Tree Reconciliation

Challenge: The evolutionary history of genes and gene families are often more complex than species phylogeny due to such processes as gene duplication, gene loss, incomplete lineage sorting and cross-species gene transfer. Gene tree-species tree reconciliation is a powerful tool that allows researchers to infer past duplication events along a species’ lineage and identify orthologous genes.

Tree reconciliation search results and GO terms

The primary goal of the Tree Reconciliation Working Group is to develop an infrastructure to perform large species-gene tree reconciliations involving thousands of taxa and thousands of gene families. Such an infrastructure, able to process datasets of this magnitude, will prove indispensable given the pace at which the genomes of the different species are being sequenced. The iPlant Tree Reconciliation platform is composed of three elements: an analytical pipeline, a database and a visualizer.


The analytical pipeline links existing tools and algorithms, porting them to a HPC environment if necessary, so computationally intensive methods like Maximum Likelihood and Bayesian approaches can be used to compute the reconciliations. The pipeline uses a known phylogeny to infer speciation and duplication events that occurred along the evolution of a given gene family. The results are then stored in a version of Ensembl’s Compara database that has been modified to store reconciliations between species and gene trees.


A web interface then allows users to query the database either through BLAST searches or by using functional annotations and to download the underlying data. A feature of this platform is the custom visualization developed in collaboration with the Tree Visualization Working Group that allows users to intuitively navigate the species tree and the reconciled gene tree synchronously and to visually identify the relationships between the two.

Working Group Members

Name Role Institution
Todd Vision Working Group Lead

University of North Carolina, Chapel Hill/NESCent

Cecile Ane Collaborator University of Wisconsin, Madison
Jamie Estill Postdoc University of Georgia
John Kerry Graduate Student University of Georgia
Jim Leebens-Mack Collaborator University of Georgia
Naim Matasci Engagement Team Analyst iPlant Collaborative, The University of Arizona
Sheldon McKay Scientific Lead iPlant Collaborative, Cold Spring Harbor Laboratory
Daniel Packer Scientific Programmer