Paper Info
Title
RecPhyloXML: a format for reconciled gene trees.
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.
Year
DOI
Venue
2018
10.1093/bioinformatics/bty389
BIOINFORMATICS
Field
DocType
Volume
Data mining,Gene,Annotation,Phylogenetic tree,Information retrieval,Computer science,Tree species,Software,Gene duplication
Journal
34
Issue
ISSN
Citations 
21
1367-4803
0
PageRank 
References 
Authors
0.34
11
21
Name
Order
Citations
PageRank
Wandrille Duchemin131.44
Guillaume Gence200.34
Anne-Muriel Arigon Chifolleau3141.78
Lars Arvestad422217.51
Mukul S. Bansal529423.97
Vincent Berry623116.37
Bastien Boussau700.34
François Chevenet81018.66
Nicolas Comte910.73
Adrián A. Davín1000.34
Christophe Dessimoz1137830.12
David Dylus1250.78
Damir Hasic1321.76
Diego Mallo1400.68
Rémi Planel1520.77
David Posada1600.34
Celine Scornavacca1721618.80
Gergely J Szöllosi18785.49
Louxin Zhang1989096.47
Eric Tannier2049737.25
Vincent Daubin211185.65