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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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Empirical and semi-empirical models of codon evolution

Empirical and semi-empirical models of codon evolution

Chapter:
(p.34) Chapter 3 Empirical and semi-empirical models of codon evolution
Source:
Codon Evolution
Author(s):

Adrian Schneider

Gina M. Cannarozzi

Publisher:
Oxford University Press
DOI:10.1093/acprof:osobl/9780199601165.003.0003

This chapter first describes the empirical codon model presented by Schneider et al. in 2005, demonstrating its advantages over amino acid models for aligning coding sequences. It then outlines two models, proposed in 2007, that introduce parameters to empirical models in order to combine the advantages of empirical and parametric models. Doron-Faigenboim and Pupko (2007) presented a ‘combined empirical and mechanistic’ model of codon evolution in which empirical transition rates between amino acids formed the basis for a parametric codon model. Another version of a combination of empirical and parametric model was presented by Kosiol et al. (2007). The empirical codon matrix that is the basis for their model was derived by directly estimating a rate matrix using an expectation maximization algorithm from a set of multiple sequence alignments and trees. The chapter concludes with a study that used unsupervised learning to determine the relevant parameters in a codon model.

Keywords:   codon evolution, empirical model, parametric model, amino acids, expectation maximization algorithm

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