Faster Linkage Analysis Computations for Pedigrees with
Loops or Unused Alleles
Alejandro A. Schaffer
Human Heredity 46, 226--235 (1996)
Abstract
There seems to be no limit to the complexity of computations that
genetic linkage analysts want to do. Two primary factors that
increase the length of computations are pedigree loops and
unknown genotypes. I describe the implementation in FASTLINK
of some algorithmic improvements to partly address the problems
of pedigree loops and unknown genotypes. LINKAGE is by far
the most popular software package to do lod score computations
on disease pedigrees. FASTLINK is derived from LINKAGE 5.1
and compatible with it. In contrast to LINKAGE, FASTLINK
has the virtues that it is faster sequentially, runs well in
parallel, is more robust against errors, and includes substantial
new documentation. One of the new improvements allows the
detection of violation of Mendelian rules of inheritance in
input pedigree files with loops. This error-detection capability
was not provided in any previous version of LINKAGE or FASTLINK.
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