An Alignment-Free Heuristic For Fast Sequence Comparisons With Applications To Phylogeny Reconstruction

Alignment-free methods for sequence comparisons have become popular in many bioinformatics applications, specifically in the estimation of sequence similarity measures to construct phylogenetic trees. Recently, the average common substring measure, ACS, and its k-mismatch counterpart, ACS-k, have been shown to produce results as effective as multiple-sequence alignment based methods in phylogeny. In this work, we present a novel linear-time heuristic to approximate ACS-k, which is faster than computing the exact ACS-k while being closer to the exact ACS-k values compared to previously published linear-time greedy heuristics