The hierarchical overlap graph (HOG) is a graph that encodes overlaps from a given set P of n strings, as the overlap graph does. A best known algorithm constructs HOG in O(||P|| log n) time and O(||P||) space, where ||P|| is the sum of lengths of the strings in P. In this paper we present a new algorithm to construct HOG in O(||P||) time and space. Hence, the construction time and space of HOG are better than those of the overlap graph, which are O(||P|| + n^2).
@article{arxiv.2102.12824,
title = {A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs},
author = {Sangsoo Park and Sung Gwan Park and Bastien Cazaux and Kunsoo Park and Eric Rivals},
journal= {arXiv preprint arXiv:2102.12824},
year = {2021}
}