The best map in an existing Pareto frontier is obtained by the paretobestprint (order is given) and paretobestprintd (order and distances are given) commands. These commands have a special lambda parameter which corresponds to the expected number of breakpoints between the true order and the reference order. In general, this number is unknown (we don't know the true order!), and should be set to its minimum value (1 or the minimum number of obligate breakpoints if greater than one^{2.9}). However, if the evolutionary distance can be assessed by some external (phylogeny) methods, then the knowledge of the number of breakpoints deduced from this evolutionary distance can slightly improve the quality of the best map found by paretobestprint and paretobestprintd.
The command paretoplotg gives a graphical view of the Pareto frontier (that can be zoomed, printed or saved). It draws the traditional and comparative mapping criteria for the maps in the frontier. An example is given in Figure 2.2 (the red triangle corresponds to the best map). By clicking on any point in the frontier, a comparative mapping view can be obtained between the corresponding map and the reference order. An example is given in Figure 2.2 (the distance between adjacent markers can be fixed or proportional).
The command paretosave allows to save the current Pareto frontier, for future use.

Thomas Schiex 20091027