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EggLib: processing, analysis and simulation tools for population genetics and genomics

Stéphane De Mita12* and Mathieu Siol34

Author Affiliations

1 Institut de Recherche pour le Développement (IRD), UMR Diversité, Adaptation et Développement des Plantes (DIADE), Montpellier, France

2 Institut National de la Recherche Agronomique (INRA), UMR Interactions Arbres-Microorganismes (IAM), Nancy, France

3 Institut National de la Recherche Agronomique (INRA), UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), Montpellier, France

4 Institut National de la Recherche Agronomique (INRA), UMR Agroécologie, Dijon, France

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BMC Genetics 2012, 13:27  doi:10.1186/1471-2156-13-27

Published: 11 April 2012

Abstract

Background

With the considerable growth of available nucleotide sequence data over the last decade, integrated and flexible analytical tools have become a necessity. In particular, in the field of population genetics, there is a strong need for automated and reliable procedures to conduct repeatable and rapid polymorphism analyses, coalescent simulations, data manipulation and estimation of demographic parameters under a variety of scenarios.

Results

In this context, we present EggLib (Evolutionary Genetics and Genomics Library), a flexible and powerful C++/Python software package providing efficient and easy to use computational tools for sequence data management and extensive population genetic analyses on nucleotide sequence data. EggLib is a multifaceted project involving several integrated modules: an underlying computationally efficient C++ library (which can be used independently in pure C++ applications); two C++ programs; a Python package providing, among other features, a high level Python interface to the C++ library; and the egglib script which provides direct access to pre-programmed Python applications.

Conclusions

EggLib has been designed aiming to be both efficient and easy to use. A wide array of methods are implemented, including file format conversion, sequence alignment edition, coalescent simulations, neutrality tests and estimation of demographic parameters by Approximate Bayesian Computation (ABC). Classes implementing different demographic scenarios for ABC analyses can easily be developed by the user and included to the package. EggLib source code is distributed freely under the GNU General Public License (GPL) from its website http://egglib.sourceforge.net/ webcite where a full documentation and a manual can also be found and downloaded.