msprime
Simulation tools conditioned on a genealogy are now part of msprime.
Simulation tools conditioned on a genealogy are now part of msprime.
L Anderson-Trocmé et al, "Genes, Genealogies, and geographies of Quebec", Science 380, 849 (2023)
Software
You’ll find most of our software on the gravellab github page and Simon Gravel’s github.
VIPRS
A variational approach to polygenic risk prediction.
A variational approach to polygenic risk prediction.
S. Zabad, S. Gravel, Y. Li "Fast and Accurate Bayesian Polygenic Risk Modeling with Variational Inference." AJHG. 110, 1 (2023)
Moments.LD
Inferring complex demographic models from two-locus statistics.
Inferring complex demographic models from two-locus statistics.
A.P. Ragsdale, S. Gravel, (2019). "Models of archaic admixture and recent history from two-locus statistics." PLoS Genet. 1008204.
Moments
Inferring multipopulation demographic models from allele frequency distributions. Now bundled with moments.LD
Inferring multipopulation demographic models from allele frequency distributions. Now bundled with moments.LD
J. Jouganous, W. Long, A.P. Ragsdale, S. Gravel, (2017). "Inferring the Joint Demographic History of Multiple Populations: Beyond the Diffusion Approximation ." Genetics 206 (3).
Tracts
Inferring the timing of admixture events
Inferring the timing of admixture events
S. Gravel, (2012). "Population genetics models of local ancestry ." Genetics 191 (607).