fastsimcoal2: demographic inference under complex evolutionary scenarios

• DOI: 10.1093/bioinformatics/btab468
• Publication Date: 2021-06-22T11:10:20Z
• Authors: Laurent Excoffier; Nina Marchi; David Alexander M...; Remi Matthey-Doret; Alexandre Gouy; Vitor C Sousa
• Keywords: 0303 health sciences; 03 medical and health sciences; Genetics, Population; 570 Life sciences; biology; Computer Simulation; Applications Notes; Biological Evolution; Software; Demography

Abstract

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 populations and of large chromosomes.

Availability and implementation 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.