Admixtures

What do you think about ADMIXTURE?

  • I can make it work, just let me have a go!

    Votes: 0 0.0%

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    22
Guys you are fired.Let's see, a rookie, for example from Europe like me, what is the best calculator to start and which in turn give spectacular results, clear and easy to understand? otherwise we will end up in a mental hospital all.
 
Hello, Could someone please tell me how to use the the Dodecad program for windows, it's says unzip your file to a working directory, I don't get what it is talking about, I just can't seem to get the program to work, could someone give me some instructions that are easy to understand. Thank you aaliy06
If you need to unzip any files you can download this user-friendly software here. Just install and drag any zipped files over it to have them uncompressed. Go to documents in windows and create a file named DIYDOD. Save all your admixture calculator files in this folder. Then save your 23andme or ftdna data file to this folder. Everything should be in the same file location, namely the file that you created, named DIYDOD, in windows documents. You need to download the R console software here. You will enter your commands into this console once you have installed it. Now you are ready to enter the following four commands: setwd('DIYDOD') This command tells the program where to look for all the files, namely the DIYDOD file created in windows Documents. source('standardize.r') This command standardizes the data preparing it for the analysis. standardize('???.csv', company='ftdna') This command tells the program the name of your data file and the company where you tested. system('DIYDodecadWin dv3.par') This is the final command. Wait a few minutes for your admixture results to appear. If in future you would like to use a different calculator just add the new calculator's name in place of dv3 (eg. euro7) and download the (eg. euro7) files to your DIYDOD file in documents. Your final command for the different calculators will look like this: system('DIYDodecadWin euro7.par') For the Euro7 calculator. system('DIYDodecadWin eurasia7.par') For the Eurasia7 calculator. system('DIYDodecadWin africa9.par') For the Africa9 calculator.
 
Guys you are fired.Let's see, a rookie, for example from Europe like me, what is the best calculator to start and which in turn give spectacular results, clear and easy to understand? otherwise we will end up in a mental hospital all.
Try the K=12v3 and the Euro7 to get an aproximate idea if you don't want to run all tests. This is the easiest thing to understand.

However, I must mention the K12a, which is the latest experiment and the data Dienekes' is currently using. In my opinion is not the same clear, but for comparison with other people of similar ethnic background it's okay.
 
Hello,

I finally got it to work, so thank you so much for helping me, now I would like to know how you use the byseg and the bychr? if someone can help me on that.

Thank you
 
Hello,

I finally got it to work, so thank you so much for helping me, now I would like to know how you use the byseg and the bychr? if someone can help me on that.

Thank you

For byseg (percentages per segment on each chromosome) analysis go to the file named dv3.par that you have saved in DIYDOD. You need to change the genomewide setting to:
byseg
500
50

This will give you the percentages for individual segments of each of your 22 chromosomes.

For bychr (percentages per chromosome) you simply replace the genomewide setting with bychr.

Remember to save your changes as dv3.par once you have finished to edit the file.

Enter the same commands into the R console and wait a few minutes for your results. Your bychr results will appear in a bychr file in your DIYDOD file.
 
I'm sorry, I know you said go to the file named dv3.par, I still don't get what your saying about the genomewide settings, I don't know where to change it at. I apologize if I am bothering you or anyone else on here, I just want to learn just like everyone else.
 
We can send to them our results and you put them in his calculator, because the life has been complicated in a bad way: cannot it be simpler and the calculator bends in a pack without so many histories?
We would be grateful for it eternally and it would serve them as learning in his personal studies.
What do they say to me?
 
I'm sorry, I know you said go to the file named dv3.par, I still don't get what your saying about the genomewide settings, I don't know where to change it at. I apologize if I am bothering you or anyone else on here, I just want to learn just like everyone else.
Using the Do-It-Yourself Dodecad v 2.1 that you can find here [includes the Dodecad v3 calculator files]
The DIY Dodecad v 2.1 software includes the dv3 calculator files, and the dv3.par file was downloaded together with the DIY dodecad v 2.1 program files. When you saved the DIY Dodecad files after unzipping them, you unknowingly also saved a file name dv3.par in the same directory; as you have been able to run the admixture program successfully. The dv3.par file is one of the files that you downloaded as part of the DIY Dodecad program. Look in your DIY dodecad file registry and you will find a file named dv3.par Once you have found it open it using notepad or any other program that allows you to read the few lines (settings) that it has. In the dv3.par file you will see the word 'genomewide'. Delete this word and write 'bychr' in its place. Save the file as dv3.par and go to the R console where you continue with the command prompts as you have done before. This will work, however you will find the results in your DIY dodecad directory with all the other program files in a new file generated from the analysis named 'bychr.doc'. Follow the same procedure for byseg results.
We can send to them our results and you put them in his calculator, because the life has been complicated in a bad way: cannot it be simpler and the calculator bends in a pack without so many histories? We would be grateful for it eternally and it would serve them as learning in his personal studies. What do they say to me?
If you cannot manage and want me to calculate your bychr and byseg percentages send me a personal message. I am happy to help where I can.
 
Dorianfinder
If you cannot manage and want me to calculate your bychr and byseg percentages send me a personal message. I am happy to help where I can.

Thank you very much, very friendly. I sent a private message.
 
K7b and K12b calculators available

Download the K7b calculator here.
Download the K12b calculator here.

Download the new Dodecad Oracle for K12b here.
 
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There are two more calculators from Dienekes aka the Dodecad Ancestry Project.

Download the weac2 calculator files here.
Download the K10a calculator here.
 
Hi Zanipolo, no it is not possible to use STR data with the current admixture setup. Autosomal DNA is used by reading SNP data and comparing it with individuals from specific regions. Primary component analysis (PCA) is used to give each SNP a value indicating it's significance as an ancestral marker. You need to do an autosomal DNA test (aDNA) if you want to know what your ancestral percentages are. This is the region that excludes the sex chromosomes (X & Y). Your STR values were taken from your Y chromosome. I hope this helps!
 
Hi Zanipolo, no it is not possible to use STR data with the current admixture setup. Autosomal DNA is used by reading SNP data and comparing it with individuals from specific regions. Primary component analysis (PCA) is used to give each SNP a value indicating it's significance as an ancestral marker. You need to do an autosomal DNA test (aDNA) if you want to know what your ancestral percentages are. This is the region that excludes the sex chromosomes (X & Y). Your STR values were taken from your Y chromosome. I hope this helps!

thanks

this was recently done for me by a person in the know
Uploaded with ImageShack.us

I am the Treviso noted one and the message - 5 clusters blah blah refers only to me.

It was done to measure myself with South Tyrol people...............I seem slightly out ( my opinion)
 
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There's going to be a new calculator on GED Match soon, a revised version of Eurogenes K13 featuring two ancient genomes, MA-1 and La Brana. As soon as John restores the server on GED Match. We'll be able to use the calculator.
 
There's going to be a new calculator on GED Match soon, a revised version of Eurogenes K13 featuring two ancient genomes, MA-1 and La Brana. As soon as John restores the server on GED Match. We'll be able to use the calculator.
Sweet, thanks Dorianfinder.
 
is it possible to run your raw data on DODECAD outside GEDmatch platform? some other websites?
 
previus DODECAD calculators will still available?
 
Why isn't the french admixture split in many admixture tests?

Clearly its a huge land too solely be basically under one marker
 

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