Duchemin W., Gence G., Chifolleau A. M. A., Arvestad L., Bansal M. S., Berry V., Boussau B., Chevenet François, Comte N., Davin A. A., Dessimoz C., Dylus D., Hasic D., Mallo D., Planel R., Posada D., Scornavacca C., Szollosi G., Zhang L. X., Tannier E., Daubin V. (2018). RecPhyloXML : a format for reconciled gene trees. Bioinformatics, 34 (21), p. 3646-3652. ISSN 1367-4803.
Titre du document
RecPhyloXML : a format for reconciled gene trees
Année de publication
2018
Auteurs
Duchemin W., Gence G., Chifolleau A. M. A., Arvestad L., Bansal M. S., Berry V., Boussau B., Chevenet François, Comte N., Davin A. A., Dessimoz C., Dylus D., Hasic D., Mallo D., Planel R., Posada D., Scornavacca C., Szollosi G., Zhang L. X., Tannier E., Daubin V.
Source
Bioinformatics, 2018,
34 (21), p. 3646-3652 ISSN 1367-4803
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.
Plan de classement
Sciences fondamentales / Techniques d'analyse et de recherche [020]
;
Informatique [122]
Localisation
Fonds IRD [F B010074453]
Identifiant IRD
fdi:010074453
