dadi 2.0.1

Fit population genetic models of demography and selection using diffusion approximations to the allele frequency spectrum

Diffusion Approximation for Demographic Inference

∂a∂i implements methods for demographic history and selection inference from genetic data, based on diffusion approximations to the allele frequency spectrum. One of ∂a∂i's main benefits is speed: fitting a two-population model typically takes around 10 minutes, and run time is independent of the number of SNPs in your data set. ∂a∂i is also flexible, handling up to three simultaneous populations, with arbitrary timecourses for population size and migration, plus the possibility of admixture and population-specific selection.

Originally ∂a∂i was initially developed by Ryan Gutenkunst in the labs of Scott Williamson and Carlos Bustamante (https://bustamantelab.stanford.edu/) in Cornell's Department of Biological Statistics and Computational Biology. Ryan is now faculty in Molecular and Cellular Biology at the University of Arizona, and his group continues to work on ∂a∂i and other topics (http://gutengroup.mcb.arizona.edu).

If you use ∂a∂i in your research, please cite RN Gutenkunst, RD Hernandez, SH Williamson, CD Bustamante "Inferring the joint demographic history of multiple populations from multidimensional SNP data" PLoS Genetics 5:e1000695 (2009).

Getting started

See the manual (https://bitbucket.org/gutenkunstlab/dadi/src/master/doc/manual/manual.pdf) and the example files in the source distribution. Full API documenation is available (https://bb.githack.com/gutenkunstlab/dadi/raw/master/doc/api/dadi/index.html) and is in the source distribution, under doc/api/dadi/index.html .

Also, please sign up for our mailing list, where we help the community with ∂a∂i. Please do search the archives before posting. Many questions come up repeatedly. (http://groups.google.com/group/dadi-user)