.. egglib documentation master file, created by sphinx-quickstart on Tue Nov 10 21:49:03 2009. ==================== EggLib documentation ==================== 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 :ref:`manual` section. .. note:: EggLib version 2.1 is now in archive mode while EggLib version 3.0 is in beta. Bugs in EggLib 2.1 will be fixed if they are reported but we encourage users to try the new version of EggLib in order to report bugs or incorrect results. `Go to EggLib 3 web site `_. **Get EggLib:** :ref:`instructions ` -- `download `_. **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 `_. ------------ What's new ? ------------ * March 4, 2016: Release of version 2.1.11 (in which an occasional bug if eggcoal is fixed). * March 23, 2014: Version 2.1.10 supports Bio++ 2.2.0 and higher but does not support earlier versions of Bio++. Note that this version also fix a minor problem with the coalescent simulator that only appears when you deal directly from low-level classes. Only the source code is released. * October 04, 2014: Version 2.1.9 is out to fix a rather minor error affecting the Staden parser only (in particular ``staden2fasta``). * September 23, 2014: Version 2.1.8 is out to fix a heavy error affecting the ``abc_sample`` command and more precisely the ``TPS``, ``TPF`` and ``TPK`` summary statistics sets. The error was that the program used only the last locus for computing per-population :math:`\pi` (ignoring all previous ones). The three summary statistics sets are fixed. This error did not affect other summary statistics sets or the other statistics of those three summary statistics sets. Since this behaviour was consistent for both observed data sets and simulations, the consequence of the error was, in principle, a complete lack of resolution of these summary statistics sets rather than erroneous results, but it is much likely that results using these summary statistics sets were inaccurate. Also: version 2.2.0 has been elevated to version 3 due to large-scale changes in the interface. A preliminary package of version 3 is `out `_ (for testing purpose). * November 20, 2013: The pre-compiled package of version 2.1.7 is available for Python 2.7 32 bits. * November 7, 2013: Version 2.1.7 (source only, at the moment) is out to include minor changes. Warning: If you use non-standard genetic codes, you must update because there was an error preventing the code argument to be passed to underlying polymorphism analysis routines in egglib-py. .. * 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. .. * February 8, 2012: Release of version 2.1.2 with several bug corrections (especially one concerning the number of orientable sites). .. * January 26, 2012: Release of version 2.1.1 with updated links in the documentation and a single small change. .. 2.1.1 is still beta and available in the `future `_ directory. .. The default version (available in the `current `_ directory) has the bugs that were fixed in 2.1.0 and 2.1.1 (see :ref:`History `). .. * January 26, 2012: EggLib moved from seqlib.sourceforge.net to egglib.sourceforge.net. .. * January 24, 2012: Version 2.1.0 is available in the `future `_ directory. .. This version includes parallel computing, a test suite and a large number of bug fixes. More changes (including programming .. interface changes) are planned for the next version 2.1.1. .. * November 7, 2011: Release of the slightly improved version 2.0.3. .. * September 16, 2011: Release of version 2.0.2: the behaviour of methods :meth:`polymorphism` and :meth:`polymorphismBPP` of :class:`Align` is .. changed and some statistics are now longer returned when they are not defined. See :ref:`History ` for more details and a full list .. of changes. .. * May 11, 2011: Pre-compiled Windows modules are available. -------- Synopsis -------- - An underlying :ref:`egglib-cpp` which might be used independently. - Two standalone programs: - :ref:`eggcoal`: an extensive coalescent simulator. - :ref:`eggstats`: a simple command line tool for analyzing diversity in fasta files. - A flexible Python module bringing together the C++ library and additional high-level tools: :ref:`egglib-py`. - A script ``egglib`` providing a number of modular tools for processing and analyzing sequence data (and others). See :ref:`apps`. ------------- Documentation ------------- 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 `_. ================= Detailed contents ================= .. toctree:: :maxdepth: 4 installation manual eggcoal eggstats egglib-cpp egglib-py documentation-utils authors acknowledgments history ================== Indices and tables ================== * :ref:`genindex` * :ref:`modindex` * :ref:`search`