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Published on: October 1, 2013
RecPhyloXML: a format for reconciled gene trees
Wandrille Duchemin1,2,3,4, Guillaume Gence1, Anne-Muriel Arigon Chifolleau5,6
1Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, F-69622 Villeurbanne, France.
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/.
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