Alignment-free sequence analyses have been applied to problems ranging from whole-
genome phylogeny to the classification of protein families, identification of horizontally …

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

The plastid genome of plants is the smallest and most gene‐rich of the three genomes in
each cell and the one generally present in the highest copy number. As a result, obtaining …

The development of data-dependent heuristics and representations for biological
sequences that reflect their evolutionary distance is critical for large-scale biological …

Motivation: Alignment-free methods for sequence comparison are increasingly used for
genome analysis and phylogeny reconstruction; they circumvent various difficulties of …

The ability to inexpensively describe taxonomic diversity is critical in this era of rapid climate
and biodiversity changes. The recent genome-skimming approach extends current …

Genetic tools are increasingly used to identify and discriminate between species. One key
transition in this process was the recognition of the potential of the ca 658bp fragment of the …

Motivation: A standard approach to classifying sets of genomes is to calculate their pairwise
distances. This is difficult for large samples. We have therefore developed an algorithm for …

Placing a new species on an existing phylogeny has increasing relevance to several
applications. Placement can be used to update phylogenies in a scalable fashion and can …

With sharp increasing in biological sequences, the traditional sequence alignment methods
become unsuitable and infeasible. It motivates a surge of fast alignment-free techniques for …