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Inferring Trees

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Bioinformatics

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 452))

Abstract

Molecular phylogenetics examines how biological sequences evolve and the historical relationships between them. An important aspect of many such studies is the estimation of a phylogenetic tree, which explicitly describes evolutionary relationships between the sequences. This chapter provides an introduction to evolutionary trees and some commonly used inferential methodology, focusing on the assumptions made and how they affect an analysis. Detailed discussion is also provided about some common algorithms used for phylogenetic tree estimation. Finally, there are a few practical guidelines, including how to combine multiple software packages to improve inference, and a comparison between Bayesian and maximum likelihood phylogenetics.

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Acknowledgments

S.W. is funded by EMBL. Comments and suggestions from Nick Goldman, Lars Jermiin, Ari Loytynoja, and Fabio Pardi all helped improve previous versions of the manuscript.

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Authors and Affiliations

  1. University of Manchester, Manchester, United Kingdom

    Simon Whelan (Faculty of Life Sciences)

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  1. Simon Whelan
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Editors and Affiliations

  1. School of Mathematical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia

    Jonathan M. Keith PhD

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© 2008 Humana Press, a part of Springer Science+Business Media, LLC

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Whelan, S. (2008). Inferring Trees. In: Keith, J.M. (eds) Bioinformatics. Methods in Molecular Biology™, vol 452. Humana Press. https://doi.org/10.1007/978-1-60327-159-2_14

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  • DOI: https://doi.org/10.1007/978-1-60327-159-2_14

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-707-5

  • Online ISBN: 978-1-60327-159-2

  • eBook Packages: Springer Protocols

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