{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T00:51:22Z","timestamp":1774399882404,"version":"3.50.1"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T00:00:00Z","timestamp":1771891200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"University of Brussels"},{"DOI":"10.13039\/501100002749","name":"Belgian Science Policy Office","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002749","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,2,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>We report the second version of the R package \u201cseraphim\u201d, a toolbox developed to process and analyze the output of spatially explicit phylogeographic reconstructions. This approach \u2013 also known as continuous phylogeographic inference \u2013 is commonly used in molecular epidemiology to reconstruct the dispersal history and spatiotemporal dynamics of rapidly evolving pathogens. The \u201cseraphim\u201d 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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The package is openly available (https:\/\/github.com\/sdellicour\/seraphim) along with a series of tutorials describing the different analytical procedures it implements.<\/jats:p>\n                  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R","family":"Faria","sequence":"additional","affiliation":[{"name":"MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London , London W12 0BZ,","place":["United Kingdom"]},{"name":"Institute of Tropical Medicine, University of S\u00e3o Paulo , S\u00e3o Paulo 05403-000,","place":["Brazil"]}]},{"given":"Rebecca","family":"Rose","sequence":"additional","affiliation":[{"name":"BioInfoExperts LLC, Sid Martin Biotech, University of Florida , Alachua, FL 32615,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2826-5353","authenticated-orcid":false,"given":"Philippe","family":"Lemey","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven , Leuven 3000,","place":["Belgium"]}]},{"given":"Oliver G","family":"Pybus","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Oxford , Oxford OX1 3RB,","place":["United Kingdom"]},{"name":"Department of Pathobiology and Population Science, Royal Veterinary College , Hatfield AL9 7TA,","place":["United Kingdom"]}]}],"member":"286","published-online":{"date-parts":[[2026,2,24]]},"reference":[{"key":"2026032419570159900_btag093-B1","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/j.coviro.2018.08.009","article-title":"Recent advances in computational phylodynamics","volume":"31","author":"Baele","year":"2018","journal-title":"Curr Opin Virol"},{"key":"2026032419570159900_btag093-B2","doi-asserted-by":"crossref","first-page":"1653","DOI":"10.1038\/s41592-025-02751-x","article-title":"BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference","volume":"22","author":"Baele","year":"2025","journal-title":"Nat Methods"},{"key":"2026032419570159900_btag093-B3","doi-asserted-by":"crossref","first-page":"e2411582121","DOI":"10.1073\/pnas.2411582121","article-title":"Modeling the velocity of 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