This repository implements the algorithm and results in this paper. In particular, it 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.

Prerequisites:

• Scientific distribution of Python 2.7, e.g. Anaconda, Enthought Canopy
  • Alternatively, custom installation of pip, and the SciPy stack
• gcc

To install, simply type

pip install momi

See tutorial.py to get started.

The results from the paper are implemented in paper_results/.

The current version of momi is 1.2.3. Upcoming features for the next version (2.0.0) of momi are:

• Pulse migration/admixture
• Parameter inference via gradient descent, automatic differentiation
• Improvements to user interface

Version 2.0 will be released in early 2016, to be accompanied with a second paper.