simulator_msms {coala}

Simulator: msms

Description

This adds the simulator 'msms' to the list of available simulators. To add msms, you need to download the jar file and have Java installed on your system.

Usage

activate_msms(jar = NULL, java = NULL, priority = 200, download = FALSE)

Arguments

jar

The path of the msms jar file.

java

The path of the java executable on your system.

priority

The priority for this simulator. If multiple simulators can simulate a model, the one with the highest priority will be used.

download

If set to TRUE, coala will try to download the msms jar file. In that case, the jar argument is not required.

References

Gregory Ewing and Joachim Hermisson. MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus. Bioinformatics (2010) 26 (16): 2064-2065 doi:10.1093/bioinformatics/btq322

See Also

Other simulators: simulator_ms, simulator_scrm, simulator_seqgen

Examples

# Download and activate msms (requires Java)
## Not run: activate_msms(download = TRUE)