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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

Corresponding Author:[email protected]

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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 2022Submission Checks Completed
09 May 2022Assigned to Editor
11 May 2022Reviewer(s) Assigned
09 Jun 2022Review(s) Completed, Editorial Evaluation Pending
04 Jul 2022Editorial Decision: Revise Minor
25 Aug 20221st Revision Received
25 Aug 2022Review(s) Completed, Editorial Evaluation Pending
29 Aug 2022Reviewer(s) Assigned
21 Nov 2022Editorial Decision: Revise Minor
29 Nov 2022Review(s) Completed, Editorial Evaluation Pending
29 Nov 20222nd Revision Received
30 Nov 2022Editorial Decision: Accept