LinDen is a tool for detecting pairwise statistical epistasis between single nucleotide polymorphisms in genome wide association studies.
LinDen greatly increases the speed of a complete pairwise epistasis screen by reducing the number of statistical tests performed.
Loci are hierarchically grouped into trees based their linkage disequilibrium.
Rather than testing all pairs of loci, LinDen evaluates all pairs of LD-Trees utilizing branch and bound pruning in order to quickly detect the most significant locus pairs.
LinDen is implemented in C++, the source code is is available from the above tab.