StAMPP: an R package for calculation of genetic differentiation and structure of mixed-ploidy level populations

被引：551
作者：
Pembleton, Luke W. [1 ,2 ,3 ]
Cogan, Noel O. I. [1 ,2 ]
Forster, John W. [1 ,2 ,3 ]
机构：
[1] La Trobe Univ, Dept Environm & Primary Ind, AgriBio, Bundoora, Vic 3083, Australia
[2] La Trobe Univ, Dairy Futures Cooperat Res Ctr, AgriBio, Bundoora, Vic 3083, Australia
[3] La Trobe Univ, Bundoora, Vic 3083, Australia
来源：
MOLECULAR ECOLOGY RESOURCES | 2013年 / 13卷 / 05期
关键词：
F-ST; genetic distance; genomic relationship matrix; polyploidy; EVOLUTION; SNPS; ACCURACY;
D O I：
10.1111/1755-0998.12129
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
Statistical Analysis of Mixed-Ploidy Populations (StAMPP) is a freely available R package for calculation of population structure and differentiation based on single nucleotide polymorphism (SNP) genotype data from populations of any ploidy level, and/or mixed-ploidy levels. StAMPP provides an advance on previous similar software packages, due to an ability to calculate pairwise F-ST values along with confidence intervals, Nei's genetic distance and genomic relationship matrixes from data sets of mixed-ploidy level. The software code is designed to efficiently handle analysis of large genotypic data sets that are typically generated by high-throughput genotyping platforms. Population differentiation studies using StAMPP are broadly applicable to studies of molecular ecology and conservation genetics, as well as animal and plant breeding.
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收藏
页码：946 / 952
页数：7
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