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Gene Phylogenies and Orthologous Groups

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Comparative Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1704))

Abstract

This chapter covers the theory and practice of ortholog gene set computation. In the theoretical part we give detailed and formal descriptions of the relevant concepts. We also cover the topic of graph-based clustering as a tool to compute ortholog gene sets. In the second part we provide an overview of practical considerations intended for researchers who need to determine orthologous genes from a collection of annotated genomes, briefly describing some of the most popular programs and resources currently available for this task.

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Notes

  1. 1.

    Certain papers in the literature use the term co-ortholog instead of simply ortholog, to emphasize that this is not always a one-to-one relation. However, the literature also records the usage of co-orthologs in the sense of paralogs [24]. To avoid confusion, we use the simpler term.

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Acknowledgements

This work was funded in part by the Deutsche Forschungsgemeinschaft (Proj. No. MI439/14-1) (to PFS) and a CNPq fellowship (to JCS).

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Authors and Affiliations

  1. Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP, 05508-000, Brazil

    João C. Setubal

  2. Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany

    Peter F. Stadler

  3. Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04103, Leipzig, Germany

    Peter F. Stadler

  4. Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, Leipzig, 04103, Germany

    Peter F. Stadler

  5. Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, Wien, A-1090, Austria

    Peter F. Stadler

  6. Center for Non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, Frederiksberg C, DK-1870, Denmark

    Peter F. Stadler

  7. Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM, 87501, USA

    Peter F. Stadler

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  1. João C. Setubal
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Correspondence to João C. Setubal .

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Editors and Affiliations

  1. Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, São Paulo, Brazil

    João C. Setubal

  2. Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany

    Jens Stoye

  3. Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany

    Peter F. Stadler

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Setubal, J.C., Stadler, P.F. (2018). Gene Phylogenies and Orthologous Groups. In: Setubal, J., Stoye, J., Stadler, P. (eds) Comparative Genomics. Methods in Molecular Biology, vol 1704. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7463-4_1

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  • DOI: https://doi.org/10.1007/978-1-4939-7463-4_1

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