Computer simulations: tools for population and evolutionary genetics

S Hoban, G Bertorelle, OE Gaggiotti - Nature Reviews Genetics, 2012 - nature.com
Computer simulations are excellent tools for understanding the evolutionary and genetic
consequences of complex processes whose interactions cannot be analytically predicted …

Efficient ancestry and mutation simulation with msprime 1.0

F Baumdicker, G Bisschop, D Goldstein, G Gower… - Genetics, 2022 - academic.oup.com
Stochastic simulation is a key tool in population genetics, since the models involved are
often analytically intractable and simulation is usually the only way of obtaining ground-truth …

Efficient coalescent simulation and genealogical analysis for large sample sizes

J Kelleher, AM Etheridge… - PLoS computational …, 2016 - journals.plos.org
A central challenge in the analysis of genetic variation is to provide realistic genome
simulation across millions of samples. Present day coalescent simulations do not scale well …

OpenMendel: a cooperative programming project for statistical genetics

H Zhou, JS Sinsheimer, DM Bates, BB Chu… - Human genetics, 2020 - Springer
Statistical methods for genome-wide association studies (GWAS) continue to improve.
However, the increasing volume and variety of genetic and genomic data make …

SLiM: simulating evolution with selection and linkage

PW Messer - Genetics, 2013 - academic.oup.com
SLiM is an efficient forward population genetic simulation designed for studying the effects of
linkage and selection on a chromosome-wide scale. The program can incorporate complex …

[PDF][PDF] Coalescent simulation with msprime

J Kelleher, K Lohse - Statistical Population Genomics, 2020 - library.oapen.org
Coalescent simulation is a fundamental tool in modern population genetics. The msprime
library provides unprecedented scalability in terms of both the simulations that can be …

Simulation of molecular data under diverse evolutionary scenarios

M Arenas - PLoS computational biology, 2012 - journals.plos.org
This study is intended for evolutionary biologists interested in strategies for the simulation of
molecular data under diverse evolutionary scenarios. It begins with a brief background on …

Demes: a standard format for demographic models

G Gower, AP Ragsdale, G Bisschop, RN Gutenkunst… - Genetics, 2022 - academic.oup.com
Understanding the demographic history of populations is a key goal in population genetics,
and with improving methods and data, ever more complex models are being proposed and …

Simulation of genes and genomes forward in time

A Carvajal-Rodríguez - Current genomics, 2010 - ingentaconnect.com
The importance of simulation software in current and future evolutionary and genomic
studies is just confirmed by the recent publication of several new simulation tools. The …

Next generation analytic tools for large scale genetic epidemiology studies of complex diseases

LE Mechanic, HS Chen, CI Amos… - Genetic …, 2012 - Wiley Online Library
Over the past several years, genome‐wide association studies (GWAS) have succeeded in
identifying hundreds of genetic markers associated with common diseases. However, most …