gadma 2.0.0rc14

Genetic Algorithm for Demographic Inference

GADMA

Welcome to GADMA v2!

GADMA implements methods for automatic inference of the joint demographic history of multiple populations from the genetic data.

GADMA is a command-line tool. Basic pipeline presents a series of launches of the genetic algorithm folowed by local search optimization and infers demographic history from the Allele Frequency Spectrum of multiple populations (up to three).
GADMA features variuos optimization methods (global and local search algorithms) which may be used for any general optimization problem.

GADMA provides choice of several engines of demographic inference (this list will be extended in the future):

• ∂a∂i developed by Ryan Gutenkunst
• moments developed by Simon Gravel

GADMA is implemented by Ekaterina Noskova ([e-mail])

GADMA is now of version 2! See Changelog.

Documentation

Please see documentation for more information including installation instructions, usage, examples and API.

Contributors

• Ekaterina Noskova

• Vladimir Ulyantsev

• Pavel Dobrynin

Getting help

F.A.Q.

Please don't be afraid to contact me for different problems and offers via email [e-mail]. I will be glad to answer all questions.

Also you are always welcome to create an issue on the GitHub page of GADMA with your question.

Citations

Please see full list of citations in documentation.

If you use GADMA in your research please cite:

Ekaterina Noskova, Vladimir Ulyantsev, Klaus-Peter Koepfli, Stephen J O’Brien, Pavel Dobrynin, GADMA: Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data, GigaScience, Volume 9, Issue 3, March 2020, giaa005, https://doi.org/10.1093/gigascience/giaa005