Cocos: Constructing multi-domain protein phylogenies

M. Homilius, J. Wiedenhoeft, S. Thieme, C. Standfuß, 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).

Pubmed ID: 21686311. DOI: 10.1371/currents.RRN1240.