linkage user's guide (version 5.2)
1.1 General Features
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. Incomplete penetrance and liability
(risk) classes can be specified for affection-status phenotypes,
and several correlated quantitative measurements can be incorporated
simultaneously. 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 following is a quick guide to the programs available for some
common applications:
-
Estimation of recombination rates and calculation of the
maximum lod score:
-
ILINK for general pedigrees;
CILINK for three-generation
reference pedigrees.
-
Lod score tables and risk analysis:
-
MLINK .
-
Location scores:
-
LINKMAP for general pedigrees;
CMAP for three-generation reference pedigrees.
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