{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T06:37:37Z","timestamp":1780555057412,"version":"3.54.1"},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2017,5,19]],"date-time":"2017-05-19T00:00:00Z","timestamp":1495152000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Comparative and evolutionary studies utilize phylogenetic trees to analyze and visualize biological data. Recently, several web-based tools for the display, manipulation and annotation of phylogenetic trees, such as iTOL and Evolview, have released updates to be compatible with the latest web technologies. While those web tools operate an open server access model with a multitude of registered users, a feature-rich open source solution using current web technologies is not available.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we present an extension of the widely used PhyloXML standard with several new options to accommodate functional genomics or annotation datasets for advanced visualization. Furthermore, PhyD3 has been developed as a lightweight tool using the JavaScript library D3.js to achieve a state-of-the-art phylogenetic tree visualization in the web browser, with support for advanced annotations. The current implementation is open source, easily adaptable and easy to implement in third parties\u2019 web sites.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>More information about PhyD3 itself, installation procedures and implementation links are available at http:\/\/phyd3.bits.vib.be and at http:\/\/github.com\/vibbits\/phyd3\/.<\/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\/btx324","type":"journal-article","created":{"date-parts":[[2017,5,18]],"date-time":"2017-05-18T16:41:53Z","timestamp":1495125713000},"page":"2946-2947","source":"Crossref","is-referenced-by-count":269,"title":["PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization"],"prefix":"10.1093","volume":"33","author":[{"given":"\u0141ukasz","family":"Kreft","sequence":"first","affiliation":[{"name":"VIB Bioinformatics Core, VIB, Ghent, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander","family":"Botzki","sequence":"additional","affiliation":[{"name":"VIB Bioinformatics Core, VIB, Ghent, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Frederik","family":"Coppens","sequence":"additional","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium"},{"name":"VIB-UGent Center for Plant Systems Biology, Ghent, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Klaas","family":"Vandepoele","sequence":"additional","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium"},{"name":"VIB-UGent Center for Plant Systems Biology, Ghent, Belgium"},{"name":"Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michiel","family":"Van Bel","sequence":"additional","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium"},{"name":"VIB-UGent Center for Plant Systems Biology, Ghent, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,5,19]]},"reference":[{"key":"2023020206413286000_btx324-B1","doi-asserted-by":"crossref","first-page":"356.","DOI":"10.1186\/1471-2105-10-356","article-title":"phyloXML: XML for evolutionary biology and comparative genomics","volume":"10","author":"Han","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023020206413286000_btx324-B2","doi-asserted-by":"crossref","first-page":"W236","DOI":"10.1093\/nar\/gkw370","article-title":"Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees","volume":"44","author":"He","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023020206413286000_btx324-B3","doi-asserted-by":"crossref","first-page":"W22","DOI":"10.1093\/nar\/gkt389","article-title":"aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity","volume":"41","author":"Kuraku","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023020206413286000_btx324-B4","doi-asserted-by":"crossref","first-page":"W242","DOI":"10.1093\/nar\/gkw290","article-title":"Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees","volume":"44","author":"Letunic","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023020206413286000_btx324-B5","doi-asserted-by":"crossref","first-page":"e12267.","DOI":"10.1371\/journal.pone.0012267","article-title":"jsPhyloSVG: a javascript library for visualizing interactive and vector-based phylogenetic trees on the web","volume":"5","author":"Smits","year":"2010","journal-title":"Plos One"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/18\/2946\/49041134\/bioinformatics_33_18_2946.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/18\/2946\/49041134\/bioinformatics_33_18_2946.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T01:41:44Z","timestamp":1675302104000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/18\/2946\/3835380"}},"subtitle":[],"editor":[{"given":"Janet","family":"Kelso","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2017,5,19]]},"references-count":5,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2017,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx324","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/107276","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,9,15]]},"published":{"date-parts":[[2017,5,19]]}}}