Structure instructions

We went over how to run Structure pretty quickly on Friday, and I've heard from a couple of people who are having some problems. Here's a list of instructions so it's all in the same place.

• Double click on the Structure icon and start the program
• From the  "File" menu, select "New project".You'll get a "Project Wizard" box labeled "Step 1 of 4".
• Give your project a name, e.g., "humans" (without the double quotes)
• Select the directory where you want the results to be stored, probably the directory where you downloaded the file humans.stru.
• Select the humans.stru file and click "Next >>". You'll get a "Project Wizard" box labeled "Step 2 of 4"
• There are 263 individuals in the data set, the ploidy is 2 (diploid), the number of loci is 100, and the missing data value is -9. Enter those values in the respective boxes and click "Next >>". You'll get a "Project Wizard" box labeled "Step 3 of 4".
• Check the box labeled "Row of marker names", and click "Next >>". You'll get a "Project Wizard" box labeled "Step 4 of 4".
• Check the box labeled "Putative population origin for each individual", check the box "Other extra columns", enter 2 in the box labeled, "Number of extra columns",and click "Next >>". You'll get a "Confirmation" box. Click "Proceed" and you sho uld have the data appearing as a spreadsheet in Structure.

At this point you have the data loaded into Structure and you're (almost) ready to begin the analysis. First, you have to set up a "Parameter set".

• To do that select "Parameter Set -> New". You'll get a "New Parameter Set" box popping up.
  
• We want a burnin of 10,000 iterations and a sample of 50,000 iterations. Enter those numbers in the respective boxes and click "Ok".
• You'll get an "Input" box popping up asking you for the name of your parameter set. You can pick anything you want. I usually pick "default". Enter the name you want in the box and hit "Ok". The box will disappear, and you'll see in the list of things on the left side of the screen a new Parameter set with the name that you just provided.

Now you're ready to run the analysis.

• Select "Project -> Start a job", and a "Structure Scheduler" box will pop up.
• Highlight the parameter set you created, set K from 2 to 10 by entering the numbers in the appropriate boxes. Leave the number of iterations set at 1.
  
• Click "Start". The "Strucutre Scheduler" box should disappear, a "Structure Job Log" box should appear, and you'll start seeing numbers appearing in the black box at the bottom of the screen.

It will probably take 10-12 hours for the analysis to finish. If you need to stop it along the way, select "Project -> Kill Running Job". You can pick up where you left off by selection "File -> Open Project", setting the "Structure Scheduler" to start with the K you had when you started the analysis and clicking "Start".

Since we need results from this analysis by Tuesday morning so that we can post the results, it would be a very good idea to see if you can get the analysis running today so that we can go over any problems tomorrow, even if you don't finish the analysis tonight.