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Appendices

Ziheng Yang.

in Molecular Evolution

May 2014; p ublished online August 2014 .

Chapter. Subjects: Biomathematics and Statistics; Evolutionary Biology. 4488 words.

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Bayesian computation (MCMC)

Ziheng Yang.

in Molecular Evolution

May 2014; p ublished online August 2014 .

Chapter. Subjects: Biomathematics and Statistics; Evolutionary Biology. 32739 words.

This chapter provides a detailed introduction to modern Bayesian computation. The Metropolis–Hastings algorithm is illustrated using a simple example of distance estimation between two...

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Bayesian phylogenetics

Ziheng Yang.

in Molecular Evolution

May 2014; p ublished online August 2014 .

Chapter. Subjects: Biomathematics and Statistics; Evolutionary Biology. 27279 words.

This chapter discusses the implementation of various models of genetic sequence evolution in Bayesian phylogenetic analysis. It discusses the specification of priors for parameters in such...

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Bayesian theory

Ziheng Yang.

in Molecular Evolution

May 2014; p ublished online August 2014 .

Chapter. Subjects: Biomathematics and Statistics; Evolutionary Biology. 18645 words.

This chapter summarizes the Frequentist–Bayesian controversy in statistics, and introduces the basic theory of Bayesian statistical inference, such as the prior, posterior, and Bayes’...

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Coalescent theory and species trees

Ziheng Yang.

in Molecular Evolution

May 2014; p ublished online August 2014 .

Chapter. Subjects: Biomathematics and Statistics; Evolutionary Biology. 32207 words.

This chapter introduces Kingman’s coalescent process, which describes the genealogical relationships within a sample of DNA sequences taken from a population, and forms the basis for...

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Comparison of phylogenetic methods and tests on trees

Ziheng Yang.

in Molecular Evolution

May 2014; p ublished online August 2014 .

Chapter. Subjects: Biomathematics and Statistics; Evolutionary Biology. 17404 words.

This chapter summarizes the criteria for comparing different tree reconstruction methods, such as consistency and efficiency, as well as computer simulation studies that evaluate the...

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Maximum likelihood methods

Ziheng Yang.

in Molecular Evolution

May 2014; p ublished online August 2014 .

Chapter. Subjects: Biomathematics and Statistics; Evolutionary Biology. 31441 words.

This chapter describes the pruning algorithm for calculating the likelihood on a tree, as well as extensions under complex substitution models, including the gamma and covarion models of...

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Models of amino acid and codon substitution

Ziheng Yang.

in Molecular Evolution

May 2014; p ublished online August 2014 .

Chapter. Subjects: Biomathematics and Statistics; Evolutionary Biology. 20482 words.

This chapter discusses Markov chain models of amino acid replacement and codon substitution. It then discusses the various methods for estimating the numbers of synonymous and nonsynonymous...

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Models of nucleotide substitution

Ziheng Yang.

in Molecular Evolution

May 2014; p ublished online August 2014 .

Chapter. Subjects: Biomathematics and Statistics; Evolutionary Biology. 21271 words.

This chapter discusses Markov chain models of nucleotide substitution, such as JC69, K80, HKY85 and the general time-reversible (GTR) model, and their use in the calculation of the distance...

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Molecular clock and estimation of species divergence times

Ziheng Yang.

in Molecular Evolution

May 2014; p ublished online August 2014 .

Chapter. Subjects: Biomathematics and Statistics; Evolutionary Biology. 16641 words.

This chapter discusses the hypothesis of the molecular clock and its use to date species divergences. It introduces various tests of the molecular clock as well as strategies to relax the...

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