k-mer-based methods are widely used in bioinformatics, but there are many gaps in our
understanding of their statistical properties. Here, we consider the simple model where a …

Alignment-based methods have faced disadvantages in sequence comparison and
phylogeny reconstruction due to their high computational complexity. Alignment-free …

Classification of viruses into their taxonomic ranks (eg, order, family, and genus) provides a
framework to organize an abundant population of viruses. Next-generation metagenomic …

Recently developed MinHash-based techniques were proven successful in quickly
estimating the level of similarity between large nucleotide sequences. This article discusses …

Background The development of sequencing technology increases the number of genomes
being sequenced. However, obtaining a quality genome sequence remains a challenge in …

Motivation Tracking disease outbreaks by whole-genome sequencing leads to the collection
of large samples of closely related sequences. Five years ago, we published a method to …

Background In many fields of biomedical research, it is important to estimate phylogenetic
distances between taxa based on low-coverage sequencing reads. Major applications are …

Pairwise global alignment is a fundamental step in sequence analysis. Optimal alignment
algorithms are quadratic—slow especially on long sequences. In many applications that …

Word-based or 'alignment-free'methods for phylogeny inference have become popular in
recent years. These methods are much faster than traditional, alignment-based approaches …

Motivation The k-mer frequency in whole genome sequences provides researchers with an
insightful perspective on genomic complexity, comparative genomics, metagenomics and …