Evolutionary Genetics and Genomics Library
Project description
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.
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