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

Protocol 1 

Primates data

Example script (Jukes-Cantor )

Example script (GTR-Gamma )

Protocol 2 

Primates data

Example script (Jukes-Cantor )

Example script (GTR-Gamma )

Protocol 3 

Primates data

Example script (Jukes-Cantor )

Example script (GTR-Gamma )

Tutorials

Manual

The complete manual containing all tutorials. 

Introduction

Getting Started

Getting Started with RevBayes. 

Rev basics

Basic language features and simple statistical (Poisson) regression model example. 

Tutorial

Basic Introduction to Markov chain Monte Carlo. 

Example script (Simple MCMC)

Example script (Moves)

Example script (RevBayes MCMC)

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)

MCMC Strategies and Model Selection

Tutorial

Running and diagnosing an MCMC analysis 

Tutorial

Compute marginal likelihoods to selection between models 

Primates data

Example script

More substitution models, data partitioning, and discrete morphology

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)

Tutorial

Models of morphological character evolution (substitution models). 

Bears data

Example scripts.

Precooked Output

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

Divergence time estimation using tip-dating 

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

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

Character-dependent diversification rate estimation. 

Primates phylogeny and morphology

Example MCMC script.

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

Species tree estimation

Tutorial

Concatenation of multiple genes 

Primates data

Example script

Tutorial

Multi-species coalescent analysis 

Primates data

Example script

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

Model Fit

Tutorial

Assessing Phylogenetic Reliability 

Example data

Example scripts