This list shows all of the RevBayes tutorials for learning various aspects of RevBayes and Bayesian phylogenetic analysis. Each one explicitly walks you through model specification and analysis set-up for different phylogenetic methods. These tutorials have been written for new users to learn RevBayes at home, at workshops, and in courses taught at the undergraduate and graduate levels. You may find that the styles are somewhat different between tutorials and that some have overlapping content.
Please see the Tutorial Format guide for details about how to read the tutorials.
Please see Recommended Software for links to various software programs you may need to download in order to follow the tutorials.
Getting Started with RevBayes and Rev Language Syntax
Overview of introductory topics
Getting Started with RevBayes
A very basic overview on how to use RevBayes
Rev Language Syntax
A very short introduction to the Rev language
Introduction to Graphical Models
A gentle introduction to graphical models, probabilistic programming, and MCMC using a simple linear regression example.
Setting Up RevBayes
Preparing your computer to work with phylogenetic data in RevBayes
Introduction to RevGadgets
Plotting the output of RevBayes analyses in the R package RevGadgets.
Using RevBayes with Docker
Using a platform-independent container to run RevBayes on your computer or a computing cluster
Introduction to Markov chain Monte Carlo (MCMC) Sampling
Overview of topics on MCMC methods in RevBayes
Introduction to MCMC
A simple Poisson regression example
Introduction to MCMC using RevBayes
Introduction to MCMC Simulation using a simple Binomial Model
Introduction to MCMC using RevBayes
A simple Archery example for building a hierarchical model and sampling under Markov Chain Monte Carlo
Overview of Moves in MCMC
Guidelines and Recommendation
Debugging your Markov chain Monte Carlo (MCMC)
Practical guidelines for issues with MCMC for Bayesian phylogenetic inference
Convergence assessment
Phylogenetic convergence assessment using the R package Convenience
General Introduction to Model selection
Comparing relative model fit with Bayes factors
Model selection of common substitution models for one locus
Comparing relative model fit with Bayes factors
Model selection of partition models
Comparing relative model fit with Bayes factors
Model averaging of substitution models
Reversible-jump MCMC over substitution models
Introduction to Posterior Prediction
Assessing the fit of Normal distributions to trait data
Assessing Phylogenetic Reliability Using RevBayes and $P^{3}$
Model adequacy testing using posterior prediction (Data Version).
Assessing Phylogenetic Reliability Using RevBayes and $P^{3}$
Model adequacy testing using posterior prediction (Inference Version).
Assessing Phylogenetic Reliability Using RevBayes and $P^{3}$
Model adequacy testing using posterior prediction (Morphological Models).
Understanding Continuous-Time Markov Models
Simulating DNA sequence evolution with a die
Nucleotide substitution models
Phylogenetic inference of nucleotide data using RevBayes
Partitioned data analysis
Current Protocols in Bioinformatics - Phylogenetic Inference using RevBayes (Protocol #2)
Discrete morphology - Multistate Characters
Phylogenetic inference with discrete morphological data
Discrete morphology - Tree Inference
Phylogenetic inference with discrete morphological data
Dating trees
Estimating species divergence times using RevBayes
Relaxed Clocks & Time Trees
Comparing relaxed clock models & estimating rooted time trees
Sequential Bayesian inference of phylogeny
Example sequential Bayesian analysis for divergence time estimation in RevBayes
Polymorphism-aware phylogenetic models with balancing selection
Species tree inference and identification of preferred allele frequency for balancing selection in RevBayes
Polymorphism-aware phylogenetic models
Species tree inference with allele frequency data in RevBayes
Dating with Relative Constraints
Constraining the relative order of nodes when dating a phylogeny
Combined-Evidence Analysis and the Fossilized Birth-Death Process for Analysis of Extant Taxa and Fossil Specimens
Joint inference of divergence times and phylogenetic relationships of fossil and extant taxa
Introduction to Discrete Morphology Evolution
Overview of types of Analyses
Discrete morphology - Ancestral State Estimation
The Equal Rates Markov Model
Discrete morphology - Ancestral State Estimation with the independent rates model
Testing for Unequal Rates
Discrete morphology - Ancestral State Estimation and Irreversibility
Testing for Irreversibility
Discrete morphology - Stochastic Character Mapping and Hidden Rates
Mapping Character Transitions and Testing for Rate Variation
Discrete morphology - Correlation among Characters
Testing for Correlation
Discrete morphology - Ancestral State Estimation (Mammals & Placenta Type)
Ancestral State Estimation and Testing for Irreversibility
Introduction to Models of Continuous-Character Evolution
Overview of Standard Models of Continuous-Character Evolution
Simple Brownian Rate Estimation
Estimating rates of Brownian-motion evolution
Relaxed Brownian Rate Estimation
Estimating branch-specific rates of Brownian-motion evolution
State-Dependent Brownian Rate Estimation
Estimating state-dependent rates of Brownian-motion evolution
Multivariate Brownian Motion
Accounting for correlations among continuous traits
Simple Ornstein-Uhlenbeck Models
Estimating optima under Ornstein-Uhlenbeck evolution
Relaxed Ornstein-Uhlenbeck Models
Estimating lineage-specific optima under Ornstein-Uhlenbeck evolution
Reconstructing Host Repertoire Evolution
Inference of ancestral ecological interactions
Introduction to Diversification Rate Estimation
Overview of Analyses, Models and Theory
Simple Diversification Rate Estimation
Comparing different constant-rate models of lineage diversification
Episodic Diversification Rate Estimation
Estimating Rate-Variation Through Time in Diversification Rates
Environmental-dependent Speciation & Extinction Rates
Estimating Correlation between Diversification Rates and Environmental Characters
Mass Extinction Estimation
Estimating Mass Extinctions from Phylogenies with Fossil and Extant Taxa
Branch-Specific Diversification Rate Estimation
How to estimate branch-specific shifts in diversification rates
Background on state-dependent diversification rate estimation
An introduction to inference using state-dependent speciation and extinction (SSE) branching processes
State-dependent diversification with BiSSE and MuSSE
Inference using the binary/multiple state-dependent speciation and extinction (BiSSE/MuSSE) branching process
State-dependent diversification with HiSSE
Inference using the hidden character binary/multiple state-dependent speciation and extinction with (HiSSE) branching process
State-dependent diversification with the ClaSSE model
Accommodating both cladogenetic and anagenetic changes
Assumptions of Diversification Rate Estimation
Choices and impact of conditions of the birth-death process
Diversification Rate Estimation with Missing Taxa
How to estimate diversification rates with incomplete taxon sampling
Chromosome Evolution
Modeling chromosome evolution with ChromEvol, BiChroM, and ChromoSSE
Introduction to phylogenetic biogeography with the DEC model
Overview of the Dispersal-Extinction-Cladogenesis (DEC) model
Simple phylogenetic analysis using the DEC model
Estimating ancestral ranges using the Dispersal-Extirpation-Cladogenesis (DEC) model
Advanced phylogenetic analysis using the DEC model
Ancestral range estimates using DEC with time- and region-dependent effects on dispersal rates
Biogeographic dating using the DEC model
Estimating divergence times with molecular, biogeographic, and paleogeographic evidence with the DEC model
Introduction to phylogenetic biogeography with the FIG model
Using the feature-informed geographic state-dependent speciation-extinction (FIG) model for phylogenetic biogeography
Feature-informed geographic state-dependent speciation-extinction (FIG) model
A phylogenetic model where GeoSSE event rates are informed by regional features
Geographic state-dependent speciation-extinction (GeoSSE) model
A phylogenetic model of biogeographic dispersal, extinction, and speciation
Time-heterogeneous FIG (TimeFIG) model
A FIG model with paleogeographically varying regional features
Biogeographic dating using the TimeFIG model
Using the TimeFIG model to jointly infer divergence times and biogeographic history
Coalescent Analyses
Estimating Demographic Histories with Bayesian Coalescent Skyline Plot Models
StairwayPlot Analyses
Estimating Demographic Histories from SNP data with Bayesian StairwayPlot Approach