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#编者信息
熊荣川
明湖实验室
xiongrongchuan@126.com
http://blog.sciencenet.cn/u/Bearjazz
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。 |
https://cran.r-project.org/web/views/Phylogenetics.html |
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