Getting Started in Structural Phylogenomics

Structural phylogenomics refers to the combined use of evolutionary and structural information in a bioinformatics analysis. The term phylogenomics refers to two distinct tasks: reconstructing a species phylogeny using multiple genes (for a review, see [1]) and predicting protein function by estimating the evolutionary history of a family of related sequences (i.e., a gene tree or multi-gene tree including gene duplication events) [2]–[4]. In this “Getting Started” article, we focus on the latter task, restricting our discussion to the construction and analysis of phylogenetic trees for amino acid data, and including protein structure data and structure prediction to improve the accuracy of functional annotation. We address the following questions: Why perform a complicated structural phylogenomic analysis when simpler approaches are available? What are the fundamental underlying assumptions of this approach, and what are the implications of any conflicts with these assumptions? What technical challenges do we need to address to achieve the full potential of these ideas?

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