{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T11:32:51Z","timestamp":1761823971021,"version":"3.37.3"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2017,8,26]],"date-time":"2017-08-26T00:00:00Z","timestamp":1503705600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003130","name":"FWO","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003130","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004418","name":"VUB","doi-asserted-by":"publisher","award":["VUB\/OZR2714"],"award-info":[{"award-number":["VUB\/OZR2714"]}],"id":[{"id":"10.13039\/501100004418","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Clinicians, health officials and researchers are interested in the epidemic spread of pathogens in both space and time to support the optimization of intervention measures and public health policies. Large sequence databases of virus sequences provide an interesting opportunity to study this spread through phylogenetic analysis. To infer knowledge from large phylogenetic trees, potentially encompassing tens of thousands of virus strains, an efficient method for data exploration is required. The clades that are visited during this exploration should be annotated with strain characteristics (e.g. transmission risk group, tropism, drug resistance profile) and their geographic context.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>PhyloGeoTool implements a visual method to explore large phylogenetic trees and to depict characteristics of strains and clades, including their geographic context, in an interactive way. PhyloGeoTool also provides the possibility to position new virus strains relative to the existing phylogenetic tree, allowing users to gain insight in the placement of such new strains without the need to perform a de novo reconstruction of the phylogeny.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/rega-cev\/phylogeotool (Freely available: open source software project).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx535","type":"journal-article","created":{"date-parts":[[2017,8,25]],"date-time":"2017-08-25T19:09:59Z","timestamp":1503688199000},"page":"3993-3995","source":"Crossref","is-referenced-by-count":18,"title":["PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context"],"prefix":"10.1093","volume":"33","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3906-758X","authenticated-orcid":false,"given":"Pieter","family":"Libin","sequence":"first","affiliation":[{"name":"Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven \u2013 University of Leuven, Leuven, Belgium"},{"name":"Department of Computer Science, Vrije Universiteit Brussel, Brussels, Belgium"}]},{"given":"Ewout","family":"Vanden Eynden","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven \u2013 University of Leuven, Leuven, Belgium"}]},{"given":"Francesca","family":"Incardona","sequence":"additional","affiliation":[{"name":"EuResist Network, Rome, Italy"}]},{"given":"Ann","family":"Now\u00e9","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Vrije Universiteit Brussel, Brussels, Belgium"}]},{"given":"Antonia","family":"Bezenchek","sequence":"additional","affiliation":[{"name":"InformaPRO, Rome, Italy"}]},{"name":"EucoHIV Study Group","sequence":"additional","affiliation":[]},{"given":"Anders","family":"S\u00f6nnerborg","sequence":"additional","affiliation":[{"name":"Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden"}]},{"given":"Anne-Mieke","family":"Vandamme","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven \u2013 University of Leuven, Leuven, Belgium"},{"name":"Center for Global Health and Tropical Medicine, Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal"}]},{"given":"Kristof","family":"Theys","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven \u2013 University of Leuven, Leuven, Belgium"}]},{"given":"Guy","family":"Baele","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven \u2013 University of Leuven, Leuven, Belgium"}]}],"member":"286","published-online":{"date-parts":[[2017,8,26]]},"reference":[{"key":"2023020207504466500_btx535-B1","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkp455","article-title":"A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences","volume":"37","author":"Alcantara","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2023020207504466500_btx535-B2","doi-asserted-by":"crossref","first-page":"2952","DOI":"10.1093\/bioinformatics\/btm410","article-title":"CTree: comparison of clusters between phylogenetic trees made easy","volume":"23","author":"Archer","year":"2007","journal-title":"Bioinformatics"},{"key":"2023020207504466500_btx535-B3","doi-asserted-by":"crossref","first-page":"e2001624.","DOI":"10.1371\/journal.pbio.2001624","article-title":"Lifemap: exploring the entire tree of life","volume":"14","author":"de Vienne","year":"2016","journal-title":"PLoS Biol"},{"key":"2023020207504466500_btx535-B4","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1093\/cid\/civ963","article-title":"Transmission of HIV drug resistance and the predicted effect on current first-line regimens in Europe","volume":"62","author":"Hofstra","year":"2016","journal-title":"Clin. 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