Clusthaplo: a plug-in for MCQTL to enhance QTL detection using ancestral alleles in multi-cross design.

We enhance power and accuracy of QTL mapping in multiple related families, by clustering the founders of the families on their local genomic similarity. MCQTL is a linkage mapping software application that allows the joint QTL mapping of multiple related families. In its current implementation, QTLs are modeled with one or two parameters for each parent that is a founder of the multi-cross design.