Related Experiment Video
Updated: Feb 21, 2026

A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
A biologist's guide to Bayesian phylogenetic analysis
Fabrícia F Nascimento1,2, Mario Dos Reis3, Ziheng Yang4
1Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK. f.nascimento@imperial.ac.uk.
None:
Bayesian methods have become very popular in molecular phylogenetics due to the availability of user-friendly software implementing sophisticated models of evolution. However, Bayesian phylogenetic models are complex, and analyses are often carried out using default settings, which may not be appropriate. Here, we summarize the major features of Bayesian phylogenetic inference and discuss Bayesian computation using Markov chain Monte Carlo (MCMC), the diagnosis of an MCMC run, and ways of summarising the MCMC sample. We discuss the specification of the prior, the choice of the substitution model, and partitioning of the data. Finally, we provide a list of common Bayesian phylogenetic software and provide recommendations as to their use.
Related Concept Videos
Evolutionary Relationships through Genome Comparisons
Phylogenetic Trees
Phylogeny
Gene Evolution - Fast or Slow?
In contrast, regions which code...
Gene Evolution - Fast or Slow?
Applications of Molecular Taxonomy

