SERAPHIM 2.0: an extended toolbox for studying phylogenetically informed movements.
other · Level V
Where this comes from
- Record sourced from PubMed, PMID 41734272.
- Also identified by DOI 10.1093/bioinformatics/btag093 and PMC identifier 13012800.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
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.
Medical subject headings
- Software
- Phylogeny
- Computational Biology