SPREAD is a user-friendly, cross-platform application to analyze and visualize Bayesian
phylogeographic reconstructions incorporating spatial–temporal diffusion. The software maps …

The 2013–2016 West African epidemic caused by the Ebola virus was of unprecedented
magnitude, duration and impact. Here we reconstruct the dispersal, proliferation and decline of …

Abstract Model-based phylogenetic reconstructions increasingly consider spatial or
phenotypic traits in conjunction with sequence data to study evolutionary processes. Alongside …

Information on global human movement patterns is central to spatial epidemiological models
used to predict the behavior of influenza and other infectious diseases. Yet it remains …

10.7554/eLife.12217.001 Swine influenza presents a substantial disease burden for pig
populations worldwide and poses a potential pandemic threat to humans. There is considerable …

… For tip nodes in F, we assign forumla to either 0 or 1 depending on whether trait i is (partially)
observed or not. Finally, the full likelihood of F becomes forumla where x 2N−1 is the root …

Motivation: Statistical methods for comparing relative rates of synonymous and non-synonymous
substitutions maintain a central role in detecting positive selection. To identify selection, …

Since its isolation in 1966 in Kenya, rice yellow mottle virus (RYMV) has been reported
throughout Africa resulting in one of the economically most important tropical plant emerging …

Phylogeographic analyses aim to extract information about pathogen spread from genomic
data, and visualising spatio-temporal reconstructions is a key aspect of this process. Here we …

Background Simulated nucleotide or amino acid sequences are frequently used to assess
the performance of phylogenetic reconstruction methods. BEAST, a Bayesian statistical …