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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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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:
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
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author Excoffier, Laurent
Marchi, Nina
Marques, David Alexander
Matthey-Doret, Remi
Gouy, Alexandre
Sousa, Vitor C
author_facet Excoffier, Laurent
Marchi, Nina
Marques, David Alexander
Matthey-Doret, Remi
Gouy, Alexandre
Sousa, Vitor C
author_sort Excoffier, Laurent
collection PubMed
description 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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spelling pubmed-86657422021-12-13 fastsimcoal2: demographic inference under complex evolutionary scenarios Excoffier, Laurent Marchi, Nina Marques, David Alexander Matthey-Doret, Remi Gouy, Alexandre Sousa, Vitor C Bioinformatics Applications Notes 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. Oxford University Press 2021-06-23 /pmc/articles/PMC8665742/ /pubmed/34164653 http://dx.doi.org/10.1093/bioinformatics/btab468 Text en © The Author(s) 2021. Published by Oxford University Press. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Excoffier, Laurent
Marchi, Nina
Marques, David Alexander
Matthey-Doret, Remi
Gouy, Alexandre
Sousa, Vitor C
fastsimcoal2: demographic inference under complex evolutionary scenarios
title fastsimcoal2: demographic inference under complex evolutionary scenarios
title_full fastsimcoal2: demographic inference under complex evolutionary scenarios
title_fullStr fastsimcoal2: demographic inference under complex evolutionary scenarios
title_full_unstemmed fastsimcoal2: demographic inference under complex evolutionary scenarios
title_short fastsimcoal2: demographic inference under complex evolutionary scenarios
title_sort fastsimcoal2: demographic inference under complex evolutionary scenarios
topic Applications Notes
url 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
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