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Contents
Elements of phylogenetic theory
Subsections
Phylogenetic trees
Unrooted phylogenies
String representation of a tree
Branch lengths
Nucleotide substitution models
A Markov model of substitution
Transition matrices
Nucleotide substitution models implemented in
PHASE
JC69
model (Jukes-Cantor, 69)
K80
model (Kimura, 80)
HKY85
model (Hasegawa-Kishino-Yano, 85)
TN93
model (Tamura-Nei, 93)
REV
model (Yang, 94)
Paired-site substitution models
RNA secondary structure
Theory of compensatory substitutions
Base-paired substitution models implemented in
PHASE
RNA6A
model
RNA6B
model (Tillier, 94)
RNA7A
model
RNA7D
model (Tillier, 98)
RNA16A
model
Refinements to substitution models
Invariant and discrete gamma models
The
MIXED
model
Bayesian phylogenetics
Bayes' theorem
Markov chain Monte-Carlo (MCMC)
Priors and proposals
Uniform priors ?
Proposals for the parameters
Proposals for the tree
Pitfalls of Markov chain Monte-Carlo techniques
Gowri-Shankar Vivek 2003-04-24
