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 and MCMC

Rev Language Syntax

A very short introduction to the Rev language

Getting Started with RevBayes

A very basic overview on how to use RevBayes

Introduction to Graphical Models

A gentle introduction to graphical models, probabilistic programming, and MCMC using a simple linear regression example.

Introduction to MCMC using RevBayes

A simple Archery example for building a hierarchical model and sampling under Markov Chain Monte Carlo

Introduction to MCMC using RevBayes

Introduction to MCMC Simulation using a simple Binomial Model

Understanding Continuous-Time Markov Models

Simulating DNA sequence evolution with a die

Basic introduction to Rev & MCMC

General Rev language features and simple Poisson regression example

Diagnosing MCMC performance

How to assess the performance of MCMC simulations

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 averaging of substitution models

Reversible-jump MCMC over substitution models

Model selection of partition models

Comparing relative model fit with Bayes factors

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

Substitution Models

Phylogenetic inference of nucleotide data using RevBayes

Molecular dating

Estimating species divergence times using RevBayes

Partitioned data analysis

Current Protocols in Bioninformatics - Phylogenetic Inference using RevBayes (Protocol #2)

Relaxed Clocks & Time Trees

Comparing relaxed clock models & estimating rooted time trees

Discrete morphology - Tree Inference

Phylogenetic inference with discrete morphological data

Phylogenetic Inference using RevBayes

Continuous trait evolution with Ornstein-Uhlenbeck models

Gene tree - species tree reconstruction

Incomplete lineage sorting and the multispecies coalescent

Alignment concatenation

Species tree estimation from multiple concatenated gene sequence alignments

Discrete morphology - Ancestral State Estimation

Ancestral State Estimation and Testing for Irreversibility

Complex hierarchical models for phylogenetic inference

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

Combined-Evidence Analysis and the Fossilized Birth-Death Process for Analysis of Fossil and Extant Specimens

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

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

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 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

Comparative methods

Continuous trait evolution and Brownian motion

Phylogenetic analysis of continous characters and the comparative method

Chromosome Evolution

Modeling chromosome evolution with ChromEvol, BiChroM, and ChromoSSE

Biogeography

Introduction to Historical Biogeography

Phylogeographic analysis under the dispersal-extinction-cladogenesis process

Historical Biogeographic Analysis using a Simple DEC Model

Ancestral range estimation of the silverswords under the dispersal-extinction-cladogenesis process

Historical Biogeographic Analysis using an epoch DEC Model

Ancestral range estimation of the silverswords under the dispersal-extinction-cladogenesis process

Biogeographic dating analysis

Biogeographic dating analysis under the dispersal-extinction-cladogenesis process