Bioinformatics.: co-auth.: group Dessimoz

Bioinformatics. 2018 May 14. doi: 10.1093/bioinformatics/bty389. [Epub ahead of print]

RecPhyloXML – a format for reconciled gene trees.

Duchemin W1,2,3,4Gence G1Arigon Chifolleau AM5,6Arvestad L7,8Bansal MS9,10Berry V5,6,11Boussau B1Chevenet F5,12Comte N2Davín AA1,3,4Dessimoz C13,14,15,16Dylus D13Hasic D17Mallo D18Planel R19Posada D20Scornavacca C6,11Szöllosi G3,4Zhang L1,2Tannier É1,2Daubin V1.



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.


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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PMID: 29762653