ArticleBioinformatics (Oxford, England)2026
SERAPHIM 2.0: an extended toolbox for studying phylogenetically informed movements.
Article in Bioinformatics (Oxford, England), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
5 citing papers in PubMed.
- One Health genomic surveillance reveals structured urban rabies transmission and major surveillance gaps.bioRxiv : the preprint server for biology · 2026Article
- Article
- HIV Transmission Dynamics in Greater Mexico City are Shaped by Dense Spatial Mixing.Research square · 2026Article
- HIV Transmission Dynamics in Greater Mexico City are Shaped by Dense Spatial Mixing.medRxiv : the preprint server for health sciences · 2026Article
- Phylodynamic analyses reveal persistence and extensive intermixing of Usutu virus in the Netherlands.Virus evolution · 2026Article
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Authors and funding
5 authors.
Funding
Abstract
summaryWe 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.