All simuPOP documents, including a user's guide, a reference manual, and documents of internal (C++ level) classes and functions are available online. The online version of the simuPOP user's guide and reference manual make use of the Python docutils and reStructuredText. The HTML pages are prepared by sphinx. These documents are also available in PDF format.
A book about forward-time simulations and simuPOP
A monograph Forward-Time Population Genetics Simulations: Methods, Implementation, and Applications by Bo Peng, Marek Kimmel and Christopher I Amos has been published by Wiley & Sons Inc, and is available from bookstores such as amazon. This book systematically describes the methods and applications of forward-time population genetics simulations, and uses simuPOP to simulate all examples. Compared to the user's guide and reference manual, this book provides a better introduction to what simuPOP can do. If you have used simuPOP, please consider purchasing this book to support the development of simuPOP.
The simuPOP userís guide shows you how to install and use simuPOP using a large number of examples. It describes all concepts and features of simuPOP and shows you how to use them in a simuPOP script. It is recommended that all simuPOP users read this guide, at least the second chapter, before you start using simuPOP.
The simuPOP reference manual is the authoritative reference for all simuPOP classes and functions. Unlike the user's guide that is organized by features and concepts, this manual is organized by classes and functions. There is no example in this document.
Documentation for previous simuPOP releases
The PDF version of simuPOP user's guide and reference manual are available in the doc directory of all simuPOP packages available at the sourceforge download page. If you are interested only in the documents, you can locate them from the subversion tags of these releases. You will need to select the release you want, choose doc, and then userGuide.pdf or refManual.pdf.
The latest PDF versions of the simuPOP user's guide and reference manual are available from the simuPOP subversion server. The lastest HTML versions of the simuPOP user's guide and reference manual are also available online.
NOTE: The developmental version of simuPOP may not be compatible with the latest release.
simuPOP uses doxygen to document its large number of classes and functions. The web version of these documents provides annotated definitions of all classes and functions. All simuPOP source codes are also listed.
Note: This page lists the latest version of the simuPOP documents. If you are using a previous version of simuPOP, please refer to the documents under the doc directory of the distribution.