Specify a threshold for the grouping value of the estimated recombination fraction when using Minimum Recombination Grouping. Linkage groups are formed by assigning a marker to a group only if the marker has a recombination fraction less than or equal to this specified value with at least one marker already in the linkage group. If a marker is not linked to any markers in a linkage group based on this value, then that marker is placed in a new linkage group. This value determines the number of linkage groups.
The Minimum Spanning Tree algorithm builds a tree connecting markers with edges proportional to their recombination fraction (the markers with the smallest recombination values are joined first). Once the minimum length of a potential edge between markers becomes larger than the specified threshold or the minimum number of linkage groups value (equal to the number of framework groups when Minimum Recombination Grouping is used only with a framework) is surpassed, the algorithm stops forming edges between markers, and linkage groups are then comprised of markers with connected edges.
Note: If a Framework Linkage Group Variable is specified, the minimum number of linkage groups is automatically set to the number of defined framework groups.
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