 PAPR is an open-source software package designed for the analysis of data from ad-mixed, clonal, mixed, and or sexual populations. It provides unique tools for analysis of data from such populations, including functions for calculating brovus distances for micro-satellite markers, batch analysis of the index of association with several indices of genotypic diversity, and graphing including dendrograms with bootstrap support and minimum spanning networks. Additionally, functions for genotypic diversity and clone censoring are specific for clonal populations, but several functions found in PAPR are applicable to any population. The package is available on CRAN and documentation and tutorials can be found online. This article was authored by Jianen Kambar, Javier F. Tabima, and Nicholas J. Grunwald.