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

Please consider subscribing to my channel by hitting the "Subscribe" button. It is absolutely free and there are no charges. But if you like what I am doing and you do want to support my channel, consider making a voluntary donation at / joshbanta . It helps me to deliver more content and to keep this channel active.
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 Virt...
The instructions for Mac computers are here (from 0:00 to 5:37):
• How to Install Windows...
This tutorial assumes you have already installed the following software:
1) MrBayes: nbisweden.githu...
2) FigTree: tree.bio.ed.ac....
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:
mrbayes.sourcef...
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 B...
2) Second, you must create a new phylogeny using R, and then customize it using a program such as Inkscape:
• How to make a customiz...
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 m...
Mac: • Ubuntu 20.04 virtual m...

[@Tmillar321]

Josh, Great video. I came to learn about some basic commands with Mr. Bayes. I did want to comment that if you add those packages to your path variable you can run them from wherever you are at on the file system. Certainly it would save some time and headache from needing to jump around the file system looking for the right software.

[@florian4513]

Thank you, very clear and pedagogic.

[@hoaninh4045]

Thanks so much for your video, Im a beginer, and I wonder that how can we continue this annalys if we have a problem with the power (may be shut down the computer) while the cmd is running?

[@gemijuine]

Hi Josh! I am now following your awesome tutorial for my study. It is very clear and easy to follow esp fr beginners like me. The prottest3 gave me the +F (observed amino acid frequencies); however, as I am not very well-versed with bioinformatics (even after reading the manual) , I do not know how to set this argument/option in MrBayes. Any idea how to do this? Everyone in could jump in and answer. Thanks!

[@alyrababy]

Thanks so much for this

[@shaguftaperveen5273]

Hi ..will you plz help me to perform multi gene phylogenetic tree by mr bayes..from very start like which softaware i should install ? How to convert my fasta file .... I have my 5 gene sequence file in fasta format .plz help me

[@inesgalan5332]

First of all, thank you for your video! I am trying to get my outgroup to be monophyletic, but I don’t know how to specify this in the prompts… can someone help me here? Thank you

[@DrJBanta]

Hello, I am not sure I understand your question. You should only use a single specimen for your outgroup. If you have multiple specimens for your outgroup, only include one of them and remove the others. Choose one at random. Best wishes, Josh

[@ThePunkPatriot]

Can you talk more about how to generate a nexus file? Is that a multisequence alignment, like in PHYLIP? Or does MrBayes do an MSA on the FASTA/Nexus files? I have presently FASTA files for chloroplast rRNA from NCIB in a txt format, and I've been banging my head against the wall getting an MSA to run in Clustal Omega. My professor ran it for me because neither of us can figure out why it isn't working, and then I used PHYLIP to generate a consensus tree, but the final product is really quite incorrect. I'm trying to teach myself MrBayes now, because PHYLIP is so frustrating.

[@DrJBanta]

Hello, you can follow my tutorial for converting between PHYLIP and Nexus file formats here: kzbin.info/www/bejne/pnaknamdjdSei5o

[@kanansheth337]

Hello, thank you very much for such an informative video. I am a beginner, hence I wanted to know, Instead of Figtree can another software such as MEGA be used for visualization of the phylogenetic tree?

[@DrJBanta]

Hi, yes, any of those may be used! Best, Josh

[@kanansheth337]

@@DrJBanta Can you guide me as to how MEGA can be used for phylogenetic tree visualization after I have obtained results from Mr.Bayes? Because I think the .nex files do not open in MEGA. Thank you.

[@DrJBanta]

@@kanansheth337 See this video: kzbin.info/www/bejne/pHnIeZKlhax8f6M Best, Josh