Tutorials

PDF	Description	Data	Scripts
Manual	The complete manual containing all tutorials.
Introduction
Getting Started	Getting Started with RevBayes.
Rev basics	Basic language features.
Rev syntax	General Rev language features and simple statistical (Poisson) regression model example.
Bayesian Inference and MCMC simulation
Tutorial	Basic Introduction to Markov chain Monte Carlo using an Archery Example.		Example script (Simple MCMC) Example script (Moves) Example script (RevBayes MCMC)
Tutorial	Basic Introduction to Markov chain Monte Carlo using a Coin-Flip Example.		Example script (Simple MCMC) Example script (Moves) Example script (RevBayes MCMC)
Tutorial	Running and diagnosing an MCMC analysis
Model Selection and Model Fit (Adequacy)
Tutorial	Compute marginal likelihoods to selection between models	Primates data	Example script
Tutorial	Assessing Phylogenetic Reliability	Example data	Example scripts
Basic phylogeny reconstruction and substitution models
Tutorial	Models of molecular character evolution (substitution models).	Primates data	Example script (Jukes-Cantor) Example script (GTR+Gamma+Inv)
Tutorial	Strategies for partitioning molecular data matrices, e.g., by genes and codon position.	Primates cytB data Primates cox2 data	Example script for MCMC (uniform partition) Example script for MCMC (by-gene partition) Example script for MCMC (by-codon partition) Example script for marginal likelihood (uniform partition)
Divergence Time Estimation
Tutorial	Divergence time estimation and node calibrations	Primates data	Example scripts.
Tutorial	Divergence time estimation and relaxed clocks	Primates data	Example scripts.
Tutorial	Time trees and divergence time estimation using relaxed clocks	Bears data Bears tree
Tutorial	FBD divergence dating using morphology and molecular data	Bears data Scripts
Species tree estimation
Tutorial	Concatenation of multiple genes	Primates data	Example script
Tutorial	Multi-species coalescent analysis	Primates data	Example script
Diversification Rate Estimation
Tutorial	Basic diversification using constant-rate pure birth and birth-death models.	Primates phylogeny	Example scripts.
Tutorial	Diversification rates through-time using episodic birth-death models.	Primates phylogeny	Example scripts.
Tutorial	Incomplete taxon sampling.	Primates phylogeny	Example scripts.
Tutorial	Branch-specific diversification rate estimation.	Primates phylogeny	Example scripts.
Tutorial	State-dependent diversification rate estimates using SSE models	Example data	Example scripts
Discrete morphology
Tutorial	Models of morphological character evolution (substitution models).	Bears data	Example scripts.	Precooked Output
Biogeography
Tutorial	Biogeographic dating under the DEC model	Silversword data	Example scripts Example output
Chromosome Evolution
Tutorial	Models of chromosome number evolution	Example data	Example scripts
Continuous trait evolution
Tutorial	Continuous trait evolution models: Brownian Motion	Primates data	Example script
Tutorial	Continuous trait evolution models: Ornstein-Uhlenbeck models	Primates data	Example scripts

RevBayes

Bayesian graphical models

Data and analysis files for Current Protocols in Bioninformatics: Phylogenetic Inference using RevBayes

Tutorials