# SERAPHIM 2.0: an extended toolbox for studying phylogenetically informed movements

## TL;DR

The SERAPHIM 2.0 toolbox helps study how pathogens spread over time and space by analyzing genetic data and environmental influences.

## Contribution

SERAPHIM 2.0 introduces new tools for visualizing, simulating, and testing phylogeographic hypotheses influenced by environmental factors.

## Key findings

- The package now includes visualization tools and dispersal metrics for phylogeographic analysis.
- It offers hypothesis testing to assess how environmental factors affect pathogen dispersal dynamics.
- Several phylogeographic simulators are implemented for modeling lineage movements.

## Abstract

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.

The package is openly available (https://github.com/sdellicour/seraphim) along with a series of tutorials describing the different analytical procedures it implements.