The wavelet matrix: An efficient wavelet tree for large alphabets

•We improve current wavelet tree representations on large alphabets.•We reduce the number of operations needed to solve access, rank and select queries.•We introduce Huffman compression on the sequence to further reduce space and time.•We show that the resulting structures are the most efficient to represent sequences on large alphabets in most aspects.

The wavelet tree   is a flexible data structure that permits representing sequences S[1,n]S[1,n] of symbols over an alphabet of size σ, within compressed space and supporting a wide range of operations on S. When σ is significant compared to n, current wavelet tree representations incur in noticeable space or time overheads. In this article we introduce the wavelet matrix, an alternative representation for large alphabets that retains all the properties of wavelet trees but is significantly faster. We also show how the wavelet matrix can be compressed up to the zero-order entropy of the sequence without sacrificing, and actually improving, its time performance. Our experimental results show that the wavelet matrix outperforms all the wavelet tree variants along the space/time tradeoff map.