Simon Dellicour, Nuno R. Faria, Rebecca Rose, Philippe Lemey, Oliver G. Pybus
SUMMARY: We report the second version of the R package "seraphim", a toolbox developed to process and analyze the output of spatially explicit phylogeographic reconstructions. This approach - also known as continuous phylogeographic inference - is commonly used in molecular epidemiology to reconstruct the dispersal history and spatiotemporal dynamics of rapidly evolving pathogens. The "seraphim" package now implements a broad range of features including (i) visualization of phylogeographic inferences, (ii) estimation of lineage dispersal metrics, (iii) several phylogeographic simulators, and (iv) hypothesis testing procedures to investigate the impact of environmental factors on variables such as diffusion velocity, dispersal location, and dispersal frequency of phylogenetic lineages. AVAILABILITY AND IMPLEMENTATION: The package is openly available (https://github.com/sdellicour/seraphim) along with a series of tutorials describing the different analytical procedures it implements.