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; Bensal 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.

Working Group Members

Todd Vision, Team Lead, University of North Carolina
Cecile Ane, Collaborator, University of Wisconsin-Madison