{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T21:38:59Z","timestamp":1770327539127,"version":"3.49.0"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2018,5,14]],"date-time":"2018-05-14T00:00:00Z","timestamp":1526256000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Agence Nationale pour la Recherche","award":["ANR-10-BINF-01-01"],"award-info":[{"award-number":["ANR-10-BINF-01-01"]}]},{"name":"Institut de Biologie Computationnelle","award":["ANR-11-BINF-0002"],"award-info":[{"award-number":["ANR-11-BINF-0002"]}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Union\u2019s Horizon 2020","award":["714774"],"award-info":[{"award-number":["714774"]}]},{"DOI":"10.13039\/501100001711","name":"Swiss National Science Foundation","doi-asserted-by":"publisher","award":["150654"],"award-info":[{"award-number":["150654"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>A reconciliation is an annotation of the nodes of a gene tree with evolutionary events\u2014for example, speciation, gene duplication, transfer, loss, etc.\u2014along with a mapping onto a species tree. Many algorithms and software produce or use reconciliations but often using different reconciliation formats, regarding the type of events considered or whether the species tree is dated or not. This complicates the comparison and communication between different programs.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we gather a consortium of software developers in gene tree species tree reconciliation to propose and endorse a format that aims to promote an integrative\u2014albeit flexible\u2014specification of phylogenetic reconciliations. This format, named recPhyloXML, is accompanied by several tools such as a reconciled tree visualizer and conversion utilities.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>http:\/\/phylariane.univ-lyon1.fr\/recphyloxml\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty389","type":"journal-article","created":{"date-parts":[[2018,5,9]],"date-time":"2018-05-09T11:39:17Z","timestamp":1525865957000},"page":"3646-3652","source":"Crossref","is-referenced-by-count":30,"title":["RecPhyloXML: a format for reconciled gene trees"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8854-7235","authenticated-orcid":false,"given":"Wandrille","family":"Duchemin","sequence":"first","affiliation":[{"name":"Univ Lyon, Universit\u00e9 Lyon 1, CNRS, Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive UMR5558, F-69622 Villeurbanne, France"},{"name":"INRIA Grenoble Rh\u00f4ne-Alpes, F-38334 Montbonnot, France"},{"name":"MTA-ELTE Lend\u00fclet Evolutionary Genomics Research Group, Budapest, Hungary"},{"name":"Department of Biological Physics, E\u00f6tv\u00f6s Lor\u00e1nd University, Budapest, Hungary"}]},{"given":"Guillaume","family":"Gence","sequence":"additional","affiliation":[{"name":"Univ Lyon, Universit\u00e9 Lyon 1, CNRS, Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive UMR5558, F-69622 Villeurbanne, France"}]},{"given":"Anne-Muriel","family":"Arigon Chifolleau","sequence":"additional","affiliation":[{"name":"LIRMM, Universit\u00e9 de Montpellier, CNRS, Montpellier, France"},{"name":"Institut de Biologie Computationnelle (IBC), Montpellier, France"}]},{"given":"Lars","family":"Arvestad","sequence":"additional","affiliation":[{"name":"Department of Mathematics, Stockholm University, Stockholm, Sweden"},{"name":"Swedish e-Science Research Centre (SeRC), Stockholm, Sweden"}]},{"given":"Mukul S","family":"Bansal","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA"},{"name":"Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA"}]},{"given":"Vincent","family":"Berry","sequence":"additional","affiliation":[{"name":"LIRMM, Universit\u00e9 de Montpellier, CNRS, Montpellier, France"},{"name":"Institut de Biologie Computationnelle (IBC), Montpellier, France"},{"name":"ISEM, CNRS, Universit\u00e9 de Montpellier, IRD, EPHE, Montpellier, France"}]},{"given":"Bastien","family":"Boussau","sequence":"additional","affiliation":[{"name":"Univ Lyon, Universit\u00e9 Lyon 1, CNRS, Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive UMR5558, F-69622 Villeurbanne, France"}]},{"given":"Fran\u00e7ois","family":"Chevenet","sequence":"additional","affiliation":[{"name":"LIRMM, Universit\u00e9 de Montpellier, CNRS, Montpellier, France"},{"name":"MIVEGEC, CNRS 5290, IRD 224, Universit\u00e9 de Montpellier, Montpellier, France"}]},{"given":"Nicolas","family":"Comte","sequence":"additional","affiliation":[{"name":"INRIA Grenoble Rh\u00f4ne-Alpes, F-38334 Montbonnot, France"}]},{"given":"Adri\u00e1n A","family":"Dav\u00edn","sequence":"additional","affiliation":[{"name":"Univ Lyon, Universit\u00e9 Lyon 1, CNRS, Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive UMR5558, F-69622 Villeurbanne, France"},{"name":"MTA-ELTE Lend\u00fclet Evolutionary Genomics Research Group, Budapest, Hungary"},{"name":"Department of Biological Physics, E\u00f6tv\u00f6s Lor\u00e1nd University, Budapest, Hungary"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2170-853X","authenticated-orcid":false,"given":"Christophe","family":"Dessimoz","sequence":"additional","affiliation":[{"name":"Department of Computational Biology, University of Lausanne, Lausanne, Switzerland"},{"name":"Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland"},{"name":"Department of Genetics, Evolution and Environment, University College London, London, UK"},{"name":"Department of Computer Science, University College London, London, UK"},{"name":"Swiss Institute of Bioinformatics, Lausanne, Switzerland"}]},{"given":"David","family":"Dylus","sequence":"additional","affiliation":[{"name":"Department of Computational Biology, University of Lausanne, Lausanne, Switzerland"}]},{"given":"Damir","family":"Hasic","sequence":"additional","affiliation":[{"name":"Department of Mathematics, Faculty of Science, University of Sarajevo, Sarajevo, Bosnia and Herzegovina"}]},{"given":"Diego","family":"Mallo","sequence":"additional","affiliation":[{"name":"Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA"}]},{"given":"R\u00e9mi","family":"Planel","sequence":"additional","affiliation":[{"name":"Laboratoire d\u2019Analyse Bio-informatique en G\u00e9nomique et M\u00e9tabolisme CNRS-UMR 8030, Commissariat \u00e0 l\u2019\u00c9nergie Atomique (CEA), Institut de G\u00e9nomique, Genoscope, Evry, France"}]},{"given":"David","family":"Posada","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain"}]},{"given":"Celine","family":"Scornavacca","sequence":"additional","affiliation":[{"name":"Institut de Biologie Computationnelle (IBC), Montpellier, France"},{"name":"ISEM, CNRS, Universit\u00e9 de Montpellier, IRD, EPHE, Montpellier, France"}]},{"given":"Gergely","family":"Sz\u00f6ll\u0151si","sequence":"additional","affiliation":[{"name":"MTA-ELTE Lend\u00fclet Evolutionary Genomics Research Group, Budapest, Hungary"},{"name":"Department of Biological Physics, E\u00f6tv\u00f6s Lor\u00e1nd University, Budapest, Hungary"}]},{"given":"Louxin","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Mathematics, National University of Singapore, Singapore, Singapore"}]},{"given":"\u00c9ric","family":"Tannier","sequence":"additional","affiliation":[{"name":"Univ Lyon, Universit\u00e9 Lyon 1, CNRS, Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive UMR5558, F-69622 Villeurbanne, France"},{"name":"INRIA Grenoble Rh\u00f4ne-Alpes, F-38334 Montbonnot, France"}]},{"given":"Vincent","family":"Daubin","sequence":"additional","affiliation":[{"name":"Univ Lyon, Universit\u00e9 Lyon 1, CNRS, Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive UMR5558, F-69622 Villeurbanne, France"}]}],"member":"286","published-online":{"date-parts":[[2018,5,14]]},"reference":[{"key":"2023012712350750300_bty389-B1","doi-asserted-by":"crossref","first-page":"5714","DOI":"10.1073\/pnas.0806251106","article-title":"Simultaneous Bayesian gene tree reconstruction and reconciliation analysis","volume":"106","author":"\u00c5kerborg","year":"2009","journal-title":"Proc. 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