Abstract

An absent word (or a forbidden word) is a word that does not appear in a given sequence. It is a minimal absent word if all its proper factors occur in the given sequence. In this paper, we propose a linear-time algorithm to compute the minimal absent words for DNA sequence using a suffix automaton. This method outputs the whole set of minimal absent words. We apply a Neighbor-Joining method to construct phylogenetic tree based on the minimal absent words.