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Codon Evolution: Mechanisms and Models

Gina M. Cannarozzi and Adrian Schneider


Codon-based models of evolution are a relatively new addition to the toolkit of computational biologists, and in recent years remarkable progress has been made in this area. The study of evolution at the codon level captures information contained in both amino acid and synonymous DNA substitutions. By combining these two types of information, codon analyses are more powerful than those of either amino acid or DNA evolution alone. This is a clear benefit for most evolutionary analyses, including phylogenetic reconstruction, detection of selection, ancestral sequence reconstruction, and alignmen ... More

Keywords: codon evolution, amino acid, DNA substitutions, codon analyses, evolutionary analyses, genetic sequences, codon models

Bibliographic Information

Print publication date: 2012 Print ISBN-13: 9780199601165
Published to Oxford Scholarship Online: May 2015 DOI:10.1093/acprof:osobl/9780199601165.001.0001


Affiliations are at time of print publication.

Gina M. Cannarozzi, editor
University of Bern, Switzerland

Adrian Schneider, editor
University of Utrecht, The Netherlands

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Part I Modelling codon evolution

Chapter 1 Background

Adrian Schneider and Gina M. Cannarozzi

Chapter 5 Likelihood-based clustering (LiBaC) for codon models

Hong Gu, Katherine A. Dunn, and Joseph P. Bielawski

Chapter 6 Detecting and understanding natural selection

Maria Anisimova and David A. Liberles

Chapter 7 Codon models as a vehicle for reconciling population genetics with inter-specific sequence data

Jeffrey L. Thorne, Nicolas Lartillot, Nicolas Rodrigue, and Sang Chul Choi

Chapter 9 Simulation of coding sequence evolution

Miguel Arenas and David Posada

Chapter 11 The future of codon models in studies of molecular function: ancestral reconstruction and clade models of functional divergence

Belinda S. W. Chang, Jingjing Du, Cameron J. Weadick, Johannes Müller, Constanze Bickelmann, D. David Yu, and James M. Morrow

Part II Codon usage bias

Chapter 13 Measuring codon usage bias

Alexander Roth, Maria Anisimova, and Gina M. Cannarozzi

End Matter