fastsimcoal2: demographic inference under complex evolutionary scenarios

Laurent Excoffier; Nina Marchi; David Alexander Marques; Remi Matthey-Doret; Alexandre Gouy; Vitor C Sousa

doi:10.1093/bioinformatics/btab468

fastsimcoal2: demographic inference under complex evolutionary scenarios

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

Authors

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

¹ Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.
² Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
³ Life Science Division, Natural History Museum Basel, 4051 Basel, Switzerland.
⁴ Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.
⁵ Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland.
⁶ Gouy Data Consulting, 1026 Denges, Switzerland.
⁷ cE3c-Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, University of Lisbon, Campo Grande, 1749-016 Lisbon, Portugal.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Biological Evolution
Computer Simulation
Demography
Genetics, Population*
Software*