Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent
years with major new advances in nearly all aspects of the joint modelling of evolutionary data. …

Background Yersinia pestis has caused at least three human plague pandemics. The second
(Black Death, 14–17th centuries) and third (19–20th centuries) have been genetically …

Adaptive evolution frequently occurs in episodic bursts, localized to a few sites in a gene,
and to a small number of lineages in a phylogenetic tree. A popular class of “branch-site” …

Estimating the rates at which bacterial genomes evolve is critical to understanding major
evolutionary and ecological processes such as disease emergence, long-term host–pathogen …

Background Phylogenies are commonly used to analyse the differences between genes,
genomes and species. Patristic distances calculated from tree branch lengths describe the …

Background The performance of different programming languages has previously been
benchmarked using abstract mathematical algorithms, but not using standard bioinformatics …

10.7554/eLife.12994.001 The 14th–18th century pandemic of Yersinia pestis caused
devastating disease outbreaks in Europe for almost 400 years. The reasons for plague’s …

10.7554/eLife.05055.001 A complex interplay of viral, host, and ecological factors shapes
the spatio-temporal incidence and evolution of human influenza viruses. Although …

We investigated two mitochondrial genes (cytb and cox1), one plastid gene (tufA), and one
nuclear gene (ldh) in blood samples from 12 chimpanzees and two gorillas from Cameroon …

Wild birds have been implicated in the emergence of human and livestock influenza. The
successful prediction of viral spread and disease emergence, as well as formulation of …