Department of Computer Science
 Rutgers University

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Cocos: Constructing multi-domain protein phylogenies

M. Homilius, J. Wiedenhoeft, S. Thieme, C. StandfuƟ, I. Kel and R. Krause

PLoS Currents: Tree of Life 2011.

Phylogenies of multi-domain proteins have to incorporate macro-evolutionary events, which dramatically increases the complexity of their construction. We present an application to infer ancestral multi-domain proteins given a species tree and domain phylogenies. As the individual domain phylogenies are often incongruent, we provide diagnostics for the identification and reconciliation of implausible topologies. We implement and extend a suggested algorithmic approach by Behzadi and Vingron (2006).