RecPhyloXML: a format for reconciled gene trees - LIRMM - Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier Access content directly
Journal Articles Bioinformatics Year : 2018

RecPhyloXML: a format for reconciled gene trees


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-01800296 , version 1 (25-05-2018)




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