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Tree Reconciliation

Tree reconciliation uses an estimate of the species tree to infer the history of gene duplication and loss, lineage sorting, lateral transfer, and other events in a gene family's history (Page 2002). It thus has wide applicability in genomics and molecular biology, but has been used relatively infrequently, not because of lack of theory but of implemetations. Recently, substantial progress has been made on both algorithms and software development (Durand et al, 2006; Bansal et al. 2007 ), but important problems remain, including scaling implementations the size of the largest known gene families and species trees to be estimated, and handling uncertainty in the reconstruction of both gene and species trees. This working group is developing tools for inferring gene family histories in the context of species trees by scaling available algorithms and addressing data heterogeneity issues between species and gene phylogenies.

Intro presentation (PDF ) by Vision to iPlant engagement team (July 1, 2009).

Working Group Members

The group includes Todd Vision (University of North Carolina & NESCent), Cecile Ane (University of Wisonsin-Madison) and Jim Leebens-Mack (University of Georgia), along with a wider group of collaborators. The iPlant engagement team includes Sheldon McKay, Michael B. Gonzales, and others.

The working group mailing list is Members of this mailing list include:
Todd Vision
Cecile Ane
William Piel
Zhenyuan (Jerry) Lu
Liya Wang
Michael B. Gonzales
Sheldon McKay
Natalie Henriques
Adam Kubach
Jim Leebens-Mack
John Bowers
Jamie Estill
Andrew Lenards

See also: "Phylogenetic tools for plant comparative genomics" project charter

We have a postdoc position available!. Email for more information.

Progress report

The bioinformatics pipeline for gene-species tree reconciliation is complete and the database has been populated with the reconciled trees and the host-tree relationships.

A developer preview release has been completed with the following features:

  • Database containing reconciliations for over 2500 gene families in six examplar species (poplar, grape, cucumber, papaya, soybean and Arabidopsis thaliana).
  • GUI with the ability to:
    • Search by Gene Identifier or GO term
    • Perform BLAST searches
    • Visualize reconciled trees
    • Retrieve and visualize speciation and gene duplication events
    • Provide overall statistics and links to alignment and sequence files

The tool is currently being integrated into the Discovery Environment and the documentation has been written. User acceptance tests have been defined and a limited test release is planned for early November.

Cooperation with tree visualization group has been intensified with the goal to add interactivity.

The working group has started discussing the scope for Phase 2.

Background information

What is a "discovery environment"?

Assembling the Tree of Life for the Plant Sciences (iPTOL): summary (PDF), proposal (PDF), intro conference agenda, videos

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