How to perform a Bayesian Markov Chain Monte Carlo-based phylogenetic analysis using MrBayes

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This tutorial shows you how to perform a Markov Chain Monte Carlo (MCMC)-based phylogenetic analysis using the software MrBayes (Mr. Bayes) on an Ubuntu Linux machine.

Please note: MrBayes is Markov Chain Monte Carlo (MCMC)-based, NOT coalescence-based!

This tutorial assumes you are using Ubuntu Linux version 20.04 as your operating system. If you do not have a computer running Ubuntu, fear not. You can install Ubuntu as a virtual machine within your current operating system. It is all free.
The instructions for Windows computers are here:
   • Install Ubuntu on VirtualBox || Linux...  
The instructions for Mac computers are here (from 0:00 to 5:37):
   • How to Install Windows 10 in UTM (M1/...  

This tutorial assumes you have already installed the following software:
1) MrBayes: http://nbisweden.github.io/MrBayes/in...
2) FigTree: http://tree.bio.ed.ac.uk/software/fig...

Or you can just use the pre-configured virtual machine that I created. See more on that below.

Here are the commands I used from the Terminal window to begin running MrBayes. I started out in the home directory:

cd bin
cd MrBayes-3.2.7a
cd src
./mb

The webpage I referenced in the tutorial, explaining the options for the 'lset' command:
http://mrbayes.sourceforge.net/Help/l...

Once you have finished performing this tutorial, you may want to make a nice publication-ready figure for use in a journal article, presentation, or thesis. The output from FigTree, however, is clunky. I have tutorials showing you how to customize the figure to make it look how you want it to look:

1) First, you must convert the result file from MrBayes into the Newick Tree format. Mine is the only way I know if to do it right:
   • How to convert a Mr  Bayes output fil...  

2) Second, you must create a new phylogeny using R, and then customize it using a program such as Inkscape:
   • How to make a customizable publicatio...  

FYI:
I have made a Linux virtual machine that is pre-configured with population genetics and ecological niche modeling programs. I have made videos explaining how to hook up this virtual machine within your Mac or Windows computer, so that you can start using the pre-configured software without having to install any of them (and even without having to install Ubuntu Linux!).

Windows:    • Ubuntu 20.04 virtual machine for Virt...  
Mac:    • Ubuntu 20.04 virtual machine for UTM ...