Stairway Plot 2: demographic history inference with folded SNP frequency spectra

Inferring the demographic histories of populations has wide applications in population, ecological, and conservation genomics. We present Stairway Plot 2, a cross-platform program package for this task using SNP frequency spectra. It is based on a nonparametric method with the capability of handling...

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Detalles Bibliográficos
Autores principales: Liu, Xiaoming, Fu, Yun-Xin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7670622/
https://www.ncbi.nlm.nih.gov/pubmed/33203475
http://dx.doi.org/10.1186/s13059-020-02196-9
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author Liu, Xiaoming
Fu, Yun-Xin
author_facet Liu, Xiaoming
Fu, Yun-Xin
author_sort Liu, Xiaoming
collection PubMed
description Inferring the demographic histories of populations has wide applications in population, ecological, and conservation genomics. We present Stairway Plot 2, a cross-platform program package for this task using SNP frequency spectra. It is based on a nonparametric method with the capability of handling folded SNP frequency spectra (that is, when the ancestral alleles of the SNPs are unknown) of thousands of samples produced with genotyping-by-sequencing technologies; therefore, it is particularly suitable for nonmodel organisms. SUPPLEMENTARY INFORMATION: Supplementary information accompanies this paper at 10.1186/s13059-020-02196-9.
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spelling pubmed-76706222020-11-18 Stairway Plot 2: demographic history inference with folded SNP frequency spectra Liu, Xiaoming Fu, Yun-Xin Genome Biol Method Inferring the demographic histories of populations has wide applications in population, ecological, and conservation genomics. We present Stairway Plot 2, a cross-platform program package for this task using SNP frequency spectra. It is based on a nonparametric method with the capability of handling folded SNP frequency spectra (that is, when the ancestral alleles of the SNPs are unknown) of thousands of samples produced with genotyping-by-sequencing technologies; therefore, it is particularly suitable for nonmodel organisms. SUPPLEMENTARY INFORMATION: Supplementary information accompanies this paper at 10.1186/s13059-020-02196-9. BioMed Central 2020-11-17 /pmc/articles/PMC7670622/ /pubmed/33203475 http://dx.doi.org/10.1186/s13059-020-02196-9 Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Method
Liu, Xiaoming
Fu, Yun-Xin
Stairway Plot 2: demographic history inference with folded SNP frequency spectra
title Stairway Plot 2: demographic history inference with folded SNP frequency spectra
title_full Stairway Plot 2: demographic history inference with folded SNP frequency spectra
title_fullStr Stairway Plot 2: demographic history inference with folded SNP frequency spectra
title_full_unstemmed Stairway Plot 2: demographic history inference with folded SNP frequency spectra
title_short Stairway Plot 2: demographic history inference with folded SNP frequency spectra
title_sort stairway plot 2: demographic history inference with folded snp frequency spectra
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7670622/
https://www.ncbi.nlm.nih.gov/pubmed/33203475
http://dx.doi.org/10.1186/s13059-020-02196-9
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