Efficient Construction of Hierarchical Overlap Graphs.

The hierarchical overlap graph (HOG for short) is an overlap encoding graph that efficiently represents overlaps from a given set P of n strings. A previously known algorithm constructs the HOG in time and space, where is the sum of lengths of the n strings in P . We present a new algorithm of time and space to compute the HOG, which exploits the segment tree data structure. We also propose an alternative algorithm using time and space in the word RAM model of computation.