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Updated: Feb 26, 2026
12:00
A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
36.2K
SERAPHIM 2.0: an extended toolbox for studying phylogenetically informed movements.
Simon Dellicour1,2,3, Nuno R Faria4,5, Rebecca Rose6
1Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles (ULB), Brussels 1050, Belgium.
Bioinformatics (Oxford, England)
|February 24, 2026
Summary
The updated "seraphim" R package enhances phylogeographic analysis for pathogen evolution. It offers new tools for visualizing dispersal, estimating movement metrics, and testing environmental impacts on pathogen spread.
Area of Science:
- Computational Biology
- Molecular Epidemiology
- Bioinformatics
Background:
- Spatially-explicit phylogeographic reconstructions are crucial for understanding pathogen evolution.
- Continuous phylogeographic inference aids in reconstructing pathogen dispersal history and spatiotemporal dynamics.
Purpose of the Study:
- To introduce the second version of the R package "seraphim".
- To provide an enhanced toolbox for processing and analyzing spatially-explicit phylogeographic reconstructions.
Main Methods:
- The "seraphim" package offers features for visualizing phylogeographic inferences.
- Includes estimation of lineage dispersal metrics and phylogeographic simulators.
- Implements hypothesis testing for environmental factors influencing dispersal velocity, location, and frequency.
Main Results:
- The package facilitates comprehensive analysis of pathogen dispersal patterns.
- Enables detailed investigation into the drivers of pathogen spread.
Conclusions:
- The "seraphim" R package is a valuable resource for molecular epidemiology.
- Version 2 expands capabilities for analyzing pathogen spatiotemporal dynamics and environmental influences.
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