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
Descripción
Sumario: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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