A method is given to resolve pleiotropy from linkage; to detect and estimate recombination free of incomplete penetrance, etiological heterogeneity, and other phenomena; and to estimate gametic frequencies for the main and test loci jointly. Large pedigrees, a liability indicator specifying risk groups (based on age, sex, or other factors), gametic disequilibrium, different recombination values in the two sexes, multiple alleles at the test locus, and a mixture of linked and unlinked marker loci are provided for. Parametrization of the marker locus is the same as for segregation analysis with pointers. The output includes standard errors, likelihood ratio tests of hypotheses, and a standard lod table for each sex separately. A model of closely linked complementing factors which can simulate recombination is also considered.