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 reconcili...

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Detalles Bibliográficos
Autores principales: Duchemin, Wandrille, Gence, Guillaume, Arigon Chifolleau, Anne-Muriel, Arvestad, Lars, Bansal, Mukul S, Berry, Vincent, Boussau, Bastien, Chevenet, François, Comte, Nicolas, Davín, Adrián A, Dessimoz, Christophe, Dylus, David, Hasic, Damir, Mallo, Diego, Planel, Rémi, Posada, David, Scornavacca, Celine, Szöllősi, Gergely, Zhang, Louxin, Tannier, Éric, Daubin, Vincent
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Original Papers
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6198865/
https://www.ncbi.nlm.nih.gov/pubmed/29762653
http://dx.doi.org/10.1093/bioinformatics/bty389
Descripción
Sumario: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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