dadi-cli: Automated and distributed population genetic model inference from allele frequency spectra

SUMMARY: dadi is a popular software package for inferring models of demographic history and natural selection from population genomic data. But using dadi requires Python scripting and manual parallelization of optimization jobs. We developed dadi-cli to simplify dadi usage and also enable straighfo...

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Detalles Bibliográficos
Autores principales: Huang, Xin, Struck, Travis J., Davey, Sean W., Gutenkunst, Ryan N.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10312675/
https://www.ncbi.nlm.nih.gov/pubmed/37398279
http://dx.doi.org/10.1101/2023.06.15.545182
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author Huang, Xin
Struck, Travis J.
Davey, Sean W.
Gutenkunst, Ryan N.
author_facet Huang, Xin
Struck, Travis J.
Davey, Sean W.
Gutenkunst, Ryan N.
author_sort Huang, Xin
collection PubMed
description SUMMARY: dadi is a popular software package for inferring models of demographic history and natural selection from population genomic data. But using dadi requires Python scripting and manual parallelization of optimization jobs. We developed dadi-cli to simplify dadi usage and also enable straighforward distributed computing. AVAILABILITY AND IMPLEMENTATION: dadi-cli is implemented in Python and released under the Apache License 2.0. The source code is available at https://github.com/xin-huang/dadi-cli. dadi-cli can be installed via PyPI and conda, and is also available through Cacao on Jetstream2 https://cacao.jetstream-cloud.org/.
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spelling pubmed-103126752023-07-01 dadi-cli: Automated and distributed population genetic model inference from allele frequency spectra Huang, Xin Struck, Travis J. Davey, Sean W. Gutenkunst, Ryan N. bioRxiv Article SUMMARY: dadi is a popular software package for inferring models of demographic history and natural selection from population genomic data. But using dadi requires Python scripting and manual parallelization of optimization jobs. We developed dadi-cli to simplify dadi usage and also enable straighforward distributed computing. AVAILABILITY AND IMPLEMENTATION: dadi-cli is implemented in Python and released under the Apache License 2.0. The source code is available at https://github.com/xin-huang/dadi-cli. dadi-cli can be installed via PyPI and conda, and is also available through Cacao on Jetstream2 https://cacao.jetstream-cloud.org/. Cold Spring Harbor Laboratory 2023-06-16 /pmc/articles/PMC10312675/ /pubmed/37398279 http://dx.doi.org/10.1101/2023.06.15.545182 Text en https://creativecommons.org/licenses/by-nc/4.0/This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License (https://creativecommons.org/licenses/by-nc/4.0/) , which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format for noncommercial purposes only, and only so long as attribution is given to the creator.
spellingShingle Article
Huang, Xin
Struck, Travis J.
Davey, Sean W.
Gutenkunst, Ryan N.
dadi-cli: Automated and distributed population genetic model inference from allele frequency spectra
title dadi-cli: Automated and distributed population genetic model inference from allele frequency spectra
title_full dadi-cli: Automated and distributed population genetic model inference from allele frequency spectra
title_fullStr dadi-cli: Automated and distributed population genetic model inference from allele frequency spectra
title_full_unstemmed dadi-cli: Automated and distributed population genetic model inference from allele frequency spectra
title_short dadi-cli: Automated and distributed population genetic model inference from allele frequency spectra
title_sort dadi-cli: automated and distributed population genetic model inference from allele frequency spectra
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10312675/
https://www.ncbi.nlm.nih.gov/pubmed/37398279
http://dx.doi.org/10.1101/2023.06.15.545182
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