{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,8]],"date-time":"2025-10-08T15:44:57Z","timestamp":1759938297567,"version":"3.37.3"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2020,10,14]],"date-time":"2020-10-14T00:00:00Z","timestamp":1602633600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Mitacs accelaration program and Plotly Inc","award":["IT11886"],"award-info":[{"award-number":["IT11886"]}]},{"name":"Canada Research Chair [CRC Tier 2","award":["950-230577"],"award-info":[{"award-number":["950-230577"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>A phylogenetic tree reconciliation is a mapping of one phylogenetic tree onto another which represents the co-evolution of two sets of taxa (e.g. parasite\u2013host co-evolution, gene\u2013species co-evolution). The reconciliation framework was extended to allow modeling the co-evolution of three sets of taxa such as transcript\u2013gene\u2013species co-evolutions. Several web-based tools have been developed for the display and manipulation of phylogenetic trees and co-phylogenetic trees involving two trees, but there currently exists no tool for visualizing the joint reconciliation between three phylogenetic trees.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present DoubleRecViz, a web-based tool for visualizing double reconciliations between phylogenetic trees at three levels: transcript, gene and species. DoubleRecViz extends the RecPhyloXML model\u2014developed for gene\u2013species tree reconciliation\u2014to represent joint transcript\u2013gene and gene\u2013species tree reconciliations. It is implemented using the Dash library, which is a toolbox that provides dynamic visualization functionalities for web data visualization in Python.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>DoubleRecViz is available through a web server at https:\/\/doublerecviz.cobius.usherbrooke.ca. The source code and information about installation procedures are also available at https:\/\/github.com\/UdeS-CoBIUS\/DoubleRecViz.<\/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\/btaa882","type":"journal-article","created":{"date-parts":[[2020,9,29]],"date-time":"2020-09-29T21:35:55Z","timestamp":1601415355000},"page":"1920-1922","source":"Crossref","is-referenced-by-count":3,"title":["DoubleRecViz: a web-based tool for visualizing transcript\u2013gene\u2013species tree reconciliation"],"prefix":"10.1093","volume":"37","author":[{"given":"Esaie","family":"Kuitche","sequence":"first","affiliation":[{"name":"Department of Computer Science, University of Sherbrooke , Sherbrooke, QC J1K2R1, Canada"}]},{"given":"Yanchun","family":"Qi","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Sherbrooke , Sherbrooke, QC J1K2R1, Canada"}]},{"given":"Nadia","family":"Tahiri","sequence":"additional","affiliation":[{"name":"Plotly Inc , Montreal, QC H2T2A3, Canada"}]},{"given":"Jack","family":"Parmer","sequence":"additional","affiliation":[{"name":"Plotly Inc , Montreal, QC H2T2A3, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2040-4948","authenticated-orcid":false,"given":"A\u00efda","family":"Ouangraoua","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Sherbrooke , Sherbrooke, QC J1K2R1, Canada"}]}],"member":"286","published-online":{"date-parts":[[2020,10,14]]},"reference":[{"key":"2023051611453971700_btaa882-B1","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1016\/j.tcs.2019.12.024","article-title":"Visualizing co-phylogenetic reconciliations","volume":"815","author":"Calamoneri","year":"2020","journal-title":"Theor. Comput. Sci"},{"key":"2023051611453971700_btaa882-B2","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1089\/106652700750050871","article-title":"NOTUNG: a program for dating gene duplications and optimizing gene family trees","volume":"7","author":"Chen","year":"2000","journal-title":"J. Comput. Biol"},{"key":"2023051611453971700_btaa882-B3","doi-asserted-by":"crossref","first-page":"608","DOI":"10.1093\/bioinformatics\/btv625","article-title":"SylvX: a viewer for phylogenetic tree reconciliations","volume":"32","author":"Chevenet","year":"2016","journal-title":"Bioinformatics"},{"year":"2018","author":"Duchemin","key":"2023051611453971700_btaa882-B4"},{"key":"2023051611453971700_btaa882-B5","doi-asserted-by":"crossref","first-page":"3646","DOI":"10.1093\/bioinformatics\/bty389","article-title":"RecPhyloXML: a format for reconciled gene trees","volume":"34","author":"Duchemin","year":"2018","journal-title":"Bioinformatics"},{"key":"2023051611453971700_btaa882-B6","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"},{"year":"2007","author":"Heng","key":"2023051611453971700_btaa882-B7"},{"key":"2023051611453971700_btaa882-B8","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1093\/sysbio\/syy075","article-title":"Exploring and visualizing spaces of tree reconciliations","volume":"68","author":"Huber","year":"2019","journal-title":"Syst. Biol"},{"key":"2023051611453971700_btaa882-B9","doi-asserted-by":"crossref","first-page":"1635","DOI":"10.1093\/molbev\/msw046","article-title":"ETE 3: reconstruction, analysis, and visualization of phylogenomic data","volume":"33","author":"Huerta-Cepas","year":"2016","journal-title":"Mol. Biol. Evol"},{"key":"2023051611453971700_btaa882-B10","doi-asserted-by":"crossref","first-page":"1740007","DOI":"10.1142\/S0219720017400078","article-title":"Reconstructing protein and gene phylogenies using reconciliation and soft-clustering","volume":"15","author":"Kuitche","year":"2017","journal-title":"J. Bioinf. Comput. Biol"},{"key":"2023051611453971700_btaa882-B11","doi-asserted-by":"crossref","first-page":"W256","DOI":"10.1093\/nar\/gkz239","article-title":"Interactive tree of life (ITOL) v4: recent updates and new developments","volume":"47","author":"Letunic","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023051611453971700_btaa882-B12","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1109\/TCBB.2018.2846253","article-title":"An integrated reconciliation framework for domain, gene, and species level evolution","volume":"16","author":"Li","year":"2019","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinf"},{"key":"2023051611453971700_btaa882-B13","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1186\/1471-2105-8-148","article-title":"Primetv: a viewer for reconciled trees","volume":"8","author":"Sennblad","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2023051611453971700_btaa882-B14","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1093\/sysbio\/syt054","article-title":"Efficient exploration of the space of reconciled gene trees","volume":"62","author":"Sz\u00f6ll\u0151si","year":"2013","journal-title":"Syst. Biol"},{"key":"2023051611453971700_btaa882-B15","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1101\/gr.073585.107","article-title":"Ensemblcompara genetrees: complete, duplication-aware phylogenetic trees in vertebrates","volume":"19","author":"Vilella","year":"2008","journal-title":"Genome Res"},{"key":"2023051611453971700_btaa882-B16","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1111\/2041-210X.12628","article-title":"ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data","volume":"8","author":"Yu","year":"2017","journal-title":"Methods Ecol. Evol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa882\/34947851\/btaa882.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/13\/1920\/50340099\/btaa882.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/13\/1920\/50340099\/btaa882.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T11:46:49Z","timestamp":1684237609000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/13\/1920\/5922814"}},"subtitle":[],"editor":[{"given":"Yann","family":"Ponty","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,10,14]]},"references-count":16,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2021,7,27]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa882","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2021,7,1]]},"published":{"date-parts":[[2020,10,14]]}}}