Running simulations.

Now that you have a parameter set, you can start the program running by going to [Parameter Set] $\rightarrow$[Run]. You'll be asked to set the number of populations ($K$). You can also stop simulations in the same place ([Parameter Set] $\rightarrow$[Stop]). Text data will be printed to the console at the bottom of the screen (Figure 6). You can also view real-time time-series plots of various key summary statistics: $F_{ST}$, $\alpha$, likelihoods, etc, (Figure 7). Once you have more than one parameter set, you need to specify which one you want to use for new MCMC runs. At any time, one parameter set is designated as ``active'' (see the left-hand window). You can switch the active parameter set by going to [Parameter Set] $\rightarrow$[Parameter Set List], and highlighting the appropriate choice.

Figure 6: The run-time output is shown in the bottom console

Figure 7: Time series plot of $F_{ST}$.