Inferring Orthology and Paralogy

  • Adrian M. Altenhoff
  • Christophe DessimozEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 855)


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.

Key words

Orthology Paralogy Tree reconciliation Orthology benchmarking 



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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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Department of Computer ScienceETH ZurichZurichSwitzerland
  2. 2.Swiss Institute of BioinformaticsLausanneSwitzerland

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