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Codon EvolutionMechanisms and Models$
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Gina M. Cannarozzi and Adrian Schneider

Print publication date: 2012

Print ISBN-13: 9780199601165

Published to Oxford Scholarship Online: May 2015

DOI: 10.1093/acprof:osobl/9780199601165.001.0001

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(p.3) Chapter 1 Background
Codon Evolution

Adrian Schneider

Gina M. Cannarozzi

Oxford University Press

This background chapter summarizes some of the basic concepts used in molecular evolution, such as the use of Markov models in modelling sequence evolution as well as maximum-likelihood and Bayesian estimation. It also discusses comparisons of models and methods using likelihood-based tests, simulations, and empirical tests. The goal of this chapter is to provide consistent notation and common definitions, and to give the reader an introduction to those topics while avoiding repeated descriptions of the same concepts in several chapters.

Keywords:   molecular evolution, Markov models, maximum-likelihood estimation, Bayesian estimation, likelihood-based tests, simulations, empirical tests

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