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More software will be added here as and when I write suitable documentation and make it otherwise user-friendly.

LEAPFrOG (Likelihood Estimation of Admixture in Parents From Offspring Genotype, an R package)
This program provides maximum likelihood estimates of individuals' admixture proportions, based on their DNA data and DNA data for 'reference' populations (e.g. Africa, Europe, Asia) provided by the user. Furthermore, based only on these data, it provides estimates of the admixture proportions for the individuals' parents, even though their DNA is unobserved. There are two functions, one for use with 'phased' DNA data and one for unphased.
Link (on CRAN)
Paper (open access)

REGENT (Risk Estimation for Genetic and Environmental Traits, an R package)
This provides estimates of relative risks and odds ratios for diseases based on patients' DNA data, and also empirically-estimated confidence intervals for these risk ratios. A risk categorisation is performed (e.g. individuals are assigned low/medium/high risks) based on how these confidence intervals vary and overlap between individuals within a simulated population.
Link (on CRAN)
Paper (open access)
User manual (pdf)