Prune takes a genetic linkage map and a data set as input. The user can either eliminate some of the data (markers or traits), bootstrap, permute or simulate missing data. Table 2.5 summarizes the command line options for Prune.
Originally, Prune was strictly a command line program. In adding the interactive menu it became necessary to add a second level of interaction. When Prune is invoked in the interactive mode, the user will see a menu in which all the parameters of Table 2.5 can be set. The user will then proceed to another interactive menu in which data manipulation can be performed. The second menu will list actions that can be taken. The user selects an action and provides the proper values at which time the action is taken. This second menu is in a loop. The user can continue to take actions until the option to quit is chosen. At the end, the data set is printed out. A few actions can be done automatically. They are bootstrapping, permuting and simulating missing data. These are provided so that Prune can be run in a batch file for permutation tests or bootstrap experiments.
The output files of Prune may include a genetic linkage map and a data file. If markers had been eliminated, then the linkage map is regenerated to take this into account. The new output files will have the extensions .mpb and .crb, and filename stems specified by the -o option.