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RhierBAPS: An R implementation of the population clustering algorithm hierBAPS
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 instal...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
F1000 Research Limited
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6178908/ https://www.ncbi.nlm.nih.gov/pubmed/30345380 http://dx.doi.org/10.12688/wellcomeopenres.14694.1 |
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author | Tonkin-Hill, Gerry Lees, John A. Bentley, Stephen D. Frost, Simon D.W. Corander, Jukka |
author_facet | Tonkin-Hill, Gerry Lees, John A. Bentley, Stephen D. Frost, Simon D.W. Corander, Jukka |
author_sort | Tonkin-Hill, Gerry |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-6178908 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | F1000 Research Limited |
record_format | MEDLINE/PubMed |
spelling | pubmed-61789082018-10-19 RhierBAPS: An R implementation of the population clustering algorithm hierBAPS Tonkin-Hill, Gerry Lees, John A. Bentley, Stephen D. Frost, Simon D.W. Corander, Jukka Wellcome Open Res Software Tool Article 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. F1000 Research Limited 2018-07-30 /pmc/articles/PMC6178908/ /pubmed/30345380 http://dx.doi.org/10.12688/wellcomeopenres.14694.1 Text en Copyright: © 2018 Tonkin-Hill G et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Software Tool Article Tonkin-Hill, Gerry Lees, John A. Bentley, Stephen D. Frost, Simon D.W. Corander, Jukka RhierBAPS: An R implementation of the population clustering algorithm hierBAPS |
title | RhierBAPS: An R implementation of the population clustering algorithm hierBAPS |
title_full | RhierBAPS: An R implementation of the population clustering algorithm hierBAPS |
title_fullStr | RhierBAPS: An R implementation of the population clustering algorithm hierBAPS |
title_full_unstemmed | RhierBAPS: An R implementation of the population clustering algorithm hierBAPS |
title_short | RhierBAPS: An R implementation of the population clustering algorithm hierBAPS |
title_sort | rhierbaps: an r implementation of the population clustering algorithm hierbaps |
topic | Software Tool Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6178908/ https://www.ncbi.nlm.nih.gov/pubmed/30345380 http://dx.doi.org/10.12688/wellcomeopenres.14694.1 |
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