SPLATCHE2 is a program to simulate the demography of populations and the resulting molecular diversity for a wide range of evolutionary scenarios. The spatially-explicit simulation framework can account for environmental heterogeneity and fluctuations, and it can manage multiple population sources. A coalescent-based approach is used to generate genetic markers mostly used in population genetics studies (DNA sequences, SNPs, STRs, or RFLPs). Various combinations of independent, fully or partially linked genetic markers can be produced under a recombination model based on the ancestral recombination graph. Competition between two populations (or species) can also be simulated with user-defined levels of admixture between the two populations. SPLATCHE2 may be used to generate the expected genetic diversity under complex demographic scenarios and can thus serve to test null hypotheses. For model parameter estimation, SPLATCHE2 can easily be integrated into an Approximate Bayesian Computation (ABC) framework.
How to cite SPLATCHE 2
Ray N, Currat M, Foll M, Excoffier L. SPLATCHE2: a spatially-explicit simulation framework for complex demography, genetic admixture and recombination. Bioinformatics 2010, Vol 26(3): 2993-2994
New version 2.01 (released in january 2012)
- important bug correction: the transition rate parameter was not used in the simulation, but this is now corrected.
- important bug correction: when dynamic environments were considered, the specific carrying capacity and frictions attribute to rivers and coastlines were only valid during the first dynamic periods. This is now corrected and these specific values are now valid throughout the simulation and the different periods.
- minor graphical improvements or corrections.
- minor improvements in output files.
Download SPLATCHE 2.01
Graphical version: download Version 2.01 Windows Graphical.
Console version: download Version 2.01 Windows Console.
Console version: Version 2.01 Linux Console (32 and 64 bits versions).
Example settings files
Download 1 layer dataset
Download 2 layers dataset
Information about how to use SPLATCHE 2 can be found in the User Manual.
We thank Daniel Wegmann, Seraina Klopfstein, Samuel Neuenschwander, Grant Hamilton, Guillaume Laval, Pierre Berthier, Stefano Mona and Anna Sramkova for technical help and useful discussions throughout the development of SPLATCHE2. This work was partly supported by a EU/FP7 grant No 226852 (SCALES).
Read the most frequently asked questions about SPLATCHE2.
First version: SPLATCHE 1.1
The web site of version 1.1 can be found here.
Publications citing SPLATCHE
See a list of the publications citing SPLATCHE version 1 (listed in Google Scholar)
See a list of the publications citing SPLATCHE version 2 (listed in Google Scholar)
If you encounter any bug using SPLATCHE 2, please send an email to Mathias Currat.