DUMMIES GUIDE TO STRUCTURE 4.x

Install Structure 4.x with its default settings and then start up the program. Please visit softwares homepage for more information.

1. First enter your project name, project directory and datafile. Please note that the program require the project directory to be made before you make a new project. As datafile in this example we use the "22LOCI.txt" file downloadable at the end of this page. If everything is entered correcty click "Next".

2. In this example as on the screen enter the "Number of individuals:" as 1500. "Ploidy of Data" as 2. "Number of loci:" as 22 and "Missing data value:" as -9. Click "Next".

3. Select the settings as in the image.

4. Select the settings as in the image and click Next.

5. The import summary is presented, if you get a error message go back and recheck your entries. Click Next.

6. After clicking proceed above go to the "Parameter Set" menu and select "New Parameter Set" as shown below. In this example 10 000 and 20 000 have been used and this should be satisfactory for most purposes but for more accuracy numbers up 100 000 or more could be used. There is a range of other options in the parameter set, for more information about those please confer with Structure manual. I will provide links to the manuals and some literature describing details about the use of the program at the bottom of this page. In this example we leave the other parameters to their default settings and click OK.

7. After clicking OK above, please choose the name for the new parameter sets and then click OK.

8. We can now start the job. Select "Project" menu and then select "Start Job", The box below enter K=3 in both "from" and "to". Leave the iterations at default. Click Start.

9. The job should be running as shown below. Expect lower performance on the computer for other tasks. Depending on the values you entered for the new parameter set above the waiting time can be from around 5-10 minutes to several days.

10. When the job is finished you can look at the admixture rates for the different individuals and populations in the dataset and the bar and triange plot.

So how do I find my own admixture rate?

If you have managed the above ts very easy! In the "22LOCI.txt" datafile go to the end of the file and enter your own marker/loci data. You need to enter two lines with identical names as shown below, here illustrated as "JOHNDOE"  and input your markers multiplied with 10 as the program dont accept decimals only integers. If you are missing any of the markers enter "-9" in the field for that marker, it cannot be left empty or have any other value. You should change your population number to 4 meaning (1 is used for Europe, 2 for East Asian and 3 for African). This will give you a single dot with your own color in the triangle plot. If you have added your own marker data to at the end of the data file, you must make a new project and make sure that there is 1501 individuals instead of 1500 individuals as described ealier in this guide because you just entered one more individual, also make sure you have not made any bad entries when including your own data as the program will halt in the import process if the data do not have the properties as described. Then you run the same procedure again and your individual admixture can be found.

Please note that there will not be given ANY support by me for this program and its use. 22 loci datafile for Europe, East Asia and Africa. (simulated 1500 individuals) 13 loci datafile for Caucasian, Asian American, Native American and African American (real individuals)