This program takes as input an XML command file and returns as output log files. The log files record a sample of the states that the Markov chain encountered. This output must be analyzed to produce estimates of the parameters of interest (evolutionary rates, divergence times, population sizes and tree topologies). A careful examination of this output is also necessary to determine whether the Markov chain has been run long enough to obtain accurate estimates of the parameters. Part of the post-analysis is usually performed by a graphical application called Tracer.