1. Error Checking for Linkage Analyses

2. Pedcheck
Level 1 does checking on the nuclear family level. It will detect the following errors.
A child and parent's alleles are incompatible.
A person is half-typed. This is checked because current programs cannot handle this situation.
More than 4 alleles in a sibship.
More that 3 alleles in a sibship when there is a homozygous child.
The allele is out of bounds, if any is specified.
That in X-linked pedigrees, males are scored as homozygous.

3. Pedcheck
Level 2 is guaranteed to detect if there is an inconsistency. Thus, if there are NO Level 2 errors detected, then the pedigree is Mendelian consistent.
Level 3 determines the "critical genotypes". They are typed individuals who when set to "unknown" then remove the inconsistency in the pedigree.

4. ILINK
ILINK is a program for maximum likelihood estimation of recombination fractions for an arbitrary number of marker and disease loci. For two loci, the program determines the maximum lod score in addition to the recombination estimate.

5. MLINK
MLINK is a program for calculation of lod scores and risk with two or more loci.

6. Simwalk
Haplotype analysis estimates the most likely set of fully typed maternal and paternal marker haplotypes at each individual in the pedigree. This provides an estimate for the genetic descent state with the largest likelihood, i.e., the best haplotype vector for the pedigree, which is the output.

7. Merlin
MERLIN finds genotypes that provide information about gene flow in a pedigree that contradicts information provided by other available data. MERLIN considers all available data simultaneously (not just pairs of individuals) so that error detection improves in accuracy in larger pedigrees.

8. Merlin