Welcome to Genome Size Evolution project!

Scientific motivation:

This is an implementation of a model presented in the papers:

Bentkowski P, van Oosterhout C, Mock T (2015) A model of genome size evolution for prokaryotes in stable and fluctuating environments. Genome Biol Evol evv148. http://dx.doi.org/10.1093/gbe/evv148 (Open Access)

Bentkowski P, van Oosterhout C, Ashby B, Mock T. (2016). The effect of extrinsic mortality on genome size evolution in prokaryotes. ISME Journal, Epub ahead of print. https://dx.doi.org/10.1038/ismej.2016.165 (Open Access)

The "Master" branch includes the newest stable development. For the ORIGINAL code from the publication check this branch:

As_in_Bentkowski_et_al_2015_GBE

Software used:

For writing this project I have used:

• NetBeans for coding, https://netbeans.org/
• Doxygen and Doxywizard for generating documentation: http://www.stack.nl/~dimitri/doxygen/

Compilation:

To compile one needs GNU Scientific Library, http://www.gnu.org/software/gsl/ , installed. It's in any GNU/Linux repos. To read the documentation you need to download the thing first.

In the directory '00_CurrentCode' one can find nbproject directory. If you running NetBeans as well, you can load a NetBeans project from there.

Documentation:

Directory 'Doc' contains documentation in HTML format. Find file 'index.htm' and run it in a browser to view the docs. Do not alter files in Doc manually, as they are generated automatically by Doxygen. File 'Doxyfile' contains the set-up for Doxygen (you mignt need to tweek some dir paths at your local workstation - Doxywizard is a GUI front-end to Doxygen one might find useful).

Fairly accurate description what the model does can be found in the documentation (directory 'Doc') or in Chapter 2 " Construction of the model and testing the parameter space" of Piotr Bentkowski's PhD thesis: https://ueaeprints.uea.ac.uk/50553/

Auxiliary code:

Directory '01_PyScrips' contains Python scripts used for plotting and analysis of the output files. They are rather poorly documented - sorry :-(

• SigleRuns - scripts for processing single simulation.
• MultiRuns - scripts for processing and comparing a larger number of simulations, often varying in parameter set-up between each other.
• GenotypeAnalysys - scripts for counting mutations and evolution related stuff.

Acknowledgements:

All simulations were carried out on the High Performance Computing Cluster supported by the Research and Specialist Computing Support service at the University of East Anglia. http://rscs.uea.ac.uk/high-performance-computing