This repository is associated with the article "Signatures of introgression across the allele frequency spectrum" by Simon H. Martin and William Amos, in Molecular Biology and Evolution (https://doi.org/10.1093/molbev/msaa239) Empirical genotype data from six different taxa are included. All are based on previously published data, but we provide the processed genotype files and frequency spectra used for our analyses for convenience. The repository also contains the plotted values underlying all figures (both empirical and simulated results).