Background Alignment-free (AF) sequence comparison is attracting persistent interest driven
by data-intensive applications. Hence, many AF procedures have been proposed in recent …

We study the number N k of length-k word matches between pairs of evolutionarily related
DNA sequences, as a function of k. We show that the Jukes-Cantor distance between two …

The encounter of large amounts of biological sequence data generated during the last
decades and the algorithmic and hardware improvements have offered the possibility to …

Background Viruses are among the shortest yet highly abundant species that harbor
minimal instructions to infect cells, adapt, multiply, and exist. However, with the current …

Motivation k-mer counting is a common task in bioinformatic pipelines, with many dedicated
tools available. Many of these tools produce in output k-mer count tables containing both k …

Background The increasing amount of available genome sequence data enables large-
scale comparative studies. A common task is the inference of phylogenies—a challenging …

Word-based or 'alignment-free'sequence comparison has become an active research area
in bioinformatics. While previous word-frequency approaches calculated rough measures of …

The Salicornia L. has been considered one of the most taxonomically challenging genera
due to high morphological plasticity, intergradation between related species, and lack of …

Alignment-free methods for sequence comparison and phylogeny inference have attracted a
great deal of attention in recent years. Several algorithms have been implemented in diverse …

Polyploid genomes pose several inherent challenges to population genetic analyses. While
alignment‐based methods are fundamentally limited in their applicability to polyploids …