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. Availability and implementation http://phylariane.univ-lyon1.fr/recphyloxml/.
Wandrille Duchemin, Guillaume Gence, Ama Chifolleau, Lars Arvestad, Bansal, Berry, Bastien Boussau, François Chevenet, Nicolas Comte, AA Davín, C Dessimoz, David Dylus, Damir Hasić, Diego Mallo, Rémi Planel, David Posada, C Scornavacca, Gergely J. Szöllősi, L Zhang, Éric Tannier, Daubin
Discussion(0)
No comments yet. Be the first to comment.