| Token | Followed by | Means |
| -Cross | string | type of cross See (1.1.2) |
| -traits | integer | number of traits |
| -otraits | integer | number of categorical variables |
| -SampleSize | integer | sample size |
| -case | yes or no | whether comparisons are case sensitive |
| -TranslationTable | table | table for marker translation |
| -skip | Tells Rcross to skip everything until an | |
| -unskip | which is the end of the -skip. These | |
| cannot be within a -start to -stop block | ||
| -start | string | Start of a block of markers, traits or otraits |
| -stop | End of a block | |
| -end | End of the file |
The -case token changes how strings are matched. Put a yes here if comparisons are case dependant. With no, all names of individuals, markers and traits are converted to lower case to make comparisons.