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

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 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

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

Model selection

Comparing relative model fit with Bayes factors

Assessing Phylogenetic Reliability Using RevBayes and $P^{3}$

Model adequacy testing using posterior prediction (Data Version).

Standard tree inference

Substitution Models

Phylogenetic inference of nucleotide data using RevBayes

Relaxed Clocks & Time Trees

Comparing relaxed clock models & estimating rooted time trees

Discrete morphology

Phylogenetic inference with discrete morphological data

Assessing Phylogenetic Reliability Using RevBayes and $P^{3}$

Model adequacy testing using posterior prediction (Inference Version).

Gene tree - species tree reconstruction

Incomplete lineage sorting and the multispecies coalescent

Partitioned data analysis

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

Discrete morphology - Tree Inference

Phylogenetic inference with discrete morphological data

Alignment concatenation

Species tree estimation from multiple concatenated gene sequence alignments

Phylogenetic Inference using RevBayes

Continuous trait evolution with Ornstein-Uhlenbeck models

Complex hierarchical models for phylogenetic inference

Combined-Evidence Analysis and the Fossilized Birth-Death Process

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

Diversification Rate Estimation

Branch-Specific Diversification Rate Estimation

How to estimate branch-specific shifts in diversification rates

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

State-dependent diversification rate estimation in RevBayes

Inference using the binary state-dependent speciation and extinction (BiSSE) branching process

Co-estimating state-dependent diversification rates and ancestral states in RevBayes

Inference using the binary state-dependent speciation and extinction (BiSSE) branching process

Chromosome Evolution

Phylogenetic analysis with ChromoSSE models

Macroevolutionary Analysis of Stratigraphic Range Data

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

Diversification Rate Estimation with Missing Taxa

How to estimate diversification rates with incomplete taxon sampling

Comparative methods

Continuous trait evolution and Brownian motion

Phylogenetic analysis of continous characters and the comparative method

Biogeography

Historical biogeography

Phylogeographic analysis under the dispersal-extinction-cladogenesis process