• 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 utilizes: 

  • RStudio: https://rstudio.com/

  • (Rstudio also requires R: https://www.r-project.org/)

  • Mesquite: http://mesquiteproject.org

• 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.

• Files needed for tutorial

• This tutorial utilizes: 

  • RStudio: https://rstudio.com/

  • (Rstudio also requires R: https://www.r-project.org/)

• 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 utilizes: 

  • RStudio: https://rstudio.com/

  • (Rstudio also requires R: https://www.r-project.org/)

  • Mesquite: http://mesquiteproject.org

• 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.

• File needed for tutorial

• • This tutorial utilizes: 

    • Wine: https://www.winehq.org/

    • The Windows graphical user interface (GUI) version of Arlequin:

      • http://cmpg.unibe.ch/software/arlequin35/

• 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 utilizes: 

  • RStudio: https://rstudio.com/

  • (Rstudio also requires R: https://www.r-project.org/)

• 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 utilizes: 

  • Wine: https://www.winehq.org/

  • SAMOVA version 1.0:

    • http://cmpg.unibe.ch/software/samova/

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

• Files needed for tutorial

• This tutorial utilizes: 

  • RStudio: https://rstudio.com/

  • (Rstudio also requires R: https://www.r-project.org/)

• 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 utilizes: 

  • RStudio: https://rstudio.com/

  • (Rstudio also requires R: https://www.r-project.org/)

• 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.

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

• Files needed for tutorial

• This tutorial utilizes: 

  • RStudio: https://rstudio.com/

  • (Rstudio also requires R: https://www.r-project.org/)

• 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.

• Files needed for tutorial

• There is a second part to this video, which can be found here: https://youtu.be/pr4ZeYw4hmI

• This tutorial utilizes: 

  • RStudio: https://rstudio.com/

  • (Rstudio also requires R: https://www.r-project.org/)

• These programs are free of charge and can be installed on a Windows, Mac, or Linux (for instance, Ubuntu) machine.

• This video assumes you have already installed the following R libraries: lme4, qtl, devtools, and qtlTools. 

• This video illustrates how to perform the analysis using a Mac, but it should work exactly the same on a Windows machine, as well as on a Linux machine (assuming you have properly installed the packages on your Linux machine).

• Files needed for tutorial

• There is a second part to this video, which can be found here: https://youtu.be/vRgDnjXBnnc

• This tutorial utilizes: 

  • RStudio: https://rstudio.com/

  • (Rstudio also requires R: https://www.r-project.org/)

• These programs are free of charge and can be installed on a Windows, Mac, or Linux (for instance, Ubuntu) machine.

• This video assumes you have already installed the following R libraries: lme4, qtl, devtools, and qtlDesign.

• This video illustrates how to perform the analysis using a Mac, but it should work exactly the same on a Windows machine, as well as on a Linux machine (assuming you have properly installed the packages on your Linux machine).

• 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.

• Files needed for tutorial

• Files needed for tutorial

• Files needed for tutorial

• This tutorial was written by Alyssa Blanton, an undergraduate research assistant in the Banta lab.

• 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 Alyssa Blanton, an undergraduate research assistant in the Banta lab.

• Files needed for tutorial

• This tutorial was written by Alyssa Blanton, an undergraduate research assistant in the Banta lab.

• Files needed for tutorial

• This tutorial was written by Alyssa Blanton, an undergraduate research assistant in the Banta lab.

• Files needed for tutorial

• This tutorial was written by Alyssa Blanton, an undergraduate research assistant in the Banta lab.

• 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.

• Files needed for tutorial

• This tutorial utilizes: 

  • Open JDK: https://openjdk.java.net/

  • jModeltest2: https://github.com/ddarriba/jmodeltest2

• 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.

• 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.

• 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.

• 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.

• This tutorial assumes you have the following programs installed:

  • Mr. Bayes: http://nbisweden.github.io/MrBayes/

  • FigTree: http://tree.bio.ed.ac.uk/software/figtree/

• For the links referenced in the video, see 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 utilizes: 

  • RStudio: https://rstudio.com/

  • (Rstudio also requires R: https://www.r-project.org/)

• 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.

• Links you need to have open during this tutorial:

  • https://stackoverflow.com/questions/31820865/installing-rgl-on-ubuntu-and-mac-x11-not-found

  • https://stackoverflow.com/questions/20671814/non-zero-exit-status-r-3-0-1-xml-and-rcurl

  • https://github.com/ropensci/magick/issues/145

• This tutorial utilizes RStudio:

  • https://rstudio.com/

  • (Rstudio also requires R: https://www.r-project.org/)

• 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.

• Links you need to have open during this tutorial:

  • https://zoomadmin.com/HowToInstall/UbuntuPackage/libudunits2-dev

  • https://www.digitalocean.com/community/tutorials/how-to-install-r-packages-using-devtools-on-ubuntu-16-04

  • https://mothergeo-py.readthedocs.io/en/latest/development/how-to/gdal-ubuntu-pkg.html

• Code you will be using is in the show notes.

• This tutorial utilizes RStudio:

  • https://rstudio.com/

  • (Rstudio also requires R: https://www.r-project.org/)

• 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 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.

• 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

• 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 machine. VirtualBox does not work on newer (M1 and M2) Macs.

• This is for installing the program distruct on Ubuntu Linux version 20.04. distruct is used to visualize the results from the population genetics programs STRUCTURE and fastStructure.

• Links you need to have open during this tutorial:

  • https://gist.github.com/josiahaltschuler/a063e03b4197013def53f9a0abc6dfed#gistcomment-3347127

  • https://rosenberglab.stanford.edu/distructDownload.html

• 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.

• File needed for tutorial

• The username for the virtual machine account is sample

• The password for the virtual machine account is stanleysfamous.com75702

• File needed for tutorial

• The username for the virtual machine account is sample

• The password for the virtual machine account is stanleysfamous.com75702

• ArcGIS must be purchased from ESRI

• Files needed for tutorial (DO NOT DOWNLOAD THIS FOR MY CLASS! THIS IS THE WRONG ONE. KEEP LOOKING.)

• Files needed for tutorial (DO NOT DOWNLOAD THIS FOR MY CLASS! THIS IS THE WRONG ONE. KEEP LOOKING.)

• Files needed for tutorial

• Uses both ArcGIS and R

• Files needed for tutorial

• 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.

• Files needed for tutorial

• This tutorial utilizes: 

  • RStudio: https://rstudio.com/

  • (Rstudio also requires R: https://www.r-project.org/)

• Don't have Linux? No problem! You can run it as a virtual machine within your Windows PC. Or you can run Rstudio directly on your Windows or Mac without running Linux.

• See the show notes on this video for links, including for setting up a virtual Ubuntu Linux PC within your existing Windows computer.

• Files needed for tutorial

• This tutorial utilizes: 

  • RStudio: https://rstudio.com/

  • (Rstudio also requires R: https://www.r-project.org/)

• 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)

• 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.

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

• PDF version of the instructions

• Files needed for tutorial

• List of questions to answer for tutorial

• This tutorial assumes you have already installed GRASS GIS. Instructions can be found here: 

  • https://grasswiki.osgeo.org/wiki/Installation_Guide#Ubuntu

• 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.

• PDF version of the instructions

• Files needed for tutorial

• List of questions to answer for tutorial

• This tutorial assumes you have already installed GRASS GIS. Instructions can be found here: 

  • https://grasswiki.osgeo.org/wiki/Installation_Guide#Ubuntu

• 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.

• PDF version of the instructions

• Files needed for tutorial

• List of questions to answer for tutorial

• This tutorial assumes you have already installed GRASS GIS. Instructions can be found here: 

  • https://grasswiki.osgeo.org/wiki/Installation_Guide#Ubuntu

• 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.

• PDF version of the instructions

• Files needed for tutorial

• List of questions to answer for tutorial

• 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.

• Files needed for tutorial (updated)

• Files needed for tutorial (old)

• 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.

• 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.

• 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: 

  • RStudio: https://rstudio.com/

  • (Rstudio also requires R: https://www.r-project.org/)

• 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.

• 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: 

  • RStudio: https://rstudio.com/

  • (Rstudio also requires R: https://www.r-project.org/)

• 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.

• 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: 

  • RStudio: https://rstudio.com/

  • (Rstudio also requires R: https://www.r-project.org/)

• 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.

• Files needed for tutorial

• This tutorial utilizes: 

  • RStudio: https://rstudio.com/

  • (Rstudio also requires R: https://www.r-project.org/)

• 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.

• Files needed for tutorial

• This tutorial utilizes: 

  • RStudio: https://rstudio.com/

  • (Rstudio also requires R: https://www.r-project.org/)

• This tutorial also assumes you already have the R package 'sf' and all of its dependencies installed (or you can just use my preconfigured virtual machine. See 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.

• File needed for tutorial (it's just one file, and it's already unzipped)

• This tutorial requires the software GRASS GIS. See tutorials above if you are unfamiliar with this software.

• This tutorial requires the software Maxent, which is free. You can download it here.

• Files needed for tutorial

I have created a single R script to automate almost every step of performing species distribution modeling using Maxent. The script even runs Maxent for you. No more running ENMEvaluate separately to find the right model settings, and then inputing them into Maxent. No more hassle creating a bias file and then trying to incorporate it into Maxent on your own (I know a lot of you have trouble with this).

With this script, all you need are your species occurrence points, your environmental layers, and the R script. The whole process is automated for you, from choosing the model settings, making the bias file, and feeding all this information into Maxent and then running Maxent.

As an added bonus, you can also use this script to automatically forecast your results into the future!

• Files needed for tutorial

• This tutorial utilizes: 

  • RStudio: https://rstudio.com/

  • (Rstudio also requires R: https://www.r-project.org/)

• 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)

• 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 the code used in this tutorial, and 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.

• Files needed for tutorial

• This tutorial utilizes: 

  • RStudio: https://rstudio.com/

  • (Rstudio also requires R: https://www.r-project.org/)

• 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 utilizes: 

  • RStudio: https://rstudio.com/

  • (Rstudio also requires R: https://www.r-project.org/)

• This tutorial also assumes you already have the R package 'RMark' and all of its dependencies installed. It also assumes you have the program Mark installed. I have a tutorial for installing these items in the show notes (or you can just use my preconfigured virtual machine. See 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.