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Coala is an R package for simulating biological sequences accordingto a given model of evolution. It can call a number of efficientsimulators based oncoalescent theory.All simulators can be combined with the programseq-gen to simulate finitesite mutation models.Coala also directly imports the simulation results intoR, and cancalculate various summary statistics from the results.

The package can be installed from CRAN using

install.packages("coala")

If you want to use the simulation programsms,msms orseqgen,they need to be installed separately. This is described in the"Using External Simulators" vignette andinthe wiki.

Coala comes with avignettethat explains the packages concepts and is a good place to start. It also has avignette containing a few example applications.

Detailed information about coala's functions is provided via R's help system.Callhelp(_function_) in R to view them. They usually also contain examples and further links.

TheABC vignettegives an example on how coala can be used to conduct the simulations forApproximate BayesianComputation.

Also take a look at theproject wiki for additionalresources.

In the following example, we create a simple panmictic model, simulate it andcalculate the site frequency spectrum (SFS) of the simulation results:

model<- coal_model(sample_size=10,loci_number=2)+  feat_mutation(5)+  sumstat_sfs()result<- simulate(model)result$sfs# [1] 15 12  1  4  0  1  0  2  0

More examples can be found in theexamples vignette.

If you encounter problems when usingcoala, pleasefile a bug report or mail tocoala-pkg (at) googlegroups.com.

The package supports the coalescent simulatorsms,scrm andmsms.All simulators can be combined withseq-gen to simulate finite sitesmutation models. The programsmsms andseq-gen must beinstalledmanually.The R version ofscrm should be installed automatically,and the R versionms if the packagephyclust is installed.

To follow or participate in the development ofcoala, please install thedevelopment version from GitHub using

devtools::install_github('statgenlmu/coala')

on Linux and OS X. This requires that you havedevtools and a compiler orXcode installed. Bug reports and pull request on GitHub are highly appreciated.Theextending coala vignettecontains information on how to create new summary statistics and add simulatorsto coala. Thewiki also contains a fewresources for developers.