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arg

arg software from BSc thesis

arg: Distributions of times to MRCAs in the Ancestral Recombination Graph

arg is a collection of Octave/MATLAB scripts to compute numerically as well as simulate distribution functions for times to most recent common ancestors in the specific population genetics model introduced as "Ancestral Recombination Graph" (ARG) by Griffiths 1991. It was developed in the course of my B.Sc. thesis "Distributions of times to most recent common ancestors in coalescents with recombination" in mathematics at Technische Universitaet Berlin (Berlin Institute of Technology). For details on the ARG model and the concepts of times to most recent common ancestors, refer to the thesis text included in the documentation folder.

Installation and Usage

Some numerical functions of the software require the additional installation of parts of expokit by Roger Sidje. This software is not free of copyright, refer to their page for the license. To run arg with expokit, you need to download mexpv.m from http://www.maths.uq.edu.au/expokit/matlab/mexpv.m into the software subfolder of this folder and you're done.

The script run_arg.m is the main entry point to the software and manages all computations, as well as loading, saving and plotting of the results. The intended usage for this script is to change the parameters to the desired values in its code, let it run and obtain plotted distribution functions from it. Detailed documentation can be found in the Software Appendix of the thesis text, pp. 60ff.

Pre-computed results

Since computations of the generator matrices for the distributions might take very long, several pre-computed results are included in the results subfolder.

References

For references mentioned above see the References section in doc/tmrcadistributions.pdf, starting p. 48. As a general reference, refer to the text of doc/tmrcadistributions.pdf, the thesis for which this software was written.