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vcfpop : Performing population genetics analyses for autopolyploids and aneuploids based on next‐generation sequencing data sets
Author(s) -
Huang Kang,
Li Wenkai,
Yang Bing,
Wang Dan,
He Shujun,
Shen Yujia,
Ao Jincuo,
Li Yuhang,
Cui Yunxia,
Kong Yuchen,
Li Wei,
Li Nianlong,
Dunn Derek W.,
Li Baoguo
Publication year - 2025
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.13744
Subject(s) - biology , polyploid , population , genome , cluster analysis , software , hierarchical clustering , genetics , ploidy , computational biology , inheritance (genetic algorithm) , evolutionary biology , computer science , machine learning , gene , demography , sociology , programming language
Abstract Polyploids are cells or organisms with a genome consisting of more than two sets of homologous chromosomes. Polyploid plants have important traits that facilitate speciation and are thus often model systems for evolutionary, molecular ecology and agricultural studies. However, due to their unusual mode of inheritance and double‐reduction, diploid models of population genetic analysis cannot properly be applied to autopolyploids. To overcome this problem, we developed a software package entitled vcfpop to perform a variety of population genetic analyses for autopolyploids, such as parentage analysis, analysis of molecular variance, principal coordinates analysis, hierarchical clustering analysis and Bayesian clustering. We used three data sets to evaluate the capability of vcfpop to analyse large data sets on a desktop computer. This software is freely available at http://github.com/huangkang1987/vcfpop .