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并行结构:一个 R 包,用于在多核计算机上分配群体遗传程序 STRUCTURE 的并行运行。

ParallelStructure: a R package to distribute parallel runs of the population genetics program STRUCTURE on multi-core computers.

机构信息

Department of Population Genetics, Institute of Marine Research, Bergen, Norway.

出版信息

PLoS One. 2013 Jul 29;8(7):e70651. doi: 10.1371/journal.pone.0070651. Print 2013.

Abstract

This software package provides an R-based framework to make use of multi-core computers when running analyses in the population genetics program STRUCTURE. It is especially addressed to those users of STRUCTURE dealing with numerous and repeated data analyses, and who could take advantage of an efficient script to automatically distribute STRUCTURE jobs among multiple processors. It also consists of additional functions to divide analyses among combinations of populations within a single data set without the need to manually produce multiple projects, as it is currently the case in STRUCTURE. The package consists of two main functions: MPI_structure() and parallel_structure() as well as an example data file. We compared the performance in computing time for this example data on two computer architectures and showed that the use of the present functions can result in several-fold improvements in terms of computation time. ParallelStructure is freely available at https://r-forge.r-project.org/projects/parallstructure/.

摘要

这个软件包提供了一个基于 R 的框架,可在运行 STRUCTURE 群体遗传学程序中的分析时利用多核计算机。它特别针对那些使用 STRUCTURE 进行大量重复数据分析的用户,他们可以利用高效的脚本将 STRUCTURE 作业自动分配到多个处理器上。它还包含了将分析分配到单个数据集内的多个群体组合的其他功能,而无需像当前在 STRUCTURE 中那样手动生成多个项目。该软件包包含两个主要功能:MPI_structure() 和 parallel_structure() 以及一个示例数据文件。我们比较了在两种计算机体系结构上计算这个示例数据的时间性能,结果表明,使用当前的函数可以在计算时间方面提高几个数量级。ParallelStructure 可在 https://r-forge.r-project.org/projects/parallstructure/ 免费获得。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/60ff/3726640/0b6cbd2a4c87/pone.0070651.g001.jpg

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