PhyKIT: A Multitool for Phylogenomics

Jacob L. Steenwyk, Gemma I. Martínez-Redondo, Thomas J. Buida III, Emile Gluck-Thaler, Xing-Xing Shen, Toni Gabaldón, Antonis Rokas, Rosa Fernández
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Abstract

Multiple sequence alignments and phylogenetic trees are rich in biological information and are fundamental to research in biology. PhyKIT is a tool for processing and analyzing the information content of multiple sequence alignments and phylogenetic trees. Here, we describe how to use PhyKIT for diverse analyses, including (i) constructing a phylogenomic supermatrix, (ii) detecting errors in orthology inference, (iii) quantifying biases in phylogenomic data sets, (iv) identifying radiation events or lack of resolution using gene support frequencies, and (v) conducting evolution-based screens to facilitate gene function prediction. Several PhyKIT functions that streamline multiple sequence alignment and phylogenetic processing—such as renaming FASTA entries or tree tips—are also discussed. These protocols demonstrate how simple command-line operations in the unified framework of PhyKIT facilitate diverse phylogenomic data analysis and processing, from supermatrix construction and diagnosis to gaining clues about gene function. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC.

Basic Protocol 1: Installing PhyKIT and syntax for usage

Basic Protocol 2: Constructing a phylogenomic supermatrix

Basic Protocol 3: Detecting anomalies in orthology relationships

Basic Protocol 4: Quantifying biases in phylogenomic data matrices and related measures

Basic Protocol 5: Identifying polytomies

Basic Protocol 6: Assessing gene-gene coevolution as a genetic screen

Abstract Image

PhyKIT:用于系统发生组学的多功能工具
多序列比对和系统发生树蕴含着丰富的生物信息,是生物学研究的基础。PhyKIT 是一种处理和分析多序列比对和系统发生树信息内容的工具。在此,我们将介绍如何使用 PhyKIT 进行各种分析,包括:(i) 构建系统发生学超级矩阵;(ii) 检测正交推断中的错误;(iii) 量化系统发生学数据集中的偏差;(iv) 利用基因支持频率识别辐射事件或缺乏分辨率;(v) 进行基于进化的筛选以促进基因功能预测。此外,还讨论了几种简化多序列比对和系统发生学处理的 PhyKIT 功能,如重命名 FASTA 条目或树提示。这些协议展示了在 PhyKIT 的统一框架下,简单的命令行操作是如何促进从超级矩阵构建和诊断到获取基因功能线索等各种系统发生学数据分析和处理的。© 2024 作者。当前协议由 Wiley Periodicals LLC 出版。基本协议 1:安装 PhyKIT 和使用语法基本协议 2:构建系统发育组超级矩阵基本协议 3:检测正交关系中的异常基本协议 4:量化系统发育组数据矩阵中的偏差和相关度量基本协议 5:识别多瘤基本协议 6:作为基因筛选评估基因-基因共同进化
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