RDP5: a computer program for analyzing recombination in, and removing signals of recombination from, nucleotide sequence datasets.
RDP5: a computer program for analyzing recombination in, and removing signals of recombination from, nucleotide sequence datasets.
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DOI：
10.1093/ve/veaa087
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发表时间：
2021-01
期刊：
影响因子：
5.3
通讯作者：
Murrell B
中科院分区：
文献类型：
--
作者：
Martin DP;Varsani A;Roumagnac P;Botha G;Maslamoney S;Schwab T;Kelz Z;Kumar V;Murrell B
在过去的20年里，重组检测项目一直致力于开发一种快速、灵活且易于使用的基于 的重组分析工具。该工具的以前版本依赖于检测到的重组事件的大量用户中介验证，而最新的迭代RDP5具有足够的自动化程度，可以集成到分析管道中并在没有任何用户输入的情况下运行。实现这种程度自动化的主要创新是实施统计测试，以识别重组信号，这些信号可能归因于重组以外的进化过程。这些测试所需的额外分析时间已被整个程序中的算法改进所抵消，因此，相对于RDP4，RDP5的运行速度仍将提高五倍，并能够分析包含两倍(高达5000个)、长五倍(高达5000万个位点)的序列的比对。对于希望在将重组信号用于下游基于系统发育的分子进化分析之前从他们的数据集中移除重组信号的用户，RDP5可以将检测到的重组序列分解成它们的组成部分，并以不同的比对格式输出各种不同的无重组数据集。对于有兴趣探索其数据集的重组历史的用户，RDP5的所有手动验证、数据管理和数据可视化组件都已进行了广泛的更新，以最大限度地减少用户单独验证和完善程序对其检测到的每个单独重组事件的解释所需的时间。
For the past 20 years, the recombination detection program (RDP) project has focused on the development of a fast, flexible, and easy to use Windows-based recombination analysis tool. Whereas previous versions of this tool have relied on considerable user-mediated verification of detected recombination events, the latest iteration, RDP5, is automated enough that it can be integrated within analysis pipelines and run without any user input. The main innovation enabling this degree of automation is the implementation of statistical tests to identify recombination signals that could be attributable to evolutionary processes other than recombination. The additional analysis time required for these tests has been offset by algorithmic improvements throughout the program such that, relative to RDP4, RDP5 will still run up to five times faster and be capable of analyzing alignments containing twice as many sequences (up to 5000) that are five times longer (up to 50 million sites). For users wanting to remove signals of recombination from their datasets before using them for downstream phylogenetics-based molecular evolution analyses, RDP5 can disassemble detected recombinant sequences into their constituent parts and output a variety of different recombination-free datasets in an array of different alignment formats. For users that are interested in exploring the recombination history of their datasets, all the manual verification, data management and data visualization components of RDP5 have been extensively updated to minimize the amount of time needed by users to individually verify and refine the program’s interpretation of each of the individual recombination events that it detects.