R/qtl-MQM has the following advantages:

\itemize{
  \item Higher power to detect linked as well as unlinked QTL, as long as the QTL explain a reasonable amount of variation
  \item Protection against overfitting, because it fixes the residual variance from the full model. For this reason more parameters (cofactors) can be used compared to, for example, CIM
  \item Prevention of ghost QTL (between two QTL in coupling phase)
  \item Detection of negating QTL (QTL in repulsion phase)}
