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 (Better Names Pending)
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.