Institut de Recherche pour le Développement (IRD), UMR Diversité, Adaptation et Développement des Plantes (DIADE), Montpellier, France.
BMC Genet. 2012 Apr 11;13:27. doi: 10.1186/1471-2156-13-27.
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.
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.
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/ where a full documentation and a manual can also be found and downloaded.
在过去十年中，随着核苷酸序列数据的大量增长，集成和灵活的分析工具已成为必要。特别是在群体遗传学领域，需要自动化和可靠的程序来进行可重复和快速的多态性分析、合并模拟、数据处理以及在各种情况下估计人口参数。
在这种情况下，我们提出了 EggLib（进化遗传学和基因组学库），这是一个灵活而强大的 C++/Python 软件包，为核苷酸序列数据提供了高效且易于使用的计算工具，用于序列数据管理和广泛的群体遗传学分析。EggLib 是一个多方面的项目，涉及几个集成的模块：一个底层计算高效的 C++库（可以在纯 C++应用程序中独立使用）；两个 C++程序；一个 Python 包，提供了高级 Python 接口到 C++库；以及 egglib 脚本，它提供了对预编程的 Python 应用程序的直接访问。
EggLib 的设计旨在高效且易于使用。实现了广泛的方法，包括文件格式转换、序列对齐编辑、合并模拟、中性测试和通过近似贝叶斯计算（ABC）估计人口参数。用户可以轻松开发实现 ABC 分析不同人口情景的类，并将其包含在包中。EggLib 源代码可从其网站 http://egglib.sourceforge.net/ 免费分发，在那里可以找到并下载完整的文档和手册。
