Inferring Orthology and Paralogy.
- Altenhoff AM Computer Science Department, ETH Zurich, Zurich, Switzerland.
- Glover NM Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Dessimoz C Swiss Institute of Bioinformatics, Lausanne, Switzerland. Christophe.Dessimoz@unil.ch.
- 2019-07-07
Published in:
- Methods in molecular biology (Clifton, N.J.). - 2019
Orthology
Orthology benchmarking
Paralogy
Tree reconciliation
Algorithms
Animals
Computational Biology
Evolution, Molecular
Genome
Genomics
Humans
Multigene Family
Phylogeny
English
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.
- Language
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- English
- Open access status
- hybrid
- Identifiers
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- DOI 10.1007/978-1-4939-9074-0_5
- PMID 31278664
- Persistent URL
- https://sonar.ch/global/documents/2991
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