SelectionHapStats is a repository of Python scripts written to identify natural selection events in the genome and R scripts written to visualize the signatures of selective sites.
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README.md
README_selectionHapStats.pdf

README.md

SelectionHapStats README

Nandita Garud

Updated August 21, 2018

SelectionHapStats is a GitHub repository of Python scripts to identify and visualize genomic loci under natural selection using the statistics H12, H2/H1, G12, G123, and G2/G1. This work is described in the README document README_selectionHapStats.pdf and in greater detail in the following papers:

H12 and H2/H1 statistics:

Garud NR, Messer P, Buzbas E, and Petrov D. “Soft selective sweeps are the primary mode of adaptation in Drosophila.” PLoS Genetics 11: e1005004 (2015).

Garud NR and Petrov DA. “Elevated linkage disequilibrium and signatures of soft sweeps are common in Drosophila melanogaster.” Genetics (2016).

Garud NR and Rosenberg NA. “Enhancing the mathematical properties of haplotype homozygosity statistics for the detection of soft selective sweeps.” Theoretical Population Biology (2015).

G12, G123, and G2/G1 statistics:

Harris, AM, Garud NR, DeGiorgio M. “Detection and classification of hard and soft sweeps from unphased genotypes by multilocus genotype identity.” Submitted to Genetics. Currently on BioRxiv: https://www.biorxiv.org/content/early/2018/08/15/281063