POLYSAT: an R package for polyploid microsatellite analysis
POLYSAT: an R package for polyploid microsatellite analysis
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DOI：
10.1111/j.1755-0998.2011.02985.x
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发表时间：
2011-05-01
影响因子：
7.7
通讯作者：
Jasieniuk, Marie
中科院分区：
文献类型：
--
作者：
Clark, Lindsay V.;Jasieniuk, Marie
我们提出了一个R包，以帮助弥补缺乏操纵和分析同源多倍体和异源多倍体微卫星数据的软件。PolySAT可以处理任何倍性的基因型数据，包括混合倍性的群体，并假设在部分杂合子中等位基因拷贝数总是不明确的。它可以以8种不同的格式导入和导出基因数据，使用逐步突变和无限等位基因模型计算个体之间的成对距离，基于等位基因计数估计倍性，估计等位基因频率和成对F(ST)值。该软件可通过全面的R档案网络(http://cran.r-project.org/))免费获得，并包括一个全面的教程。
We present an R package to help remedy the lack of software for manipulating and analysing autopolyploid and allopolyploid microsatellite data. polysat can handle genotype data of any ploidy, including populations of mixed ploidy, and assumes that allele copy number is always ambiguous in partial heterozygotes. It can import and export genotype data in eight different formats, calculate pairwise distances between individuals using a stepwise mutation and infinite alleles model, estimate ploidy based on allele counts and estimate allele frequencies and pairwise F(ST) values. This software is freely available through the Comprehensive R Archive Network (http://cran.r-project.org/) and includes a thorough tutorial.