README.md

Minimal simuPOP example

• simupop_example.py: A simple walk-through of using with simuPOP.

Single locus example

After this, tree.hdf5 will contain a tree-sequence with a single selected loci in the middle of block of length L.

python3 examples.py -N 5000 -L 10000 -g log.txt -T 50 -t tree.hdf5

The selection coefficient is drawn from a gamma distribution (parameters can be passed to the script) but one could also edit the script, replacing the callable GammaDistributedFitness with a simple function using logic like this section and hard-coding s.

Setup

Follow the steps in the main README to set up a conda environment for ftprime.