A web server-based tool for analysing polygenic epistatic effects. PEPIS is based on a linear mixed model that has been used to predict the performance of hybrid rice. It includes two main sub-pipelines: the first for kinship matrix calculation, and the second for polygenic component analyses and genome scanning for main and epistatic effects. PEPIS was dedicatedly developed for epistatic genetic estimation. It will help overcome the bottleneck in genetic epistasis analysis.

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PEPIS classification

PEPIS specifications

Software type:
Package
Restrictions to use:
None
Input format:
TXT, CSV
License:
GNU General Public License version 3.0
Version:
1.0
Source code URL:
http://bioinfo.noble.org/PolyGenic_QTL/download/PEPIS_Source_Code.tar
Interface:
Web user interface
Input data:
A coded additive genotype data file, a coded dominance genotype data file and a quantative marker related phenotypic file
Programming languages:
C, C++
Computer skills:
Basic
Stability:
Stable

Publications

  • (Zhang et al., 2016) PEPIS: A Pipeline for Estimating Epistatic Effects in Quantitative Trait Locus Mapping and Genome-Wide Association Studies. PLOS Computational Biology.
    PMID: 27224861

Credits

Institution(s)

Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, OK, USA; School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China; Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA

Funding source(s)

This work was supported by the Samuel Roberts Noble Foundation and the National Science Foundation collaborative research grant awards (DBI- 1458597 and DBI-1458515).

Link to literature

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