RecPhyloXML: a format for reconciled gene trees.

Wandrille Duchemin,David Posada,Anne-Muriel Arigon Chifolleau,David Dylus,Nicolas Comte,François Chevenet,Guillaume Gence,Rémi Planel,Louxin Zhang,Diego Mallo,Lars Arvestad,Vincent Daubin,Christophe Dessimoz,Vincent Berry,Bastien Boussau,Adrián Davín ,Damir Hasić ,Mukul S Bansal ,Céline Scornavacca ,Gergely J Szöllősi ,Éric Tannier

doi:10.1093/bioinformatics/bty389

Abstract

MotivationA 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.ResultsHere, 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/.

Highlights

The relationships between the history of genomes or species and the history of their constituent genes are often described through reconciliation
A reconciliation consists of an association between the nodes of a gene tree and the nodes or branches of a species tree, along with different evolutionary events undergone by the gene
Reconciliation based metrics can be used as a criterion to construct better gene trees (Durand et al, 2006; Wu et al, 2013; Szöllosi et al, 2013a; Scornavacca et al, 2013; Sjöstrand et al, 2014) or better species tree (Boussau et al, 2013; Nakhleh, 2013)

Summary

Introduction

The relationships between the history of genomes or species and the history of their constituent genes are often described through reconciliation. Our format reflects the generality of this event by adopting a neutral label compatible with the different representations of transfers This notion of evolution in unsampled lineages implies the possibility of a bifurcation in the gene tree in such a lineage. The second group represents reconciliations as lists of gene tree nodes mapping to species tree nodes, making references to an implicit or external gene tree (meaning that the gene tree structure might not be included in the reconciliation) Examples of such output formats are used by ranger-DTL (Bansal et al, 2012), ecceTERA (Jacox et al, 2016), DLcoalRecon (Rasmussen and Kellis, 2012), Mowgli (Doyon et al, 2010), the visualization software SylvX (Chevenet et al, 2016) or the simulation software SimPhy (Mallo et al, 2016)

Format presentation

Availability

Conclusion