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

Published in: Genome biology (2020)

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.

Keyphrases

genome wide
single cell
genetic diversity
dna methylation
density functional theory
high throughput
high density
climate change
gene expression
gram negative
multidrug resistant
molecular dynamics
human health