EggLib 3.6.0

EggLib is software package offering a wide array of tools for automated population genetics and genomics analyses.

Table of Contents

• About

• Installation

• Cloning

• Building local documentation

• Citation

• License

About

EggLib is a Python library, largely implemented in C++, for evolutionary genetics and genomics. Main features are sequence data management, sequence polymorphism analysis, and coalescent simulations. EggLib is a flexible Python module with a performant underlying C++ library and allows fast and intuitive development of Python programs and scripts.

EggLib home page: https://www.egglib.org

Installation

EggLib is available on pip. For more information on installing EggLib or downloading source code please refer to the installation section of the documentation: https://egglib.org/install.html.

Cloning

You can clone the whole package using:

git clone https://gitlab.com/demita/egglib.git

For example, this lets you access to the current version on development:

cd egglib
git checkout dev

Building local documentation

To generate the documentation locally, you should clone the repository, install EggLib and the python-sphinx package, and run this:

python -m sphinx doc/ ../doc

The first argument is the location of the doc directory within the EggLib package. The second argument is the destination of the generated documentation. ../doc is just an example.

Citation

Siol M., T. Coudoux, S. Ravel and S. De Mita. 2022. EggLib 3: A python package for population genetics and genomics. Mol Ecol. Res. 22:3176-3187. https://doi.org/10.1111/1755-0998.13672

License

EggLib is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

EggLib is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

https://www.egglib.org/licence.html