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pophelper: an R package and web app to analyse and visualize population structure.

R M Francis1

  • 1Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden.

Molecular Ecology Resources
|February 7, 2016
PubMed
Summary
This summary is machine-generated.

The pophelper R package and web app simplify population structure analysis by processing output from programs like admixture and structure. These tools offer data tabulation, K estimation, and visualization for streamlined population genetics workflows.

Keywords:
admixtureclumppdistructstructuretesspopulation structure

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Area of Science:

  • Population genetics
  • Bioinformatics
  • Computational biology

Background:

  • Population structure analysis is crucial for understanding genetic diversity and evolutionary processes.
  • Existing software for population assignment (e.g., admixture, structure, tess) generates complex output files.
  • Efficient analysis and visualization of this output are essential for researchers.

Purpose of the Study:

  • To introduce the pophelper R package and its accompanying web application.
  • To provide user-friendly tools for analyzing and visualizing population structure data.
  • To streamline common tasks in population genetics analyses.

Main Methods:

  • The pophelper R package offers functions to parse output files from population assignment software.
  • Key functionalities include data tabulation, estimation of the optimal number of clusters (K) using the Evanno method, and generation of files for CLUMPP.
  • The web application provides an interactive platform with features like dynamic plots, cluster alignment, and individual/population sorting.

Main Results:

  • pophelper facilitates the integration of population structure analyses into standard R workflows.
  • The web app offers enhanced interactive visualization and data manipulation capabilities.
  • Both versions support the analysis and visualization of genetic admixture and population assignment results.

Conclusions:

  • pophelper provides valuable, accessible tools for population geneticists.
  • The R package and web app enhance the efficiency and ease of population structure analysis and visualization.
  • These resources aid in interpreting complex genetic data for a wide range of research applications.