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Inferring Orthology and Paralogy

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Evolutionary Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 855))

Abstract

The distinction between orthologs and paralogs, genes that started diverging by speciation versus duplication, is relevant in a wide range of contexts, most notably phylogenetic tree inference and protein function annotation. In this chapter, we provide an overview of the methods used to infer orthology and paralogy. We survey both graph-based approaches (and their various grouping strategies) and tree-based approaches, which solve the more general problem of gene/species tree reconciliation. We discuss conceptual differences among the various orthology inference methods and databases, and examine the difficult issue of verifying and benchmarking orthology predictions. Finally, we review typical applications of orthologous genes, groups, and reconciled trees and conclude with thoughts on future methodological developments.

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Acknowledgments

We thank Stefan Zoller for helpful feedback on the manuscript. Part of this chapter started as assignment for the graduate course “Reviews in Computational Biology” (263-5151-00L) at ETH Zurich.

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Authors and Affiliations

  1. Department of Computer Science, ETH Zurich, Zurich, Switzerland

    Adrian M. Altenhoff & Christophe Dessimoz

  2. Swiss Institute of Bioinformatics, Lausanne, Switzerland

    Adrian M. Altenhoff & Christophe Dessimoz

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  1. Adrian M. Altenhoff
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Correspondence to Christophe Dessimoz .

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  1. Department of Computer Science, ETH Zürich, Universitätsstr. 6, Zürich, 8092, Switzerland

    Maria Anisimova

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Altenhoff, A.M., Dessimoz, C. (2012). Inferring Orthology and Paralogy. In: Anisimova, M. (eds) Evolutionary Genomics. Methods in Molecular Biology, vol 855. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-582-4_9

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