SPLATCHE 2

SPatiaL And Temporal Coalescent in a Heterogeneous Environment, Version 2

Nicolas Ray, Mathias Currat, Matthieu Foll, Laurent Excoffier

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

NOT UPDATED ANYMORE ! New version 3 is here

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

Windows

Graphical version: download Version 2.01 Windows Graphical.

Console version: download Version 2.01 Windows Console.

Linux

Console version: Version 2.01 Linux Console (32 and 64 bits versions).

Example settings files

Download 1 layer dataset

Download 2 layers dataset

User manual

Information about how to use SPLATCHE 2 can be found in the User Manual.

Acknowledgments

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).

FAQ

Read the most frequently asked questions about SPLATCHE2.

Publications citing SPLATCHE 2

See a list of the publications citing SPLATCHE version 2 (listed in Google Scholar)

Bug report

If you encounter any bug using SPLATCHE 2, please send an email to Mathias Currat.

© 2010-2018 Mathias Currat, Nicolas Ray, Matthieu Foll, Laurent Excoffier | Last modified: 30.01.2012