JAMP (Joint Genetic Association of Multiple Phenotypes) uses raw data as input and evaluates the multivariate evidence for association of multiple phenotypes for a SNP. It also provides a family-wise corrected P-value.
The jointSeg R package implements functions to quickly segment multivariate signals into piecewise constant profiles. A typical application is the joint segmentation of total DNA copy numbers and allelic ratios obtained from Single Nucleotide Polymorphism (SNP) microarrays in cancer studies.