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VCFPOP: performing population genetics analyses for polyploids and anisoploids based on next-generation sequencing variant calling dataset
  • +6
  • Kang Huang,
  • Bing Yang,
  • Jincuo Ao,
  • Yuhang Li,
  • Yunxia Cui,
  • Yuchen Kong,
  • Yifan Wu,
  • Derek Dunn,
  • Baoguo Li
Kang Huang
Northwest University
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Bing Yang
Northwest University
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Jincuo Ao
Northwest University
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Yuhang Li
Northwest University
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Yunxia Cui
Northwest University
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Yuchen Kong
Northwest University
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Yifan Wu
Northwest University
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Derek Dunn
Northwest University
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Baoguo Li
Northwest University
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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 dou-ble-reduction, diploid models of population genetic analysis cannot properly be ap-plied to polyploids. To overcome this problem, we developed a software package en-titled 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 make this soft-ware freely available, downloadable from http://github.com/huangkang1987/vcfpop.
09 Apr 2022Submitted to Molecular Ecology Resources
09 May 2022Assigned to Editor
09 May 2022Submission Checks Completed
11 May 2022Reviewer(s) Assigned