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  \item Tree-Based method  \begin{itemize}  \item We considered two methods to assess clustering of disease status in genealogical trees: Blossoc (BLOck aSSOCiation, \cite{Mailund_2006}), which uses reconstructed trees, and a Mantel test which uses the true trees.   \item In practice, the true trees are unknown. However, the cluster statistics based on true trees represent a best case insofar as tree uncertainty is eliminated \cite{Burkett_2014}.  \item We therefore include two versions of the Mantel test as a benchmark for comparison.  \begin{itemize}  \item In the first version, the phenotype is scored according to whether or not the haplotype comes from a case. We refer to the first version as the {\em naive} Mantel test because all case haplotypes are treated the same, even those not carrying any risk variants.  \item In the second version, the phenotype is scored according to whether or not the haplotype comes from a case and carries a risk variant. We refer to the second version as the {\em informed} Mantel test because it takes into account whether or not a case haplotype carries a risk variant.   \end{itemize}  \item Reconstructed genealogical trees at each SNV (Blossoc, \citeNP{Mailund_2006}): A fast method to localize the disease-causing variants.  \begin{itemize}  \item Approximates perfect phylogenies for each site, assuming infinite site model of mutation and scores according to the non-random clustering of affected individuals.