linkage user's guide (version 5.2)
3.0 Overview
The analysis programs fall into two groups. Programs in the
first group (ILINK, MLINK, LINKMAP, LODSCORE)
are designed for calculations in general pedigrees.
Those in the second group
(CILINK, CMAP ) are optimized for three-generational pedigrees
with codominant markers; they cannot be used for general pedigrees
or for disease loci. CILINK and CMAP are the equivalent of
ILINK and LINKMAP for three-generational pedigrees. (The "C"
preface refers to the CEPH reference panel of families which has
this three-generation structure.)
Each analysis program is described in a separate section in this
chapter. Programs for preprocessing the input data
are described in Chapter 4 .
The calling sequence, i.e. the order
in which the data-preprocessing and analysis programs are invoked, is
given under the program description.
The programs contain certain constants that establish limits on
the number of loci, alleles, etc. that can be analyzed. These
constants can be changed, and the programs recompiled if larger
values are required. Important constants that recur in several
programs are described in section 3.1 .
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