This repository implements the algorithm in this paper (preprint here).
In particular, this repository computes the expected joint site frequency spectrum (SFS) for a tree-shaped demography without migration, via a multipopulation Moran model.
It also computes the "truncated site frequency spectrum" for a single population, i.e. the frequency spectrum for mutations arising after a certain point in time. This can be used in both Moran and coalescent approaches to computing the multipopulation SFS.
First, make sure you have Python 2.7, pip, and numpy installed. Then type
pip install .
from the root directory.
See tutorial.py to get started.
See this repository to reproduce the results in the paper.
This package is now superceded by momi2, which is the recommended version to use. New features include pulse migration and maximum likelihood inference.