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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.
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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.
next up previous contents
Next: Building a project. Up: Front End Previous: Download and installation.   Contents
Jonathan Pritchard 2003-07-10