Prune is part of the QTL Cartographer suite of programs.

Prune allows one to eliminate markers or traits. It removes the data from the file containing the cross and reconstructs the molecular map.
It requires a molecular map that could be a random one produced by Rmap, or a real one in the same format as the output of Rmap.

Prune also does bootstraps, permutations and simulations of missing or dominant markers.