Welcome to GADMA’s documentation!

GADMA [Noskova2020] implements methods for automatic inference of the joint demographic history of multiple populations from genetic data.

GADMA is a command-line tool. It presents a series of launches of the global and local search algorithms and infers demographic history of multiple populations. The automatic inference handles up to three populations.

GADMA provides choice of several engines for the demographic inference:

GADMA implements two base global search algorithms:

  • Genetic algorithm — the most common choice of optimization,
  • Bayesian optimization — for demographic inference with time-consuming evaluations, e.g. for four and five populations using moments or ∂a∂i.

GADMA features variuos optimization methods (global and local search algorithms) which may be used for any general optimization problem.

Base usage of GADMA via command-line:

$ gadma --help

GADMA version 2.0.0 by Ekaterina Noskova (ekaterina.e.noskova@gmail.com)
Usage:
    gadma   -p/--params     <params_file>
            -e/--extra      <extra_params_file>


Instead/With -p/--params and -e/--extra option you can set:
    -o/--output     <output_dir>            output directory.
    -i/--input      <in.fs>/<in.txt>/       input data for demographic inference
                    <in.vcf>,<popmap>       (AFS or dadi format or VCF).
    --resume        <resume_dir>            resume another launch from <resume_dir>.
    --only_models           flag to take models only from another
                            launch (--resume option).

    -h/--help               show this help message and exit.
    -v/--version            show version and exit.
    --test                  run test case.

In case of any questions or problems, please contact: ekaterina.e.noskova@gmail.com

What is parameter file of GADMA?

A parameter file is a simple text file (created in a text editor, such as Notepad), which contains a list of parameters/options/settings with their assigned values. Create a parameter file that reflects your particular options. Hereinafter, as an example, the name of your parameter file will be defined as param_file.

Note

Each section of user manual contain list of related options for parameter file with small description.

Full example of parameter file could be found in a section Example parameters file.

Indices and tables