An overview of the utility of population simulation software in molecular ecology

S Hoban - Molecular ecology, 2014 - Wiley Online Library
Stochastic simulation software that simultaneously model genetic, population and
environmental processes can inform many topics in molecular ecology. These include …

Inference of the distribution of selection coefficients for new nonsynonymous mutations using large samples

BY Kim, CD Huber, KE Lohmueller - Genetics, 2017 - academic.oup.com
The distribution of fitness effects (DFE) has considerable importance in population genetics.
To date, estimates of the DFE come from studies using a small number of individuals. Thus …

Efficient pedigree recording for fast population genetics simulation

J Kelleher, KR Thornton, J Ashander… - PLoS computational …, 2018 - journals.plos.org
In this paper we describe how to efficiently record the entire genetic history of a population in
forwards-time, individual-based population genetics simulations with arbitrary breeding …

Determining the factors driving selective effects of new nonsynonymous mutations

CD Huber, BY Kim, CD Marsden… - Proceedings of the …, 2017 - National Acad Sciences
The distribution of fitness effects (DFE) of new mutations plays a fundamental role in
evolutionary genetics. However, the extent to which the DFE differs across species has yet to …

The power to detect quantitative trait loci using resequenced, experimentally evolved populations of diploid, sexual organisms

JG Baldwin-Brown, AD Long… - Molecular biology and …, 2014 - academic.oup.com
A novel approach for dissecting complex traits is to experimentally evolve laboratory
populations under a controlled environment shift, resequence the resulting populations, and …

forqs: forward-in-time simulation of recombination, quantitative traits and selection

D Kessner, J Novembre - Bioinformatics, 2014 - academic.oup.com
forqs is a forward-in-time simulation of recombination, quantitative traits and selection. It was
designed to investigate haplotype patterns resulting from scenarios where substantial …

SELAM: simulation of epistasis and local adaptation during admixture with mate choice

R Corbett-Detig, M Jones - Bioinformatics, 2016 - academic.oup.com
SELAM is a forward time population genetic simulation program that provides a flexible
framework for simulating admixture between any number of ancestral populations. The …

Robust forward simulations of recurrent hitchhiking

LH Uricchio, RD Hernandez - Genetics, 2014 - academic.oup.com
Evolutionary forces shape patterns of genetic diversity within populations and contribute to
phenotypic variation. In particular, recurrent positive selection has attracted significant …

XSim: simulation of descendants from ancestors with sequence data

H Cheng, D Garrick, R Fernando - G3: Genes, Genomes …, 2015 - academic.oup.com
Real or imputed high-density SNP genotypes are routinely used for genomic prediction and
genome-wide association studies. Many researchers are moving toward the use of actual or …

Parallelizing Population Genetics Applications

C Montemuiño Sosa - 2021 - ddd.uab.cat
Amb la creixent disponibilitat de dades a escala de l'genoma per a la investigació genètica,
els genetistes de poblacions moleculars han de treballar amb models més complexos, el …