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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, 7 Nicolas Comte 2 Adrián Davín 6 Christophe Dessimoz 8 David Dylus 9 Damir Hasic 10 Diego Mallo 11 Rémi Planel 1 David Posada 12 Celine Scornavacca 13 Gergely Szöllősi 1 Louxin Zhang 14 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
LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558, Inria Grenoble - Rhône-Alpes, LIRIS - Laboratoire d'InfoRmatique en Image et Systèmes d'information
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 MIVEGEC-GeneSys - Du gène à l'écosystème
EPATH - Pathogènes, Environnement, Santé Humaine
8 Department of Computer Science
9 SIB - Swiss Institute of Bioinformatics [Lausanne]
10 University of Sarajevo
11 ASU - Arizona State University [Tempe]
12 Universidade de Vigo
13 UMR ISEM - Institut des Sciences de l'Evolution de Montpellier
14 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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https://hal-lirmm.ccsd.cnrs.fr/lirmm-01800296
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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 | EPHE | CIRAD | UDL | PSL

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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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