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© Research
Publication : Bioinformatics (Oxford, England)

RecPhyloXML: a format for reconciled gene trees

Member: Rémi Planel
Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Bioinformatics (Oxford, England) - 01 Nov 2018

Duchemin W, Gence G, Arigon Chifolleau AM, Arvestad L, Bansal MS, Berry V, Boussau B, Chevenet F, Comte N, Davín AA, Dessimoz C, Dylus D, Hasic D, Mallo D, Planel R, Posada D, Scornavacca C, Szöllosi G, Zhang L, Tannier É, Daubin V

Link to Pubmed [PMID] – 29762653

Bioinformatics 2018 11;34(21):3646-3652

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.