Tutorials

Genomics
  • How to convert between a PHYLIP file and FASTA file, and how to convert from a FASTA file to a Nexus file

YouTube Video

    • Files needed for tutorial
    • This tutorial utilizes: 
    • Note that there are actually two different types of PHYLIP files: interleaved and sequential. This tutorial assumes you are using sequential PHYLIP files.
      • Don't have Linux? No problem! You can run it as a virtual machine within your Windows PC or Mac.
      • See the show notes on this video for links, including for setting up a virtual Ubuntu Linux PC within your existing Windows or Mac computer.
    • How to make an Arlequin file from a FASTA file

    YouTube Video

    • How to do an Analysis of Molecular Variance (AMOVA) using Arlequin

    YouTube Video

    • How to get the pairwise FST information out of Arlequin into more convenient formats

    YouTube Video

    • How to do a Spatial Analysis of Molecular Variance (SAMOVA)

    YouTube Video

    • How to make a STRUCTURE file from a FASTA file

    YouTube Video

    • A brief overview of the program STRUCTURE for population genetic analysis

    YouTube Video

    • How to perform Bayesian clustering analysis using the program STRUCTURE

    YouTube Video

    • Files needed for tutorial
    • This tutorial assumes you have the program STRUCTURE installed. See the show notes for a tutorial to install STRUCTURE, or else use the virtual machine that I have pre-configured with STRUCTURE and other software (details which are in the show notes).
    • All other links mentioned in the tutorial can be found in the show notes.
    • Don't have Linux? No problem! You can run it as a virtual machine within your Windows PC or Mac.
    • See the show notes on this video for links, including for setting up a virtual Ubuntu Linux PC within your existing Windows or Mac computer.
    • How to decide which results from STRUCTURE to use

    YouTube Video

    • How to most easily visualize the results from STRUCTURE and make a publication-ready figure

    YouTube Video

      • File needed for tutorial
      • This tutorial assumes you have Inkscape installed on your machine. Click here for the link.
      • There is an older version of this tutorial that was made on a Windows machine using Microsoft Office. You can access that tutorial by clicking on this link.
        • Microsoft makes an online version of their office suite available for free that looks and works just like the paid version. You access it from a web browser, so it works on any computing platform, including Linux. Click here for the link to use it. The point is, if you prefer Microsoft Office, you can use it to accomplish this task.
    • How to test for the correct nucleotide substitution model using jmodeltest2

    YouTube Video

    • How to install the population genetic software PartitionFinder under Ubuntu Linux version 20.04

    YouTube Video

    • Don't have Linux? No problem! You can run it as a virtual machine within your Windows PC or Mac.
    • See the show notes on this video for links, including for setting up a virtual Ubuntu Linux PC within your existing Windows or Mac computer.
    • How to install the population genetic software jModelTest2 under Ubuntu Linux version 20.04.

    YouTube Video

      • Don't have Linux? No problem! You can run it as a virtual machine within your Windows PC or Mac.
      • See the show notes on this video for links, including for setting up a virtual Ubuntu Linux PC within your existing Windows or Mac computer.
    • How to convert an output file from MrBayes, which is in Nexus format, into the Newick tree file format for making phylogenies.

    YouTube Video

      • File needed for tutorial
      • This is tricky, because programs such as FigTree won't export the node support data (the posterior probabilities). This is the only tutorial I am aware of that shows you how to do it right, so that you don't lose the crucial node support data when you do the conversion.
      • Don't have Linux? No problem! You can run it as a virtual machine within your Windows PC or Mac.
      • See the show notes on this video for links, including for setting up a virtual Ubuntu Linux PC within your existing Windows or Mac computer.
    • How to perform a Bayes multispecies coalescent-based phylogenetic analysis using the software MrBayes.

      YouTube Video

    • How to install the R package 'phytools' under Ubuntu Linux version 20.04. 

    YouTube Video

    • How to install the R package 'pegas' under Ubuntu Linux version 20.04. 

    YouTube Video

    • How to make a publication-ready phylogeny figure using R and Inkscape (advanced). 

    YouTube Video

      • Files needed for tutorial
      • This tutorial assumes you have Inkscape installed on your machine. Click here for the link.
      • Don't have Linux? No problem! You can run it as a virtual machine within your Windows PC or Mac.
      • See the show notes on this video for links, including for setting up a virtual Ubuntu Linux PC within your existing Windows or Mac computer.
    • How to install fastStructure on Ubuntu Linux 20.04
    • YouTube Video

      • Don't have Linux? No problem! You can run it as a virtual machine within your Windows PC or Mac.
      • See the show notes on this video for links, including for setting up a virtual Ubuntu Linux PC within your existing Windows or Mac computer.
    • How to install STRUCTURE on Ubuntu Linux 20.04
    • YouTube Video

      • Files needed for tutorial
      • Don't have Linux? No problem! You can run it as a virtual machine within your Windows PC or Mac.
      • See the show notes on this video for links, including for setting up a virtual Ubuntu Linux PC within your existing Windows or Mac computer.
    • I have made a Linux virtual machine that is pre-configured with many population genetics and ecological niche modeling programs. The video below explains how to open up this virtual machine on your computer (Windows or Mac), so that you can start using the pre-configured software without having to install it (and even without having to install Ubuntu Linux!) NOTE: Virtualbox 6.1 does not seem to work! At least not on my Mac. Install 6.0 instead, which can be found here.
      • Instructions for Windows:

    YouTube Video

      • Instructions for Macs: 

    YouTube Video

      • File needed for tutorial
      • The username for the virtual machine account is sample
      • The password for the virtual machine account is stanleysfamous.com75702
      • Current list of pre-configured software on the virtual machine (the list will grow):
        • fastStructure
        • STRUCTURE (command prompt, not GUI)
        • Arlequin (GUI)
        • distruct
        • Tree Graph 2 (GUI)
        • GIMP
        • R
        • RStudio
        • Inkscape
        • PartitionFinder
        • MrBayes
        • tcs
        • FigTree
        • PhyML
        • RAxML
        • BEAST2
        • Tracer
        • jModelTest2
        • Mesquite
      • You will first need to install VirtualBox on your Windows or Mac machine. See the instructions below if you haven't installed it already. NOTE: Virtualbox 6.1 does not seem to work! At least not on my Mac. Install 6.0 instead, which can be found here.
        • Windows:

    YouTube Video

        • Mac:

    YouTube Video



    Geographic Information Systems

    • Tutorials for doing cartography in the software QGIS (although the software GRASS GIS is a part of one of the tutorials as well). Cartography refers to the making of publication-ready maps based upon GIS layers. QGIS is another open-source GIS software solution. It uses GRASS GIS under the hood to perform some of its routines, so GRASS GIS is still the most powerful open-source option. But QGIS is much better for cartography, which is why I switch to this software for the cartography tutorials.

    Species Distribution Modeling
    • How to perform species distribution modeling
    • How to make publication-quality figures of response curves from the Maxent output.