ARGON is a fast simulator of genetic data that samples from the discrete time Wright-Fisher process (DTWF) backwards in time.

The coalescent is equivalent to the DTWF process if the sample size is small compared to the effective population size, but will deviate from it as the sample size increases. ARGON can simulate long chromosomes and large samples under the DTWF, with computational time comparable to recent coalescent simulators.

It supports arbitrary demographic history, migration, variable mutation/recombination rates and gene conversion, and efficiently outputs pairwise identical-by-descent (IBD) sharing data.


ARGON: fast, whole-genome simulation of the discrete time Wright-Fisher process. P. Palamara. Bioinformatics. June 2016. [paper] [preprint]