dadi.CUDA: Accelerating Population Genetics Inference with Graphics Processing Units

dadi is a popular but computationally intensive program for inferring models of demographic history and natural selection from population genetic data. I show that running dadi on a Graphics Processing Unit can dramatically speed computation compared with the CPU implementation, with minimal user bu...

Descripción completa

Detalles Bibliográficos
Autor principal: Gutenkunst, Ryan N
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Resources
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8097298/
https://www.ncbi.nlm.nih.gov/pubmed/33480999
http://dx.doi.org/10.1093/molbev/msaa305
_version_ 1783688326021120000
author Gutenkunst, Ryan N
author_facet Gutenkunst, Ryan N
author_sort Gutenkunst, Ryan N
collection PubMed
description dadi is a popular but computationally intensive program for inferring models of demographic history and natural selection from population genetic data. I show that running dadi on a Graphics Processing Unit can dramatically speed computation compared with the CPU implementation, with minimal user burden. Motivated by this speed increase, I also extended dadi to four- and five-population models. This functionality is available in dadi version 2.1.0, https://bitbucket.org/gutenkunstlab/dadi/.
format Online
Article
Text
id pubmed-8097298
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-80972982021-05-10 dadi.CUDA: Accelerating Population Genetics Inference with Graphics Processing Units Gutenkunst, Ryan N Mol Biol Evol Resources dadi is a popular but computationally intensive program for inferring models of demographic history and natural selection from population genetic data. I show that running dadi on a Graphics Processing Unit can dramatically speed computation compared with the CPU implementation, with minimal user burden. Motivated by this speed increase, I also extended dadi to four- and five-population models. This functionality is available in dadi version 2.1.0, https://bitbucket.org/gutenkunstlab/dadi/. Oxford University Press 2021-01-22 /pmc/articles/PMC8097298/ /pubmed/33480999 http://dx.doi.org/10.1093/molbev/msaa305 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Resources
Gutenkunst, Ryan N
dadi.CUDA: Accelerating Population Genetics Inference with Graphics Processing Units
title dadi.CUDA: Accelerating Population Genetics Inference with Graphics Processing Units
title_full dadi.CUDA: Accelerating Population Genetics Inference with Graphics Processing Units
title_fullStr dadi.CUDA: Accelerating Population Genetics Inference with Graphics Processing Units
title_full_unstemmed dadi.CUDA: Accelerating Population Genetics Inference with Graphics Processing Units
title_short dadi.CUDA: Accelerating Population Genetics Inference with Graphics Processing Units
title_sort dadi.cuda: accelerating population genetics inference with graphics processing units
topic Resources
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8097298/
https://www.ncbi.nlm.nih.gov/pubmed/33480999
http://dx.doi.org/10.1093/molbev/msaa305
work_keys_str_mv AT gutenkunstryann dadicudaacceleratingpopulationgeneticsinferencewithgraphicsprocessingunits

Ejemplares similares