Wandrille Duchemin, Guillaume Gence, Anne-Muriel Arigon Chifolleau, Lars Arvestad, Mukul S Bansal, Vincent Berry, Bastien Boussau, François Chevenet, Nicolas Comte, Adrián A Davín, Christophe Dessimoz, David Dylus, Damir Hasic, Diego Mallo, Rémi Planel, David Posada, Celine Scornavacca, Gergely Szöllosi, Louxin Zhang, Éric Tannier, Vincent Daubin
Author Information
Wandrille Duchemin: Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, F-69622 Villeurbanne, France.
Guillaume Gence: Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, F-69622 Villeurbanne, France.
Anne-Muriel Arigon Chifolleau: LIRMM, Université de Montpellier, CNRS, Montpellier, France.
Lars Arvestad: Department of Mathematics, Stockholm University, Stockholm, Sweden.
Mukul S Bansal: Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA.
Vincent Berry: LIRMM, Université de Montpellier, CNRS, Montpellier, France.
Bastien Boussau: Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, F-69622 Villeurbanne, France.
François Chevenet: LIRMM, Université de Montpellier, CNRS, Montpellier, France.
Nicolas Comte: INRIA Grenoble Rhône-Alpes, F-38334 Montbonnot, France.
Adrián A Davín: Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, F-69622 Villeurbanne, France.
Christophe Dessimoz: Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
David Dylus: Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
Damir Hasic: Department of Mathematics, Faculty of Science, University of Sarajevo, Sarajevo, Bosnia and Herzegovina.
Diego Mallo: Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA.
Rémi Planel: Laboratoire d'Analyse Bio-informatique en Génomique et Métabolisme CNRS-UMR 8030, Commissariat à l'Énergie Atomique (CEA), Institut de Génomique, Genoscope, Evry, France.
David Posada: Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.
Celine Scornavacca: Institut de Biologie Computationnelle (IBC), Montpellier, France.
Gergely Szöllosi: MTA-ELTE Lendület Evolutionary Genomics Research Group, Budapest, Hungary.
Louxin Zhang: Department of Mathematics, National University of Singapore, Singapore, Singapore.
Éric Tannier: Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, F-69622 Villeurbanne, France.
Vincent Daubin: Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, F-69622 Villeurbanne, France.
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. Availability and implementation: http://phylariane.univ-lyon1.fr/recphyloxml/.
