BoPeng / simuPOP

simuPOP is a general-purpose individual-based forward-time population genetics simulation environment. Please refer to the simuPOP homepage http://simupop.sourceforge.net for details.

Installation

simuPOP is distributed under a GPL3 license. Starting from simuPOP 1.1.8, it supports only Python 3 (3.5 and up) on windows, mac and Linux systems.

simuPOP is part of the conda-forge, if you use Anaconda Python 3, you can install simuPOP with command

conda install -c conda-forge simuPOP

If you would like to use simuPOP with Python 2.5 - 2.7, please compile simuPOP from source, using either simuPOP 1.1.7, or the Python 2.x branch of simuPOP. Note that features that has been marked deprecated (e.g. simuOpt.Param, simuPOP.plotting) in simuPOP 1.1.7 and earlier are removed in simuPOP 1.1.8+, so simuPOP 1.1.7 would be your best bet for the execution of legendary simuPOP scripts.

Documenation

The user guide and reference manual of simuPOP is available at http://bopeng.github.io/simuPOP/. simuPOP is also introduced in the following two books:

1. Forward-Time Population Genetics Simulations: Methods, Implementation, and Applications by Bo Peng, Marek Kimmel and Christopher I Amos, published by Wiley & Sons Inc, and available at Amazon and other bookstores.
2. Bioinformatics with Python Cookbook by Tiago Antao, available at Amazon

Change Log since 1.1.7

simuPOP 1.1.10

• #70: Fix compatibility with Mac OS using libc++ instead of libstdc++.

simuPOP 1.1.9

• #28: Fix a segmentation fault when providing a non-existent VSP index
• #31: Allow operator DiscardIf to accept a probability in addition to True/False
• #35: Add a weightBy parameter to allow HeteroMating to produce offspring subpopulation with weights determined by not only the size of the parental subpopulation, but also by for example number of mating pairs.
• #49: Fix output of loci positions in MS and other formats.