RecPhyloXML: a format for reconciled gene trees

Wandrille Duchemin 1, 2 Guillaume Gence 1 Anne-Muriel Arigon Chifolleau 3 Lars Arvestad 4 Mukul Bansal 5 Vincent Berry 3 Bastien Boussau 1 François Chevenet 6 Nicolas Comte 2 Adrián Davín 6 Christophe Dessimoz 7 David Dylus 8 Damir Hasic 9 Diego Mallo 10 Rémi Planel 1 David Posada 11 Celine Scornavacca 12 Gergely Szöllősi 1 Louxin Zhang 13 Eric Tannier 1, 2 Vincent Daubin 1
1 BPGE - Bioinformatique, phylogénie et génomique évolutive
PEGASE - Département PEGASE [LBBE]
2 BEAGLE - Artificial Evolution and Computational Biology
LIRIS - Laboratoire d'InfoRmatique en Image et Systèmes d'information, Inria Grenoble - Rhône-Alpes, LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
3 MAB - Méthodes et Algorithmes pour la Bioinformatique
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
4 Science for Life Laboratory [Solna]
5 UCONN - University of Connecticut
6 LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
7 Department of Computer Science
8 Institute of Bioinformatics [Lausanne]
9 University of Sarajevo
10 ASU - Arizona State University [Tempe]
11 Universidate de Vigo
12 UMR ISEM - Institut des Sciences de l'Evolution de Montpellier
13 Department of Mathematics [Singapore]
Abstract : 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.
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LIRMM | CNRS | MAB | BIOENVIS | AGROPOLIS | UNIV-LYON1 | IRD | MIPS | B3ESTE | INRIA | UNIV-MONTPELLIER | ISEM | EC-LYON | UNIV-LYON2 | INSA-LYON | LIRIS | CARMEN | INSA-GROUPE | PSL | EPHE | CIRAD | UDL

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Wandrille Duchemin, Guillaume Gence, Anne-Muriel Arigon Chifolleau, Lars Arvestad, Mukul Bansal, et al.. RecPhyloXML: a format for reconciled gene trees. Bioinformatics, Oxford University Press (OUP), 2018, 34 (21), pp.3646-3652. ⟨10.1093/bioinformatics/bty389⟩. ⟨lirmm-01800296⟩

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