discoal - a coalescent simulator with selection

discoal is a coalescent simulator for generating genetic data under models with recombination, population structure, and selection. It is designed to be familiar to users of Richard Hudson’s ms program while adding the ability to simulate selective sweeps and other forms of natural selection.

Contents:

Features

  • Coalescent simulation with recombination and gene conversion

  • Multiple population models with migration and admixture

  • Various selection models including hard and soft sweeps

  • Partial sweeps and recurrent hitchhiking

  • Efficient memory usage with dynamic allocation

  • Support for up to 65,535 samples (increased from previous limit of 254)

  • Output compatible with ms format

Quick Start

# Download and compile
git clone https://github.com/kern-lab/discoal.git
cd discoal
make discoal

# Basic simulation: 10 samples, 5 replicates, 10000 sites, theta=10
./discoal 10 5 10000 -t 10

# With recombination (rho=10)
./discoal 10 5 10000 -t 10 -r 10

# With a selective sweep
./discoal 10 5 10000 -t 10 -r 10 -ws 0.01 -a 1000 -x 0.5

Citing discoal

If you use discoal in your research, please cite:

Kern, A.D. and Schrider, D.R. (2016). discoal: flexible coalescent simulations with selection. Bioinformatics, 32(24), 3839-3841.

Support

Indices and tables