Department of Plant Biotechnology and Bioinformatics, Ghent University.
Center for Plant Systems Biology, VIB.
Bioinformatics. 2019 Jun 1;35(12):2153-2155. doi: 10.1093/bioinformatics/bty915.
Ancient whole-genome duplications (WGDs) have been uncovered in almost all major lineages of life on Earth and the search for traces or remnants of such events has become standard practice in most genome analyses. This is especially true for plants, where ancient WGDs are abundant. Common approaches to find evidence for ancient WGDs include the construction of KS distributions and the analysis of intragenomic colinearity. Despite the increased interest in WGDs and the acknowledgment of their evolutionary importance, user-friendly and comprehensive tools for their analysis are lacking. Here, we present an easy to use command-line tool for KS distribution construction named wgd. The wgd suite provides commonly used KS and colinearity analysis workflows together with tools for modeling and visualization, rendering these analyses accessible to genomics researchers in a convenient manner.
wgd is free and open source software implemented in Python and is available at https://github.com/arzwa/wgd.
Supplementary data are available at Bioinformatics online.
地球上几乎所有主要生命谱系都发现了远古全基因组加倍（WGD），在大多数基因组分析中，寻找此类事件的痕迹或残余物已成为标准做法。对于植物来说尤其如此，因为远古 WGD 非常丰富。寻找远古 WGD 证据的常用方法包括构建 KS 分布和分析基因组内共线性。尽管人们对 WGD 的兴趣日益增加，并认识到它们在进化中的重要性，但缺乏用户友好且全面的分析工具。在这里，我们介绍了一种名为 wgd 的用于 KS 分布构建的易于使用的命令行工具。wgd 套件提供了常用的 KS 和共线性分析工作流程，以及用于建模和可视化的工具，以方便的方式为基因组学研究人员提供这些分析。
wgd 是免费的开源软件，用 Python 实现，可在 https://github.com/arzwa/wgd 上获得。
补充数据可在“Bioinformatics”在线获得。
