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 …

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 …

Abstract Information integration and workflow technologies for data analysis have always
been major fields of investigation in bioinformatics. A range of popular workflow suites are …

We have recently developed a distance metric for efficiently estimating the number of
substitutions per site between unaligned genome sequences. These substitution rates are called “…

Motivation Unique marker sequences are highly sought after in molecular diagnostics.
Nevertheless, there are only few programs available to search for marker sequences, compared …

Motivation: In many organisms, including humans, recombination clusters within recombination
hotspots. The standard method for de novo detection of recombinants at hotspots is …

The advent of high throughput sequencers has lead to a dramatic increase in the size of
available genomic data. Standard methods, which have worked well for many years, are not …

Abstract Bits, nucleotides and speed.

By tracking pathogen outbreaks using whole genome sequencing, medical microbiology is
currently being transformed into genomic epidemiology. This change in technology is leading …

To understand the evolutionary relationships between organisms, they are typicallypresented
in a tree-like structure, a phylogeny. In genomic studies, phylogenies aretraditionally …