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Updated: Feb 26, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

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

Simon Dellicour^1,2,3, Nuno R Faria^4,5, Rebecca Rose⁶

¹Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles (ULB), Brussels 1050, Belgium.

Bioinformatics (Oxford, England)

|February 24, 2026

Summary

This summary is machine-generated.

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.

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An Integrated Approach for Microprotein Identification and Sequence Analysis

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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.