This repository contains python modules and command line scripts to support testing for selective neutrality using relative likelihood. It enables application of the methods described in Simon and Huttley 2021 A New Likelihood-based Test for Natural Selection bioRxiv doi = 10.1101/2021.07.04.451068. For other software supporting that paper, but not required for applications, see https://github.com/helmutsimon/NeutralityTest. Functions available include:
- calculate statistic for relative neutrality, ρ, which is a relative likelihood of two models;
- generate variates corresponding to the Wright-Fisher model and the `uniform distribution' model;
- calculate Tajima's D (for comparison purposes);
- calibrate ρ, that is, find the threshold corresponding to a desired false positive (Type I error) rate; and
- generate variates corresponding to a piece-wise constant demographic history.
Installation is currently from test.pypi. Use: python3 -m pip install --index-url https://test.pypi.org/simple/ --no-deps selectiontest-helmutsimon --upgrade
See https://selectiontest.readthedocs.io/en/latest/index.html