RhierBAPS: An R implementation of the population clustering algorithm hierBAPS

Abstract

Identifying structure in collections of sequence data sets remains a common problem in genomics. hierBAPS, a popular algorithm for identifying population structure in haploid genomes, has previously only been available as a MATLAB binary. We provide an R implementation which is both easier to install and use, automating the entire pipeline. Additionally, we allow for the use of multiple processors, improve on the default settings of the algorithm, and provide an interface with the ggtree library to enable informative illustration of the clustering results. Our aim is that this package aids in the understanding and dissemination of the method, as well as enhancing the reproducibility of population structure analyses.

Cited by papers we hold 7

• Frequencies and characteristics of genome-wide recombination in Streptococcus agalactiae, Streptococcus pyogenes, and Streptococcus suis · 2022
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• Phylogeography of Nasutitermes ephratae (Termitidae: Nasutitermitinae) in neotropical region · 2022
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• Genome-wide insights into population structure and host specificity of Campylobacter jejuni · 2021
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• Persistence of Brucella abortus lineages revealed by genomic characterization and phylodynamic analysis. · 2020
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• Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa · 2020
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• Fast and flexible bacterial genomic epidemiology with PopPUNK · 2019
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• Fast hierarchical Bayesian analysis of population structure · 2019
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