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rPHG is a system to interact with and retrieve information from a Practical Haplotype Graph (PHG) - a general, graph-based, computational framework for genotype inference. This is accomplished by leveraging the Breeding and PHG APIs.


To cite rPHG, please use the following citation:

Bradbury et al. (2022). The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation. Bioinformatics, 38(15), 3698–3702,


If you do not have experience working with and setting up rJava with your R installation, it is recommended that you read the long-form documentation. This walkthrough can be found here. If you are already fairly comfortable working with Java JDK and rJava, you can follow the following commands.

Package source code can be installed directly from this BitBucket repository using the devtools package:

if (!require("devtools")) install.packages("devtools")
devtools::install_github(repo = "maize-genetics/rPHG")