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Wellcome Open Res. 2018 Jul 30;3:93. doi: 10.12688/wellcomeopenres.14694.1. eCollection 2018.

RhierBAPS: An R implementation of the population clustering algorithm hierBAPS.

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Parasites and Microbes, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK.
Department of Microbiology, New York University School of Medicine, New York, NY, 10016, USA.
The Alan Turing Institute, London, NW1 2DB, UK.
Department of Veterinary Medicine, University of Cambridge, Cambridge, Cambridgeshire, CB3 0ES, UK.
Department of Biostatistics, University of Oslo, Blindern, 0317, Norway.
Department of Mathematics and Statistics, University of Helsinki, Helsinki, 00014, Finland.


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.


R; clustering; population structure

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