popgenmethods/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

First, make sure you have Python 2.7, pip, and numpy installed. Then type

pip install .

from the root directory.

Getting started

See tutorial.py to get started.

See this repository to reproduce the results in the paper.

momi2

This package is now superceded by momi2, which is the recommended version to use. New features include pulse migration and maximum likelihood inference.

momi's Issues

'OutDegreeView' object has no attribute 'items'

Dear popgenmethods,

I have the following issue. Thanks in advance for your reply.
Best regards,
Cesar

$ git clone https://github.com/popgenmethods/momi.git
$ cd momi
$ python tutorial.py
Printing SFS entries for three epoch history
[3.46922568239798, 0.6905041803193086, 0.28925918566082426, 0.18382307646826954, 0.14630222131940324, 0.12951430246441245, 0.12025482991358812, 0.11413280441137114, 0.10950608451603584, 0.10569664740756339, 0.10239483376447593, 0.09944275368450997, 0.0967502566421602, 0.09426034418677022, 0.09193397689474075, 0.08974285562158904, 0.08766566223553252, 0.08568590655924462, 0.0837905841160356]

Printing truncated SFS for middle epoch
[0.1874478923928087, 0.08769197071896163, 0.05459923171604704, 0.038169703103527165, 0.028403412493141773, 0.021967054055764115, 0.017432083759685326, 0.014084243180327256, 0.011526734103605961, 0.009521488367390292, 0.007917017789540414, 0.0066123391320212456, 0.005537549081665744, 0.004642724239263062, 0.0038912611130865783, 0.003255713614919281, 0.00271509967519516, 0.0022531056531559686, 0.0018568577754385516]
Traceback (most recent call last):
File "tutorial.py", line 46, in
demo3 = Demography.from_newick(newick_str)
File "/media/cesarpc/momi/demography.py", line 13, in from_newick
t = cls(_newick_to_nx(newick, default_lineages))
File "/media/cesarpc/momi/demography.py", line 25, in init
if not all('lineages' in nd[k] for k in self.leaves):
File "/media/cesarpc/momi/util.py", line 44, in get
value = obj.dict[self.func.name] = self.func(obj)
File "/media/cesarpc/momi/demography.py", line 66, in leaves
return set([k for k, v in self.out_degree().items() if v == 0])
AttributeError: 'OutDegreeView' object has no attribute 'items'