Background De novo genome assembly relies on two kinds of graphs: de Bruijn graphs and
overlap graphs. Overlap graphs are the basis for the Celera assembler, while de Bruijn …

Constructing the suffix array for a string collection is an important task that may be performed
by sorting the concatenation of all strings. In this article we present algorithms g SAIS and g …

Background Sequencing technologies produce larger and larger collections of
biosequences that have to be stored in compressed indices supporting fast search …

Multiple sequence alignment (MSA) is fundamental to many biological applications. But
most classical MSA algorithms are difficult to handle large-scale multiple sequences …

Background Molecular phylogenetics studies the evolutionary relationships among the
individuals of a population through their biological sequences. It may provide insights about …

Abstract Background In [Prezza et al., AMB 2019], a new reference-free and alignment-free
framework for the detection of SNPs was suggested and tested. The framework, based on …

Background Sequencing technologies keep on turning cheaper and faster, thus putting a
growing pressure for data structures designed to efficiently store raw data, and possibly …

Background Suffix arrays, augmented by additional data structures, allow solving efficiently
many string processing problems. The external memory construction of the generalized …

Indexing huge collections of strings, such as those produced by the widespread sequencing
technologies, heavily relies on multistring generalizations of the Burrows–Wheeler transform …

We show that the Longest Common Prefix Array of a text collection of total size n on
alphabet [1,{\sigma}] can be computed from the Burrows-Wheeler transformed collection in …