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PLoS Curr. 2011 Jun 9;3:RRN1240. doi: 10.1371/currents.RRN1240.

Cocos: Constructing multi-domain protein phylogenies.

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Dept. of Computer Science, Free University of Berlin, Germany; Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany and Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics Berlin, Free University of Berlin, Germany.


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).

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