Parameters | Genetics | Define linkage groups based on the:

Define linkage groups based on the:
Use the radio buttons to specify an option for defining linkage groups.
Available options are listed in the table below:
The automated hierarchical clustering algorithm will assign markers into groups until the number of groups equals the value specified using the Number of Linkage Groups parameter.
To Specify How Linkage Groups are to be Defined:
Make sure that Automated Hierarchical Clustering is specified for Choose a linkage grouping method.