Contents

Overview.

The front end organizes data analysis into ``projects''. Each project is connected to a single data file. When creating a project, the user also provides information that specify how to read the data file (number of loci, number of individuals, etc). These are characteristics of the data file, and are always the same within this project. Each project also contains one or more ``parameter sets''. These allow the user to specify the details of the MCMC runs, including the number of repetitions, burnin length, etc, as well as specifying the model of analysis (e.g., whether to allow admixture, models of allele frequencies, etc). The user can then run the Markov chain at chosen values of $K$, for a given parameter set. Figure 1 shows an example of the components of a project called ``popdata''. 

 

 
                                                  Figure 1: Example showing the components of a project. Project Data is the data file; Project
                                                  Information specifies data file format. Simulation Summary  provides a summary of  all MCMC
                                                  simulations run as part of this project. Parameter Sets consists of three   groups of MCMC runs
                                                  that used different parameter settings: ps1, ps2, and ps3; each  of these shows the Settings, as well 
                                                  as a list of results for completed MCMC runs with these parameter values. The user can click on
                                                  any  of these to see details
                                              

The program can then be run, using these parameter values. The front end stores various summaries of the results, including a number of graphical plots, described below.