Phylogenetic inference using RevBayes by Hohna, Landis, and Heath in 2017
!RevBayes homepage
I. Getting started with RevBayes
1. Introduction
2. Introduction to RevBayes and Rev
3. Reading and manipulating data
II. Inference
4. Introduction to Markov chain Monte Carlo algorithms
III. Basic phylogeny estimation
5. Continuous time Markov model for discrete character evolution
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5.1 Overview
- See Markov Processes for Stochastic Modeling by Oliver Ibe in 2013 section 5.2 for a derivation of the solution to the stationary continuous-time Markov process in terms of the matrix exponential of the instantaneous rate matrix, which is usually named \[Q\] “5.2 Transient analysis”
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The substitution models of molecular evolution
- JC69
- F81
- HKY85
- GTR
- GTR+Gamma
- GTR+Gamma+I
- 5.2 Data and files
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5.3 Example: character evolution under the Jukes-Cantor substitution model
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Steps
- (1) setting up a Jukes-Cantor (JC) substitution model for an alignment of the cytochrome b subunit;
- (2) approximating the posterior probability of the tree topology and node ages (and all other parameters) using MCMC, and;
- (3) summarizing the MCMC output by computing the maximum a posteriori tree.
- \[t\] is the branch length in units of time
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- 5.4 The Hasegawa-Kishino-Yano (HKY) 1985 substitution model
- 5.5 The General Time-Reversible (GTR) substitution model
- 5.6 The discrete gamma model of among site rate variation
- 5.7 Modeling invariable sites