EggLib is a C++/Python library and program package for evolutionary genetics and genomics. Main features are sequence data management, sequence polymorphism analysis, coalescent simulations and Approximate Bayesian Computation. EggLib is a flexible Python module with a performant underlying C++ library (which can be used independently), and allows fast and intuitive development of Python programs and scripts. A number of pre-programmed applications of EggLib possibilities are available interactively. To get an idea of the possibilities offered by EggLib, see the Manual section.
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.
- April 22, 2013: Version 2.1.6 is out to match version 2.1.0 of Bio++. No other change has been made. Meanwhile, egglib 2.2.0 is still under development: the C++ library has been redesigned for improved performance, VCF and GFF3 support has been included population genomics analyses and we are now incorporating additional summary statistics.
- October 20, 2012: Release of version 2.1.5 incorporating small changes. Be careful if you have used or using the SM model in the ABC framework as the parameters were not named properly.
- September 4, 2012: Release of version 2.1.4 with several bug corrections. One of the bugs can be a trouble: when outgroup sequences were placed anywhere else but a the end of the alignment, some statistics (those computed by HaplotypeDiversity: Fst, Kst, Gst, Hst and Snn) were incorrect due to failing to consider the last sequences.
- August, 2012: Version 2.2.0 is now in development. The new coalescent simulator incorporating a number of additional features but mostly a hopefully faster reimplementation has been written. The rest of the C++ library is now under similar refactoring with the aim of improving performance. We will attempt to keep the interface change at the Python level to the strict minimum.
- May 10, 2012: Release of version 2.1.3 with several bug corrections. One of the bug concerned the TPF summary statistics set in ABC, and another prevented execution of the Python module in Windows systems.
An underlying C++ library which might be used independently.
A flexible Python module bringing together the C++ library and additional high-level tools: Python module.
A script egglib providing a number of modular tools for processing and analyzing sequence data (and others). See Directly executable commands.
These pages describe the Python module and the C++ library. They are available as an independent downloadable archive from the download site. A pdf version of the general description of EggLib and reference manual of egglib-py is available here and a pdf version of the reference manual of the C++ library is available there.