thomas-a-neil/momi

MOran Models for Inference

momi

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.

Installation

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

Getting started

See tutorial.py to get started.

See this repository to reproduce the results in the paper.

Upcoming features

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 2016, to be accompanied with a second paper.