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. AVAILABLITY AND IMPLEMENTATION: http://phylariane.univ-lyon1.fr/recphyloxml/.
Wandrille Duchemin, Guillaume Gence, Anne-Muriel Arigon Chifolleau, Lars Arvestad, Mukul S. Bansal, Vincent Berry, Bastien Boussau, François Chevenet, Nicolas Comte, Adrián Davín, Christophe Dessimoz, David Dylus, Damir Hasić, Diego Mallo, Rémi Planel, David Posada, Céline Scornavacca, Gergely J. Szöllősi, Louxin Zhang, Éric Tannier, Vincent Daubin
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