Resources for Kelleher et al., "Efficient pedigree recording for fast population genetics simulation"

• The C++ source code used in the paper is found in the fwdpy11_arg_example folder of this repository. The contents of that directory are a simple copy of what can be found in the repository where it was developed. You will find instructions in the README of that subdirectory.
• The flexible Python implementation (which uses simuPOP) is available in the ftprime repository as version 0.0.6
• We have generated a set of tutorials on integrating forward simulations with the simplification algorithm as implemented in msprime

Reproducibility

The results in this paper were generated with what ultimately became msprime version 0.5.0. The current version of msprime (0.6.x) contains a faster and more streamlined version of the algorithm that gives the same results.

Algorithm reference implementations

We provide some reference implementations of the algorithms described in the paper. To ensure that these will work as easily as possible in the future, they require mprime >= 0.6.0.

• The file sims/simplify-alg.py contains a direct Python implementation of the simplify algorithm (algorithm S).

• The file sims/wf-figures.py contains a direct Python implementation of Wright-Fisher forwards time simulation (algorithm W).