Diffusion Approximation for Demographic Inference
Developed by Ryan Gutenkunst in the labs of Scott Williamson and Carlos Bustamante in Cornell's Department of Biological Statistics and Computational Biology.
Ryan is now a postdoc at Los Alamos National Lab, in the Theoretical Biology and Biophysics group and the Center for Nonlinear Studies.
News
- Version 1.2.3 release; May 21, 2009
Primarily, this version fixes several small bugs. It also adds an extension of the IM model to Demographics2D, support for pulling specific populations out of an ms file, and a non-log-parameters optimization method.
- Version 1.2.2 release; March 23, 2009
Added method to import frequency spectra from SFS_CODE output. Also added the classic Isolation-Migration model to Demographics2D. Finally, some small bugfixes and additional technical features were added.
- Version 1.2.1 released; February 17, 2009
Added support for Hessian calculation, which can be used to roughly estimate uncertainties. Additionally, crashing bug related to saving spectra to file was fixed.
Example
The above plot summarizes the result of fitting a model the joint frequency spectrum of genetic variation between the Yoruba (YRI) and CEPH European (CEU) populations. The data is derived from the Environmental Genome Project SNPs database. The upper left panel is the data, and the upper right is the result of a demographic model whose parameters have been optimized using dadi. The lower left panel is the residuals between model and data (red means the model predicts too many SNPs in that bin) and the lower right is a histogram of the residuals. The model involves population growth in the ancestral population, followed by divergence of the CEU population with a bottleneck and exponential growth. It contains 7 free parameters and took a few minutes to fit using dadi.
