PSC-vs-RFI

Introduction

This website and the script hosted here is supporting the Masters thesis I wrote under supervision of Laurent Excoffier at the University of Bern.

The script hosted here is written in bash, which is the most common linux shell. This means that running the script under a Windows OS requires a bash emulator, e.g. Cygwin (http://www.cygwin.com), where the script should run without any problems.

To set simulation parameters and prior distributions, open the main script, run-psc-vs-rfi.sh, with the text editor of your choice and modify the arguments there.

References

I wrote the script in bash because the most important parts are done by other programs, which deserve most of the credits:

For ABCtoolbox and ABCSampler, please cite
Wegmann D, Leuenberger C, Neuenschwander S & Excoffier L (2009):
ABCtoolbox: A versatile toolkit for Approximate Bayesian Computation,
Bioinformatics, submitted

For Simcoal, please cite
Excoffier L, Laval G & Schneider S (2005):
Arlequin ver 3.0: An integrated software package for population genetic data analysis,
Evolutionary Bioinformatics Online, 1, 47-50

For arlsumstat and abcEst, please cite
Laval G & Excoffier L (2005):
Simcoal 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with complex history,
Bioinformatics 20, 2485-2487

For R, please cite
R Development Core Team (2009):
R: A language and environment for statistical computing,
R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org.

Download

The script with all applications is available as a zip File.
Please also have a look at the readme file.
For the most recent versions of the applications used, please use the following links: