Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Reconstructing domain compositions of ancestral multi-domain proteins
RCG'06 Proceedings of the RECOMB 2006 international conference on Comparative Genomics
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Essential cellular processes are controlled by functional interactions of protein domains, which can be inferred from their evolutionary histories. Methods to reconstruct these histories are challenged by the complexity of reconstructing macroevolutionary events. In this work we model these events using a novel network-like structure that represents the evolution of domain combinations, called plexus. We describe an algorithm to find a plexus that represents the evolution of a given collection of domain histories as phylogenetic trees with the minimum number of macroevolutionary events, and demonstrate its effectiveness in practice.