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

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.