SimOutbreakSelection

!!! SOS is still a WIP. Please be mindful that there are paths that require the user to manually change. !!!

Table of Contents

• Prerequisites
• Installation
• Citation
• Preparing Inputs
• Usage
• License

Prerequisites

SimOutbreakSelection or SOS relies on SLiM (3.3.1) , python (3.7.12), and R (4.2.2).

Crucially SOS uses the following modules within python to handle SLiM tree sequence outputs:

• tskit (0.2.3)
• msprime (0.7.4)
• pyslim (0.403)

An appropriate environment can be installed using conda or micromamba. Micromamba is highly recommended.

Installation

# Create a conda environment
micromamba env create -f environment.yml

Citation

Our preprint is available on BioRxiv.

Usage

Documentation for SOS can be found here at the SimOutbreakSelection wiki.

License

Distributed under the GNU General Public License v3.0. See the LICENSE file for more information.