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.


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.


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.


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.


SFS_CODE: A flexible forward simulator for populations subject to selection and demography.

Hernandez (2008)

A flexible forward population genetic simulation program with a bevy of features.


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