QuantiNemo 2: a Swiss knife to simulate complex demographic and genetic scenarios, forward and backward in time

Bioinformatics
Samuel NeuenschwanderJérôme Goudet

Abstract

QuantiNemo 2 is a stochastic simulation program for quantitative population genetics. It was developed to investigate the effects of selection, mutation, recombination and drift on quantitative traits and neutral markers in structured populations connected by migration and located in heterogeneous habitats. A specific feature is that it allows to switch between an individual-based full-featured mode and a population-based faster mode. Several demographic, genetic and selective parameters can be fine-tuned in QuantiNemo 2: population, selection, trait(s) architecture, genetic map for QTL and/or markers, environment, demography and mating system are the main features. QuantiNemo 2 is a C++ program with a source code available under the GNU General Public License version 3. Executables are provided for Windows, MacOS and Linux platforms, together with a comprehensive manual and tutorials illustrating its flexibility. The executable, manual and tutorial can be found on the website www2.unil.ch/popgen/softwares/quantinemo/, while the source code and user support are given through GitHub: github.com/jgx65/quantinemo. Supplementary data are available at Bioinformatics online.

References

Jul 16, 2005·Bioinformatics·Bo Peng, Marek Kimmel
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May 14, 2011·Molecular Ecology Resources·Laurent Excoffier, Heidi E L Lischer
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Citations

Nov 27, 2019·Molecular Ecology Resources·Erin L LandguthSamuel A Cushman
Jul 21, 2020·Evolutionary Applications·Glenn YannicLoïc Pellissier
Oct 18, 2020·Genetics·Marco GalimbertiDaniel Wegmann
Oct 9, 2020·Molecular Ecology Resources·Marco AndrelloStéphanie Manel
May 7, 2021·Genetics·Marco GalimbertiDaniel Wegmann
Jul 1, 2021·Molecular Ecology Resources·Jefferson F ParilAlexandre Fournier-Level

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Software Mentioned

Arlequin
quantiNemo
PLINK

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