SPREAD 4: online visualisation of pathogen phylogeographic reconstructions. Issue 2 (26th September 2022)

• Record Type: Journal Article
• Authors: Nahata, Kanika D; Bielejec, Filip; Monetta, Juan; Dellicour, Simon; Rambaut, Andrew; Suchard, Marc A; Baele, Guy; Lemey, Philippe
• Is Part Of: Virus evolution. Volume 8:Issue 2(2022)
• Publication Date: 2022-09-26
• Subjects: phylogeography -- viral spread -- BEAST -- Bayesian inference -- visualisation; Viruses -- Evolution -- Periodicals; 579.2138
• DOI: 10.1093/ve/veac088
• Languages: English
• ISSNs: 2057-1577

Abstract

Abstract: Phylogeographic analyses aim to extract information about pathogen spread from genomic data, and visualising spatio-temporal reconstructions is a key aspect of this process. Here we present SPREAD 4, a feature-rich web-based application that visualises estimates of pathogen dispersal resulting from Bayesian phylogeographic inference using BEAST on a geographic map, offering zoom-and-filter functionality and smooth animation over time. SPREAD 4 takes as input phylogenies with both discrete and continuous location annotation and offers customised visualisation as well as generation of publication-ready figures. SPREAD 4 now features account-based storage and easy sharing of visualisations by means of unique web addresses. SPREAD 4 is intuitive to use and is available online at https://spreadviz.org, with an accompanying web page containing answers to frequently asked questions at https://beast.community/spread4 .