Nonparametric statistics

Gene

Statistics

Genotype

Genome

Sociology

Demography

Single-nucleotide polymorphism

Artificial intelligence

Plot (graphics)

Allele

Genomics

Inference

Population

Mathematics

Allele frequency

Computer science

Genetics

Computational biology

Evolutionary biology

Biology

Genome biology

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.

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