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RecPhyloXML: a format for reconciled gene trees

Duchemin, W; Gence, G; Arigon Chifolleau, A-M; Arvestad, L; Bansal, MS; Berry, V; Boussau, B; ... Daubin, V; + view all (2018) RecPhyloXML: a format for reconciled gene trees. Bioinformatics , 34 (21) pp. 3646-3652. 10.1093/bioinformatics/bty389. Green open access

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Abstract

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. AVAILABLITY AND IMPLEMENTATION: http://phylariane.univ-lyon1.fr/recphyloxml/.

Type: Article
Title: RecPhyloXML: a format for reconciled gene trees
Location: England
Open access status: An open access version is available from UCL Discovery
DOI: 10.1093/bioinformatics/bty389
Publisher version: https://doi.org/10.1093/bioinformatics/bty389
Language: English
Additional information: © The Author(s) 2018. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/).
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
URI: https://discovery.ucl.ac.uk/id/eprint/10049657
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