EggLib 3.0.0

Evolutionary Genetics and Genomics Library

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, and run this (assuming the package has been installed):

python setup.py build_sphinx
python setup.py build_pdf

The first command generates the html documentation (available in the doc/build/html directory) and the second generates three pdf documents containing the main sections of the documentation (in the doc/build/latex directory).

To generate documentation, one needs:

• A LaTex processor, containing the following packages: anyfontsize, amsmath, fncychap, capt-of, needspace, framed, upquote, wrapfig (and possibly others).

• python3-sphinx

• python3-svgwrite

• latexmk

Citation

De Mita S. and M. Siol. 2012. EggLib: processing, analysis and simulation tools for population genetics and genomics. BMC Genet. 13:27. Open access

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