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Cocos: Constructing multi-domain protein phylogenies

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Wiedenhoeft,  J.
Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Thieme,  S.
Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Krause,  R.
Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Citation

Homilius, M., Wiedenhoeft, J., Thieme, S., Standfuss, C., Kel, I., & Krause, R. (2011). Cocos: Constructing multi-domain protein phylogenies. PLoS Curr, 3, RRN1240. Retrieved from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=21686311.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0010-790A-1
Abstract
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).