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Measuring Natural Selection

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Bioinformatics

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

Abstract

In this chapter, I review the basic algorithm underlying the CODEML model implemented in the software package PAML. This is intended as a companion to the software’s manual, and a primer to the extensive literature available on CODEML. At the end of this chapter, I hope that you will be able to understand enough of how CODEML operates to plan your own analyses.

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Acknowledgements

I would like to thank Alexandra Pavlova for comments and suggestions on an earlier draft of the chapter. I would like to express my deepest gratitude to my supervisor Rohan Clarke, who has given me the freedom and encouragement to explore evolution, adaptation, and bioinformatics in a whole new light, even though he would much rather I went bird-watching. I am also grateful to Paul Sunnucks, whom I had as an idol while still a bright-eyed, young, and naive biology student, and who turned out to be all that I expected and more. Finally, I would also like to thank Jonathan Keith for the opportunity, and for showing me the path to Bayesian theory in evolutionary work.

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Authors and Affiliations

  1. Microbiological Diagnostic Unit (MDU), Public Health Laboratory, Doherty Institute, 792 Elizabeth St., Melbourne, VIC, 3000, Australia

    Anders Gonçalves da Silva

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  1. Anders Gonçalves da Silva
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Correspondence to Anders Gonçalves da Silva .

Editor information

Editors and Affiliations

  1. Monash University, Melbourne, Victoria, Australia

    Jonathan M. Keith

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da Silva, A.G. (2017). Measuring Natural Selection. 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_13

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  • DOI: https://doi.org/10.1007/978-1-4939-6622-6_13

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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

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