Duchemin W. auteur aut IRD Gence G. auteur aut IRD Chifolleau A. M. A. auteur aut IRD Arvestad L. auteur aut IRD Bansal M. S. auteur aut IRD Berry V. auteur aut IRD Boussau B. auteur aut IRD Chevenet François auteur aut IRD Comte N. auteur aut IRD Davin A. A. auteur aut IRD Dessimoz C. auteur aut IRD Dylus D. auteur aut IRD Hasic D. auteur aut IRD Mallo D. auteur aut IRD Planel R. auteur aut IRD Posada D. auteur aut IRD Scornavacca C. auteur aut IRD Szollosi G. auteur aut IRD Zhang L. X. auteur aut IRD Tannier E. auteur aut IRD Daubin V. auteur aut IRD text journalArticle eng text/pdf reformatted digital access Motivation: A reconciliation is an annotation of the nodes of a gene tree with evolutionary events-for example, speciation, gene duplication, transfer, loss, etc. -along 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. Results: 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-albeit flexible-specification of phylogenetic reconciliations. This format, named recPhyloXML, is accompanied by several tools such as a reconciled tree visualizer and conversion utilities. specialized 020 122 34 21 3646-3652 2018 1367-4803 https://www.documentation.ird.fr/hor/fdi:010074453 10.1093/bioinformatics/bty389 1367-4803 [F B010074453] https://www.documentation.ird.fr/hor/fdi:010074453 https://horizon.documentation.ird.fr/exl-doc/pleins_textes/divers18-12/010074453.pdf IRD - Base Horizon / Pleins textes 2019-01-10 2023-07-11 fdi:010074453 fre