Introduction

FineMap is a computer program for refining the location of a disease
gene beyond the bounds provided by linkage analysis.  Many scientists
use the pattern of linkage disequilibrium between the disease allele
and alleles at nearby markers.  FineMap seeks to
refine location by analysis of `disease' and `normal' haplotypes,
thereby using multivariate information about linkage disequilibrium.
Assuming the disease mutation occurs in a specific gap between
adjacent markers, FineMap first combines parsimony and likelihood
to build an evolutionary tree of disease haplotypes with each node
(haplotype) separated by a single mutational or recombinational step
from its parent.  If required, latent nodes (unobserved haplotypes)
are incorporated to complete the tree.  Once the tree is built, its
likelihood is computed from probabilities of mutation and
recombination.  When each gap between adjacent markers is evaluated in
this fashion, and these results are combined with prior information,
they yield a posterior probability distribution to guide the search
for the disease mutation.  

FineMap was written by Johnny Lam.  It runs in any UNIX environment

Lam, J.C, Roeder, K. and Devlin, B. (2000)
Haplotype fine-mapping by evolutionary trees, 
American Journal of Human Genetics, in press

