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See detailCocos: Constructing multi-domain protein phylogenies.
Homilius, Max; Wiedenhoeft, John; Thieme, Sebastian et al

in PLoS Currents (2011), 3

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 ... [more ▼]

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). [less ▲]

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