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. 2018 Nov 1;34(21):3646-3652.
doi: 10.1093/bioinformatics/bty389.

RecPhyloXML: a format for reconciled gene trees

Wandrille Duchemin  1   2   3   4 , Guillaume Gence  1 , Anne-Muriel Arigon Chifolleau  5   6 , Lars Arvestad  7   8 , Mukul S Bansal  9   10 , Vincent Berry  5   6   11 , Bastien Boussau  1 , François Chevenet  5   12 , Nicolas Comte  2 , Adrián A Davín  1   3   4 , Christophe Dessimoz  13   14   15   16   17 , David Dylus  13 , Damir Hasic  18 , Diego Mallo  19 , Rémi Planel  20 , David Posada  21 , Celine Scornavacca  6   11 , Gergely Szöllosi  3   4 , Louxin Zhang  22 , Éric Tannier  1   2 , Vincent Daubin  1
Affiliations

RecPhyloXML: a format for reconciled gene trees

Wandrille Duchemin et al. Bioinformatics. .

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.

Availability and implementation: http://phylariane.univ-lyon1.fr/recphyloxml/.

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Figures

Fig. 1.
Fig. 1.
A. Representation of the <leaf> tag. B. Representation of the <speciation> tag. C. Representation of the <loss> tag. D. Representation of the <duplication> tag. The species tree is figured using black tube-like branches. The part of the gene tree the event occurs in is represented using plain lines. Additional parts of the gene tree are represented as dotted lines. Stars, squares and crosses respectively represent the beginning of a gene lineage, a gene duplication and a gene loss
Fig. 2.
Fig. 2.
A. Representation of the <branchingOut> tag. B. Representation of the <transferBack> tag. C. Representation of a <branchingOut> tag followed by a <loss> tag. D. Representation of the <bifurcationOut> tag. These figure uses the same conventions as Figure 1 with the following additions. For the <bifurcationOut> tag (D.), which is specific of the model of Szöllősi et al. (2013b), extinct/unsampled lineages are represented as branches of the species tree that do not extend all the way to the right. Diamonds and triangles respectively represent a transfer leaving and entering a branch of the species tree (note that the transfers leave a branch of the species tree that corresponds to an extinct/unsampled lineage)
Fig. 3.
Fig. 3.
A <recPhylo> object containing a species tree and one reconciled gene tree
Fig. 4.
Fig. 4.
A visualization of the reconciled gene tree of Figure 3
See this image and copyright information in PMC

References

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    1. Bansal M.S. et al. (2012) Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss. Bioinformatics, 28, i283–i291. - PMC - PubMed
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