Blossoc is a linkage disequilibrium association mapping tool that attempts to build (perfect) genealogies for each site in the input and score these according to non-random clustering of affected individuals, and judge high-scoring areas as likely candidates for containing disease affecting variation.
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Local phylogeny mapping of quantitative traits: Higher accuracy and better ranking than single marker association in genomewide scans
S. Besenbacher, T. Mailund and M.H. Schierup
Genetics 181 747-753 2009; doi:10.1534/genetics.108.092643