Codon Evolution - Mechanisms and Models

Edited by Gina M. Cannarozzi and Adrian Schneider

published by Oxford University Press now available

PART I: Modeling Codon Evolution

1 Background
Adrian Schneider and Gina M. Cannarozzi

2 Parametric models of codon evolution
Maria Anisimova

3 Empirical and semi-empirical models of codon evolution
Adrian Schneider and Gina M. Cannarozzi

4 Monte Carlo computational approaches in Bayesian codon substitution modeling
Nicolas Rodrigue and Nicolas Lartillot

5 Likelihood based clustering (LiBaC) for codon models
Hong Gu, Katherine A. Dunn and Joseph P. Bielawski

6 Detecting and understanding natural selection
Maria Anisimova and David A. Liberles

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

8 Robust estimation of natural selection using parametric codon models
Gavin A. Huttley and Von Bing Yap

9 Simulation of coding sequence evolution
Miguel Arenas and David Posada

10 Use of codon models in molecular dating and functional analysis
Steven A. Benner

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, David Yu, and James M. Morrow

12 Codon models applied to the study of fungal genomes
Gabriela Aguileta and Tatiana Giraud


PART II: CODON USAGE BIAS

13 Measuring codon usage bias
Alexander Roth, Maria Anisimova and Gina M. Cannarozzi

14 Detection and analysis of conservation at synonymous sites
Nimrod D. Rubinstein and Tal Pupko

15 Distance measures and machine learning approaches for codon usage analyses
Fran Supek and Tomislav Smuc

16 The application of population genetics in the study of codon usage bias
Kai Zeng

17 Structural and molecular features of non-standard genetic codes
Maria do Céu Santos and Manuel A. S. Santos