Additional file 1.
Analysis of Hapi's runtime complexity. A detailed discussion of Hapi's runtime complexity, including descriptions of inputs that can yield runtime that is exponential in the size of the family. Also a probabilistic analysis of the likelihood of one class of these inputs occurring in real data.
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Williams et al. Genome Biology 2010 11:R108 doi:10.1186/gb-2010-11-10-r108