To load a new dataset in CARTHAGENE, the only command is the dsload command which must be followed by the name of the file to load. The dataset loaded will get a numerical id (reported when the dataset is loaded and which can be requested later using the dsinfo command).
To do multiple populations mapping, two merging commands can be used. Each of these commands takes as arguments the numerical id of the 2 datasets merged (if you want to merge more than 2 datasets together, simply use the commands repeatedly).
These two commands can be used together and repeatedly. Imagine for example that you have 2 radiated hybrid panels with the same irradiation level along with 2 genetic datasets available. You can ``mergen'' the 2 RH datasets together (assuming that the same irradiation level will lead to the same distances) and also ``mergen'' the 2 genetic datasets. This will give you two merged datasets which can be again merged using the mergor command. This gives a single dataset that merges all 4 datasets. All mapping commands on this dataset will report two maps: one RH consensus map and one genetic consensus map with the guarantee that they use a consistent markers order.