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popdisp

population dispersals: method to estimate allele frequencies in a region considering geographical locations of sampling sites, the nonequal number of samples in locations, and, most crucially, possible ways of dispersals within a region. It utilizes hierarchical Bayesian Modeling, compositional nature of frequencies and the Wright-Fisher model of drift.

Initial data

Initial data contais two parts:
(1) covariance matrix between samples based on the hypothetical dispersals within a region: data/cov_mx
(2) allele frequencies in locations within regions data\samples

Pipeline (running the test)

To demonstrate the test, please run:

  • estim_routes.py to get estimates of allele frequencies
  • get_stat.py to get statisticks for mcmc

Requirements

To run popdisp methods, you need Python 3.4 or later. A list of required Python packages that the popdisp depends on, are in requirements.txt.

Authors

Anna Igolkina developed the popdisp package, e-mail.

License information

The popdisp package is open-sourced software licensed under the MIT license.

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