This project provides python and R scripts allowing to estimate population size histories from large samples of genome wide SNP data using approximate Bayesian computation (ABC), as described in:
S. Boitard, W. Rodríguez, F. Jay, S. Mona and F. Austerlitz (2016). Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach. PLoS Genet 12(3): e1005877. http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005877
Population size histories are modelled by a piecewise constant process including a large number of population size changes. Summary statistics used for ABC estimation are the allele frequency spectrum (AFS) and the average linkage disequilibrium (LD) at different bins of physical distance between SNP.
See the "wiki" tab for more details and the "Files" tab for downloads.
This project was partly funded by the grant Demochips (ANR-12-BSV7-0012) from Agence Nationale de la Recherche (http://www.agence-nationale-recherche.fr)