Tutorials

Genomics

How to install R and Rstudio under Ubuntu Linux version 20.04

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

  • 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

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

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

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

  • Files needed for tutorial

  • This tutorial was written by Ava Laszlo, a graduate student in the Banta lab, as part of an Evolutionary Genetics Laboratory course.

How to make a STRUCTURE file from a FASTA file

A brief overview of the program STRUCTURE for population genetic analysis

See the show notes on YouTube for the links referenced in the video

How to perform Bayesian clustering analysis using the program STRUCTURE

  • 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

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

  • 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.

  • Assuming 150bp per RAD-seq fragment -- check with SNPSaurus first!

  • Files needed for tutorial

  • This tutorial was written by Katherine Barthel, a graduate student, as part of an Evolutionary Genetics Laboratory course.

  • Files needed for tutorial

  • This tutorial was written by Nevada King, a graduate student, as part of an Evolutionary Genetics Laboratory course.

  • Files needed for tutorial

  • This tutorial was written by Sarah Senula, an graduate student, as part of an Evolutionary Genetics Laboratory course.

How to test for the correct nucleotide substitution model using jmodeltest2

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

  • 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.

  • 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.

  • 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.

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

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

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

  • 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

  • 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

  • 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.

How to install distruct on Ubuntu Linux 20.04

How to hook up and use my pre-configured Ubuntu Linux virtual machine on your 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!)

  • Instructions for Windows:

  • Instructions for Mac:

  • 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):

List of software on virtual machine
  • You will first need to install VirtualBox on your Windows or Mac machine. See the instructions below if you haven't installed it already.

  • Windows:

  • Mac: NOTE: Only works on older Macs! Not newer ones!

https://wikikeep.com/how-to-install-virtualbox-on-macos-big-sur-11/

Geographic Information Systems (GIS)

Tutorials using ArcGIS

  • ArcGIS must be purchased from ESRI

How to perform logistic regression with correction for spatial autocorrelation

How to export a points layer from ArcGIS as a shapefile so that you can send it to someone else

Tutorials using R

  • Sometimes, it may make more sense to do GIS using the open-source command-line-driven program R. This way is not intuitive and is not easy to visualize, but it can be quick and efficient. You can download R here. You'll also want to install RStudio (also free), which you can download here.

How to get hydrology data for your area of interest within the US

How to extract raster values (from Maxent or elsewhere) at point locations using R

  • Files needed for tutorial

  • This tutorial utilizes:

  • This tutorial also assumes you already have the R package 'raster' and all of its dependencies installed.

    • If you encounter difficulties installing the 'raster' package, follow my tutorials for installing the 'ENMEval' package, as this will also install the 'raster' package along the way (link here).

  • Don't have Linux? 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 computer.

    • Running Ubuntu Linux on a new Mac computer with an M1 chip will require Parallels (https://parallels.com)

Tutorials using GRASS GIS

  • GRASS GIS is one of many open-source, free software packages for using GIS. You can download GRASS GIS here. If you want to see other open-source GIS software options, there is a good list here.

Introduction to GIS and GRASS GIS

See the show notes for the links mentioned in the video.

Projections, transformations, and GPS data import

Rasters and raster manipulation

Buffering and clipping vectors

Tutorials for doing cartography using QGIS

  • 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 you'll want to know how to use it.

  • The files for this tutorial are the same as for part one (see above).

  • The purpose is to translate the knowledge from the previous lab (and prior ones) using your own data.

Species Distribution Modeling

  • Files needed for tutorial

  • This tutorial uses R-Studio. You can download it here.

  • This tutorial was written by Danielle Joerger, a graduate student in my Landscape Ecology lab in the spring of 2019.

How to install the R Package 'ENMEval' (and 'xml2,' 'tidyverse,' 'rJava') under Ubuntu Linux 20.04

  • This tutorial also installs the R package 'ENMEval,' as well as the dependency R packages 'xml2,' 'tidyverse,' and 'rJava,' under Ubuntu Linux version 20.04. The ENMEval package is used to find the best settings for running the ecological niche modeling (also known as species distribution modeling) software Maxent.

  • This tutorial utilizes:

  • 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 the code used in this tutorial, and links, including for setting up a virtual Ubuntu Linux PC within your existing Windows or Mac computer.

How to install the R Package 'ENMTools' under Ubuntu Linux 20.04

  • The ENMTools package has many tools to assist with ecological niche modeling (also known as species distribution modeling) and its analysis. For instance, an important tool is to compare the niches of two species and determine if they are significantly different from one another.

  • This tutorial utilizes:

  • This tutorial also assumes you already have the R package 'ENMEval' and all of its dependencies installed. See the link to my tutorial for installing it 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 the code used in this tutorial, and links, including for setting up a virtual Ubuntu Linux PC within your existing Windows or Mac computer.

How to adjust your environmental layers so that they have exactly the same spatial extent and resolution

  • PDF version of the instructions

  • This tutorial shows you how to make the resolutions and spatial extents of ESRI/ASCII grid rasters exactly the same. This is an important step for performing ecological niche modeling (also known as species distribution modeling). If the environmental layers (typically in the form of rasters) do not have exactly the same resolution and spatial extent, the modeling will fail! Often when you make your own rasters, even when you make them exactly the same way, they will still have slight differences in the resolutions and/or spatial extents. That is why this tutorial is so vital.

  • Files needed for tutorial

  • This tutorial utilizes:

  • This tutorial also assumes you already have the R packages 'ENMTools', 'ENMEval," and all of their dependencies installed. See the link to my tutorial for installing it 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 the code used in this tutorial, and links, including for setting up a virtual Ubuntu Linux PC within your existing Windows or Mac computer.

How to check for correlations among environmental layers and remove ones that are highly correlated (using ENMTools in R)

  • Files needed for tutorial

  • This tutorial utilizes:

  • This tutorial also assumes you already have the R package 'ENMTools' and all of its dependencies installed. See the link to my tutorial for installing it 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.

  • Files needed for tutorial

  • This tutorial assumes you already have ActivePerl installed. You can find it here.

  • This tutorial was written by Janey Dudley, Andrea Ortiz, and Samantha Rowe, graduate students in my Landscape Ecology lab in the spring of 2017 and 2019.

How to decide which settings to use when running Maxent, as well as how to make a bias file

How to perform species distribution modeling using Maxent

How to make publication-quality figures of response curves from the Maxent output

How to test whether two species distribution models are significantly different from each other (using ENMTools in R)

  • Files needed for tutorial

  • This tutorial utilizes:

  • This tutorial also assumes you already have the R package 'ENMTools' and all of its dependencies installed. See the link to my tutorial for installing it in the show notes.

  • Don't have Linux? 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 computer.

    • Running Ubuntu Linux on a new Mac computer with an M1 chip will require Parallels (https://parallels.com)