SELAM
Simulation of Epistasis and Local adaptation during Admixture with Mate choice
SELAM is a forward time population genetic simulation framework that can simulate admixture between any number of ancestral populations (or equivalently ancestral haplotypes). SELAM supports a variety of selective scenarios, complex demograpy and fully separate sexes. The paper describing this software is available here, and the manual and source code are available from github.
Ancestry_HMM
This program is design to circumvent a few issues with existing local ancestry inference methods. Specifically, this program can (1) explicitly model allele counts derived from NGS data (2) work on samples of any ploidy (3) simultaneously estimate local ancestry and the time of admixture. The paper has just been published in PLoS Genetics, and the code can be acquired here.
This program can now estimate the timing of multiple admixture pulses. To find out more about modelling and fitting multiple pulses, read our paper in Genetics and visit our github.
Ancestry_HMM-S
This program is primarily the work of Corbett-Detig lab postdoc Jesper Svedberg. It builds on our local ancestry inference framework, Ancestry_HMM, and enables users to detect and quantify the strength of natural selection acting during admixture. You can read about the theoretical model we developed with our collaborators describing the expected ancestry tract length distribution during adaptive introgression here. Our preprint describing the inference method, Ancestry_HMM-S, is on bioRxiv. Software to perform these analyses and detailed installation instructions are available via github.