The filename stem is an important concept in the usage of this package. Beginning with version 1.12, the programs utilize the filename stem qtlcart. All files are then named using this stem and filename extensions relevant to the filetype. For example, if the -X option is followed by corn, then when new files are created, they will have the stem corn followed by a logical extension. An example would be corn.map for a genetic linkage map. With some practice, you will be able to know the contents of a file by its extension.