How to perform an analysis of molecular variance (AMOVA) using the program Arlequin

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This tutorial shows you how to perform an Analysis of Molecular Variance (AMOVA) using the program Arlequin.

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:
youtube.com/watch?v=diIW3fgewhI
The instructions for Mac computers are here (from 0:00 to 5:37):
youtu.be/f6oU_JzrALk

This tutorial utilizes:

1) WINE:
winehq.org/
WINE lets us run some Windows programs on Linux.

2) The Windows graphical user interface (GUI) version of Arlequin:
cmpg.unibe.ch/software/arlequin35/
This second one may strike you as odd, since we are using Linux. Arlequin comes in a Linux version, but I prefer the Windows version, because it has friendly drop-down menus that make things much easier. We will run it on Linux using WINE. I will show you how. The version of Arlequin to download is WinArl35.zip (cmpg.unibe.ch/software/arlequin35/win/WinArl35.…).

But you can just use my pre-configured Ubuntu Linux virtual machine to save yourself the hassle of installing or configuring anything! Read more below.

This tutorial uses a file called "output.arp," which we created in another tutorial entitled, "How to convert a FASTA file to an Arlequin file." You can find that video here:
youtube.com/watch?v=z9dpRrLajCs&t=844s

This tutorial finishes with an output file called "output.xml." In another tutorial, I show you how to extract the pairwise FST values from that data file, in both tabular (matrix) and graphical formats. You can view that tutorial here:
youtube.com/watch?v=U2fj3pfPUlE

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: youtube.com/watch?v=-K8byTOpTY4
Mac: youtu.be/yGYjI2sCqIM