SPLATCHE 3

SPatiaL And Temporal Coalescent in a Heterogeneous Environment, Version 3 (2019)

Mathias Currat, Miguel Arenas, Claudio S Quilodràn, Laurent Excoffier, Nicolas Ray

SPLATCHE 3 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 serial coalescent-based approach is used to generate genetic markers used in population genetics and genomics 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. SPLATCHE 3 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, SPLATCHE 3 can easily be integrated into an Approximate Bayesian Computation (ABC) framework.

How to cite SPLATCHE 3

Currat M, Arenas M, Quilodran, CS, Excoffier L and Ray N (2019) SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal. Bioinformatics, in press.

Download SPLATCHE 3.0 (January 2019)

MS Windows

GUI: Download Version 3.0 MS Windows Graphical version (GUI).

Console: Download Version 3.0 MS Windows Console version.

Linux

Console: Download Version 3.0 Linux Console version.

MacOS

Console: Download Version 3.0 MacOS Console version.

Example settings files

Download 1 population layer input dataset

Download 2 population layers input dataset

User manual

Information about how to use SPLATCHE 3 can be found in the User Manual.

Acknowledgments

We thank Nuno Silva, Jeremy Rio, Nicolas Broccard, Stephan Peischl, Isabel Alves, Jason Brown and David Roessli for technical help and input throughout the development of SPLATCHE 3. This work was supported by the Swiss National Science Foundation [31003A-156853 to MC; 31003A_182577 to MC] and by the Spanish Government [RYC-2015-18241 to MA; ED431F 2018/08 to MA].

FAQ

Read the most frequently asked questions about SPLATCHE 3.

Previous versions

Serial SPLATCHE

Version used in Silva NM, Rio J & Currat M. "Investigating population continuity with ancient DNA under a spatially explicit simulation framework". BMC Genetics (2017) 18:114 and Silva, Rio, Kreutzer, Papageorgopoulou and Currat. ""Bayesian estimation of partial population continuity using ancient DNA and spatially explicit simulations".

SPLATCHE 2.1

The web site of version 2.1 can be found here.

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

SPLATCHE 1.1

The web site of version 1.1 can be found here.

See a list of the publications citing SPLATCHE version 1 (listed in Google Scholar)

Publications citing SPLATCHE 3

See a list of the publications citing SPLATCHE version 3 (listed in Google Scholar)*

*not currently available!

Bug report

If you encounter any bug using SPLATCHE 3, please send an email to Mathias Currat.

©2019 Mathias Currat | Last modified: 14.05.2019