How to use the program STRUCTURE
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- Опубліковано 11 жов 2024
- This tutorial shows you how to perform a Bayesian cluster analysis using the population genetic software STRUCTURE.
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 the program STRUCTURE installed. You can follow my step-by-step instructions here:
• How to install and run...
Or you can simply use the virtual machine that I have made available that has the program pre-configured (see below).
This tutorial assumes you already have a file in STRUCTURE format, or that you will be using the sample tutorial data. To make your own STRUCTURE file for your own data, see my tutorial for converting a FASTA file to a STRUCTURE file:
• How to convert a FASTA...
After this tutorial, you will need to choose which results from STRUCTURE to present, as there are many different results files. I have made a separate tutorial to help you decide which results to choose, which you can view here:
• How to use 'pophelper'...
Finally, after you have selected the appropriate results, you will want to visualize them graphically and make a figure that is suitable for publication. See my tutorial for how to do that:
• How to most easily vis...
If you want to gain a better background about the program STRUCTURE, as in what it does and what it is used for, I suggest my video entitled, "Brief overview of STRUCTURE for population genetics and what it is used for." The video can be accessed below. This video will also help you to interpret your results from STRUCTURE.
• Brief overview of the ...
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...
Thanks so much for posting these tutorials, Josh! They are a tremendous help for my work with my thesis. I will be sure to cite your website and add you within the acknowledgments section!
Hi, Thank you for some amazing tutorials, they are very helpful. Is it possible to add location/coordinates to the data, as an extra characteristic? and if so, how would one do that?
Dear Leo, This is a great question. You can feed location data to STRUCTURE by using the LOCPRIOR and USEPOPINFO flags in the settings. See the STRUCTURE manual: www.ccg.unam.mx/~vinuesa/tlem09/docs/structure_doc.pdf
This would require adding columns to your dataset corresponding to the location information, as indicated in the manual.
That said, I think what you really want to do is a SAMOVA. See my tutorial here: ua-cam.com/video/a0pVLcglcgU/v-deo.html
@@DrJBanta Thanks for a fast and good answer. I have done a SAMOVA aswell but since I'm looking at fish larva spread with the currents, and where they settle depending on their PLD, I was a bit worried that the SAMOVA puts value in that the location should be "geographically adjacent" (if i have understood how the SAMOVA works correctly). SInce the larvae follow the current and then settle after a certain, unknown, time, it is not sure that locations closer together should have more genetic similarity than one farther away.
But i may very well have misunderstood the SAMOVAs calculations.
@@leonasstrom1917 Got it. It sounds like playing with those settings in STRUCTURE will do what you are looking to do. Essentially you want to use the population assignments corresponding to location as priors, and then only assign those individuals to other populations if it really looks that way genetically.
Sorry teacher I have a question, when I add code ./structure -K 1 -o k1run1.txt;....into Windows terminal, it didnot show the information like you that after I press enter the Windows terminal ran and showed "PS C:\Users\user\Pictures\console>" again. I hope you can help me solve this problem. Thank you a lot.
Hello, the easiest way to ensure STRUCTURE will run properly is to use my preconfigured virtual machine using VirtualBox. ua-cam.com/video/-K8byTOpTY4/v-deo.html
@@DrJBanta thank you teacher, I already make the Structure from your tutorial, it is so great😍
Thanks, when I run the ./structure it says is not recognized as an internal or external command,
Are you using my preconfigured virtual machine using VirtualBox? ua-cam.com/video/-K8byTOpTY4/v-deo.html
The tutorial files provided in the video are not available in the website.
Dear Arjun, can you try again? I just tried and I was able to access them.
@@DrJBanta It is showing that the page you are looking for cannot be found
@@arjunpal8340 Can you try a different browser?
@@DrJBanta It is the same with different browser
@@arjunpal8340 Try this link: drive.google.com/file/d/1XnbwAz6llZXNcz1bTYhBjPEMF8mma6vW/view