Selscan: an efficient multi-threaded program to perform EHH-based scans for positive selection.
Szpiech & Hernandez (2014)
A program that implements EHH, iHS, and XP-EHH.
Download cFET: Comparing Evolutionary Rates Using An Exact Test for 2 × 2 Tables with Continuous Cell Entries.
Thompson et al. (2014)
An efficient implementation of Fisher’s Exact Test, with extensions to contingency tables with continuous cell entries.
Download A MOSAIC of methods: Improving ortholog detection through the integration of algorithmic diversity.
Maher & Hernandez. (2013)
A tool for combining information from multiple ortholog detection methods for better inference.
Download Robust forward simulation of recurrent positive selection.
Uricchio & Hernandez. (2013)
This directory includes python scripts for rescaling parameters under the recurrent hitchhiking model, and for calculating the probability of fixation using the Galton-Watson process described in our paper.
Download SFS_CODE: A flexible forward simulator for populations subject to selection and demography.
A flexible forward population genetic simulation program with a bevy of features.
Download Context Dependence, Ancestral Misidentification, and Spurious Signatures of Natural Selection.
Hernandez et al. (2007)
R script to correct your site frequency spectrum for ancestral misidentification