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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...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
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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. |
format | Online Article Text |
id | pubmed-8665742 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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