fastsimcoal2: demographic inference under complex evolutionary scenarios

Laurent Excofffier, Nina Marchi, David Alexander Marques, Remi Matthey-Doret, Alexandre Gouy, Vitor C Sousa, Russell Schwartz
2021 Bioinformatics  
Motivation fastsimcoal2 extends fastsimcoal, a continuous time coalescent-based genetic simulation program, by enabling the estimation of demographic parameters under very complex scenarios from the site frequency spectrum under a maximum-likelihood framework. Results Other improvements include multi-threading, handling of population inbreeding, extended input file syntax facilitating the description of complex demographic scenarios, and more efficient simulations of sparsely structured
more » ... ons and of large chromosomes. Availability fastsimcoal2 is freely available on http://cmpg.unibe.ch/software/fastsimcoal2/. It includes console versions for Linux, Windows and MacOS, additional scripts for the analysis and visualization of simulated and estimated scenarios, as well as a detailed documentation and ready-to-use examples.
doi:10.1093/bioinformatics/btab468 pmid:34164653 pmcid:PMC8665742 fatcat:l66enjyxbrayxmxfruvvr2w7gu