The programs for general pedigrees allow linkage analysis with an arbitrary number of loci, either sex-linked or autosomal. In addition to marker loci, affection-status or quantitative phenotypes can be considered. Program options allow for mutation at a single locus, with separate male and female mutation rates, and for linkage disequilibrium between different loci.
Pedigrees can contain one or more inbreeding loops.
Other programs in the analysis package are optimized for rapid likelihood calculations with codominant data, in reference three-generation families.