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. 2021 Dec 11;37(24):4882-4885.
doi: 10.1093/bioinformatics/btab468.

fastsimcoal2: demographic inference under complex evolutionary scenarios

Laurent Excoffier  1   2 , Nina Marchi  1   2 , David Alexander Marques  3   4   5 , Remi Matthey-Doret  1   2 , Alexandre Gouy  1   6 , Vitor C Sousa  1   7
Affiliations

fastsimcoal2: demographic inference under complex evolutionary scenarios

Laurent Excoffier et al. Bioinformatics. .

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.

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Figures

Fig. 1.
Fig. 1.
Speed comparison between different versions of fsc2. fsc21: released in 2013, single-threaded. fsc2603: released in 2017, multi-threading but no log acceleration. fsc27: current release, log acceleration, optimized for large chromosomes and highly subdivided populations. (A) Simulation of 100 1 Gb chromosomes, r = 1e-7. (B) Simulation of 100 haploid genomes consisting of 1 million unlinked segments of 100 bp, u = 1.4e-8. (C) Simulation of 2 haploid genomes of 10 000 unlinked segments of 100 bp in a 2D stepping-stone of 10×10 demes. (D) Simulation of 2 haploid genomes of 1000 unlinked segments of 100 bp in a 2D stepping-stone of 20×20 demes. In the two top cases, the mutation rate u = 1.4e-8 per bp, and the haploid population size is 20 000. In the two bottom cases, u = 1.25e-8, m = 0.05 to each of the 4 adjacent demes and the haploid population size of each deme is 200. The numbers above the bars indicate the speed gain factor as compared to fsc21
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References

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