The analysis programs are divided into two groups. The first group can be used for general pedigrees with marker and disease loci. The programs for general pedigrees allow linkage analysis with an arbitrary number of loci, either sex-linked or autosomal. 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. The pedigree and genotypic data must be entered into a single file. If you are entering data with a text editor, please consult section 2.8 of this manual for the format to use. Please consult section 2.6 for the format of this file. Verify that your problem does not exceed the limits established when the program was compiled.