fastsimcoal2: demographic inference under complex evolutionary scenarios

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 mu...

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Detalles Bibliográficos
Autores principales: Excoffier, Laurent, Marchi, Nina, Marques, David Alexander, Matthey-Doret, Remi, Gouy, Alexandre, Sousa, Vitor C
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8665742/
https://www.ncbi.nlm.nih.gov/pubmed/34164653
http://dx.doi.org/10.1093/bioinformatics/btab468
Descripción
Sumario: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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