acceleration, and   predicting elements based on conservation or custom phylogenetic hidden   Markov models. SigTree finds   branches that are responsive to some treatment, while allowing correction for   multiple comparisons. dendextend can   manipulate dendrograms, including subdividing trees, adding leaves, and   more. apex can   handle multiple gene DNA alignments making their use and analysis for tree   inference easier in ape and phangorn. aphid can   weight sequences based on a phylogeny and can use hidden Markov models (HMMs)   for a variety of purposes including multiple sequence alignment.

实用函数：这些R语言包包括操作树或相关数据的函数。ape具有随机解析多岐分支树、创建支系长度、获取有关树大小或其他属性的信息、从GenBank中提取数据等功能。phylobase具有遍历一棵树的功能（即只从一个特定节点的两个后代推导出该节点的所有后代），geiger可以将树和数据修剪成一组重叠的分类群。tidytree可以将树对象转换为整洁的数据框，并具有其他简洁的方法来处理树数据。evobiR可以对名称进行模糊匹配（以允许一定差异）。rphast实现了与PHAST的R交互接口，该接口可用于比较基因组学和进化基因组学中的多种分析，例如根据序列数据估计进化模型、为保守或加速进化给序列比对打分，预测基于保守或自定义系统发育隐马尔可夫模型的相关因素。SigTree发现对某些处理有响应的分支，同时允许对多个比较进行修正。dendextend可以操纵树图，包拆分系统发育树、添加末梢节点等等。apex可以处理多基因序列比对，使其在ape和phangorn中用作树推断和分析更容易。aphid可以根据系统发育对序列进行加权，并可以将隐马尔可夫模型（HMMS）用于多种目的，包括多序列比对。