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Updated: Mar 23, 2026

Manipulation of Ploidy in Caenorhabditis elegans
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SHEsisPlus, a toolset for genetic studies on polyploid species.

Jiawei Shen1,2,3, Zhiqiang Li1,3, Jianhua Chen1,3

  • 1Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai 200030, P.R. China.

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|April 7, 2016
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Summary

SHEsisPlus offers genetic analysis for polyploid species, improving upon limited existing software. This free toolset enhances haplotype inference and epistasis detection for quantitative traits in diverse organisms.

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Area of Science:

  • Genetics
  • Bioinformatics
  • Computational Biology

Background:

  • Genetic analysis software for diploid organisms is established, but tools for polyploid species are scarce.
  • Polyploid species analysis requires specialized algorithms for complex genetic structures.

Purpose of the Study:

  • To introduce SHEsisPlus, a comprehensive online toolset for genetic analysis in polyploid species.
  • To provide tools for both dichotomous and quantitative trait analysis, including haplotype inference and epistasis detection.
  • To offer a free, open-source solution compatible with haploid, diploid, and polyploid organisms.

Main Methods:

  • Developed a novel, efficient haplotype inference algorithm for polyploid genomes.
  • Proposed an entropy-based algorithm for detecting epistasis in quantitative trait genetic analysis.
  • Integrated these algorithms into the SHEsisPlus web-based toolset, also supporting linkage disequilibrium, Hardy-Weinberg equilibrium, and single locus association tests.

Main Results:

  • The new haplotype inference algorithm demonstrated superior speed and accuracy compared to existing methods on simulated and real datasets.
  • The entropy-based epistasis detection algorithm showed significantly higher statistical power than conventional approaches for quantitative traits.
  • SHEsisPlus provides a versatile platform for various genetic analyses, optimized for multiple-allele datasets.

Conclusions:

  • SHEsisPlus addresses a critical gap in genetic analysis tools for polyploid species.
  • The developed algorithms offer significant advancements in accuracy and efficiency for polyploid genetic studies.
  • The freely available SHEsisPlus toolset empowers researchers in diverse fields of genetic analysis.