gammaMap

gammaMap is a program for detecting natural selection in sequence data from one or more species. It is based on a combined population genetics-phylogenetics model of selection. gammaMap estimates the distribution of selection coefficients, and allows localization of the signal of selection using a Bayesian sliding window approach. The signature of selection is detected from the contrast in the dN/dS ratio within and between species. The method and modelling approach are described in

Wilson, D. J., R. D. Hernandez, P. Andolfatto and M. Przeworski (2011)
A population genetics-phylogenetics approach to inferring natural selection in coding sequences.
PLoS Genetics 7: e1002395. (abstract pdf)

The software is available to download from code.google.com/p/gcat-project/. A singularity container is available here and its definition is here.