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Updated: Feb 26, 2026

A Practical Guide to Phylogenetics for Nonexperts

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Published on: February 5, 2014

SERAPHIM 2.0: 分類学的情報に基づいた移動を研究するための拡張ツールボックス

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

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

Bioinformatics (Oxford, England)

|February 24, 2026

要旨

Summary:

We report the second version of the R package "seraphim", a toolbox developed to process and analyse 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) visualisation 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.

Supplementary Information:

Supplementary data are available at Bioinformatics online.

キーワード:

系統地理学病原体進化分子疫学 Rパッケージ計算生物学バイオインフォマティクス

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