bgc: software for Bayesian estimation of genomic clines. This software implements Bayesian estimation of genomic clines and can be used to estimate hybrid index and quantify genome-wide variation in introgression. Locus-specific measures of introgression can be used to study the genetics of adaptation and speciation. This software is compatible with traditional genetic data and next-generation sequence data with genotype uncertainty. An updated version of this program will be available soon!
gbs2ploidy: software for inference of ploidy from GBS data. This R package contains functions for inference of ploidy from GBS data, including a function to infer allelic ratios and allelic proportions in a Bayesian framework. A paper describing the methods implemented in this software package is currently under review. E-mail me if you want the current draft. The package will also be available from CRAN.
introgress: software for analysis of introgression. This R software package provides functions for quantifying introgression between hybridizing populations. This includes a likelihood-based method for estimating genomic clines using multilocus data and testing for deviations from null expectations. This software also implements a maximum likelihood estimate of hybrid index and provides several graphical summaries of genome-wide introgression.
spatpg: software to infer selection from genetic time series. This program can be used to estimate variance effective population size and environment-dependent selection from genetic time-series data (allele frequencies) from multiple populations. Selection is allowed to vary among populations and from generation to generation. Inference is made in a Bayesian framework.