RecPhyloXML: a format for reconciled gene trees

Bioinformatics
Wandrille DucheminVincent Daubin

Abstract

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. 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. http://phylariane.univ-lyon1.fr/recphyloxml/.

Citations

Oct 1, 2019·Bioinformatics·Adrián A DavínGergely J Szöllősi
Oct 22, 2020·Bioinformatics·Nicolas ComteDavid P Parsons

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Software Mentioned

Treerecs
PhyloXML
DLcoalRecon
recPhylo
RANGER
recGeoXML
recSpeciesTreeXML
DTL
ALE
PrIME

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