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Bioinformatics pp 461–478Cite as

Species Tree Estimation from Genome-Wide Data with guenomu

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1525))

Abstract

The history of particular genes and that of the species that carry them can be different for a variety of reasons. In particular, gene trees and species trees can differ due to well-known evolutionary processes such as gene duplication and loss, lateral gene transfer, or incomplete lineage sorting. Species tree reconstruction methods have been developed to take this incongruence into account; these can be divided grossly into supertree and supermatrix approaches. Here we introduce a new Bayesian hierarchical model that we have recently developed and implemented in the program guenomu. The new model considers multiple sources of gene tree/species tree disagreement. Guenomu takes as input posterior distributions of unrooted gene tree topologies for multiple gene families, in order to estimate the posterior distribution of rooted species tree topologies.

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Author information

Authors and Affiliations

  1. Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain

    Leonardo de Oliveira Martins & David Posada

  2. Department of Materials, Imperial College London, London, UK

    Leonardo de Oliveira Martins

Authors
  1. Leonardo de Oliveira Martins
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  2. David Posada
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Corresponding author

Correspondence to Leonardo de Oliveira Martins .

Editor information

Editors and Affiliations

  1. Monash University, Melbourne, Victoria, Australia

    Jonathan M. Keith

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de Oliveira Martins, L., Posada, D. (2017). Species Tree Estimation from Genome-Wide Data with guenomu. In: Keith, J. (eds) Bioinformatics. Methods in Molecular Biology, vol 1525. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6622-6_18

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  • DOI: https://doi.org/10.1007/978-1-4939-6622-6_18

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6620-2

  • Online ISBN: 978-1-4939-6622-6

  • eBook Packages: Springer Protocols

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