RevBayes Tutorials


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.

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Introduction to RevBayes

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 MCMC

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

Convergence assessment

Phylogenetic convergence assessment using the R package Convenience

Model Selection and Testing

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).

Standard tree inference

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

Molecular dating

Estimating species divergence times using RevBayes

Relaxed Clocks & Time Trees

Comparing relaxed clock models & estimating rooted time trees

Complex hierarchical models for phylogenetic inference

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

Combined-Evidence Analysis and the Fossilized Birth-Death Process for Stratigraphic Range Data

Joint inference of divergence times and phylogenetic relationships of fossil and extant taxa

Diversification Rate Estimation

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

Background on state-dependent diversification rate estimation

An introduction to inference using state-dependent speciation and extinction (SSE) branching processes

Branch-Specific Diversification Rate Estimation

How to estimate branch-specific shifts in diversification rates

Diversification Rate Estimation with Missing Taxa

How to estimate diversification rates with incomplete taxon sampling

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 HiSSE and ClaSSE

Hidden state and cladogenetic state-dependent speciation and extinction (HiSSE & ClaSSE) branching process

Macroevolutionary Analysis of Stratigraphic Range Data

Inference of diversification rates using the fossilized birth-death range process

Chromosome Evolution

Modeling chromosome evolution with ChromEvol, BiChroM, and ChromoSSE

Comparative methods

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

Discrete morphology - Ancestral State Estimation

Ancestral State Estimation and Testing for Irreversibility

Biogeography

Introduction to Phylogenetic Models of Discrete Biogeography

Overview of the Dispersal-Extirpation-Cladogenesis (DEC) model

Simple Phylogenetic Analysis of Historical Biogeography

Estimating ancestral ranges using the Dispersal-Extirpation-Cladogenesis (DEC) model

Advanced Phylogenetic Analysis of Historical Biogeography

Ancestral range estimates using the Dispersal-Extirpation-Cladogenesis (DEC) model while incorporating time-dependent and region-dependent effects on dispersal rates

Biogeographic Dating of Divergence Times

Estimating divergence times with molecular, biogeographic, and paleogeographic evidence under the Dispersal-Extirpation-Cladogenesis (DEC) model