Merlin

Efforts to find disease genes using high-density single-nucleotide polymorphism
(SNP) maps will produce data sets that exceed the limitations of current
computational tools. Here we describe a new, efficient method for the analysis of
dense genetic maps in pedigree data that provides extremely fast solutions to
common problems such as allele-sharing analyses and haplotyping. We show that
sparse binary trees represent patterns of gene flow in general pedigrees in a
parsimonious manner, and derive a family of related algorithms for pedigree
traversal. With these trees, exact likelihood calculations can be carried out
efficiently for single markers or for multiple linked markers. Using an
approximate multipoint calculation that ignores the unlikely possibility of a
large number of recombinants further improves speed and provides accurate
solutions in dense maps with thousands of markers. Our multipoint engine for
rapid likelihood inference (Merlin) is a computer program that uses sparse
inheritance trees for pedigree analysis; it performs rapid haplotyping, genotype
error detection and affected pair linkage analyses and can handle more markers
than other pedigree analysis packages.

Merlin--rapid analysis of dense genetic maps using sparse gene flow trees.

Merlin (multipoint engine for rapid likelihood inference) is a tool for pedigree analysis. The Merlin algorithm uses sparse trees to represent gene flow in pedigrees and the tool is useful for LD and association analyses, ibd, kinship, haplotyping, detection of errors, and simulations.

Merlin

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