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Dorianfinder
26-09-11, 01:49
Latest version of Admixture http://www.genetics.ucla.edu/software/admixture/download.html

ADMIXTURE is a computer software program that once calibrated by a knowledgeable tutor, is used to estimate an individual's ancestral composition by analyzing the allele frequencies from autosomal SNP data.

The ADMIXTURE program is used to estimate the number of underlying populations through a process of cross-correlation experiments. To do this, individuals of known ancestry are exploited to yield more precise ancestry estimates.

Once ancestral components have been uncovered, small admixture coefficients are eradicated for each individual, encouraging model parsimony and often yielding more interpretable results for small data-sets or data-sets with dissimilar populations.
BMC Bioinformatics 2011, 12:246doi:10.1186/1471-2105-12-246

ADMIXTURE is currently the platform used by most hobbyists and amateur population geneticists.

Dorianfinder
04-11-11, 11:18
Here are the free tools available for calculating admixture percentages using 23andMe, FTDNA and deCODEme genotype data.

Using the Do-It-Yourself Dodecad v 2.1 that you can find here (http://dodecad.blogspot.com/2011/09/do-it-yourself-dodecad-v-21.html) [includes the Dodecad v3 calculator files]

You are able to calculate your autosomal admixture percentages using the following calculators:

Download the Dodecad v3 calculator here (https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=0B7AJcY18g2GaZGU4OWQ5OWItMzY2NC00NzI1LWIzNWM tMzUxYWI4NjRmMTlk&hl=en_US)
Download the Euro7 calculator by Dodecad here
(https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=0B7AJcY18g2GaM2ZlOGQ0NjMtYzRlMS00YjA5LWIzZmU tM2RkMDIyNDEzZWZm&hl=en_US)Download the BAT calculator by Dodecad here
(https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=0B7AJcY18g2GaNjhkYTlhZTItMWZjZS00N2VmLWFkOWM tNjhmMWQxOGU1YmYz&hl=en_US)Download the weac calculator by Dodecad here
(https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=0B7AJcY18g2GaYzI1MDZlNmQtOGU1ZC00MmE3LThhOTA tMzcyNGE1NjU0ZDQ2&hl=en_US)Download the Africa9 calculator by Dodecad here
(https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=0B7AJcY18g2GaOWNmZDVlZDItZmIyZC00OGYzLTlmNGM tNjgzMzliOTg1Yzc5&hl=en_US)Download the Eurasia7 calculator by Dodecad here (https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=0B7AJcY18g2GaOTYyZTQ0ZDAtNGRkYi00ZjUyLTg3NmU tODNmMjI5MzQwM2Yy&hl=en_US)
Download the Euro-DNA-Calc111 calculator by Dodecad here (https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=0B8-Sh-LdY4_HYjc5ODZiMjktOGExYy00ZWQyLWE0YTItMWZjZjg0NjY1 ZTBl&hl=en_US)
Download the Eurogenes Eurasian K=10 by Davidski here
(https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=0B9o3EYTdM8lQYzQxMDM3NDctMzc3ZC00ZWY2LWFkM2Q tZGE4ZDI5NDgyZDQx&hl=en_US)Download the Eurogenes K=14 by Davidski here (https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=0B8-Sh-LdY4_HYTkxYTAxMzEtNzRlOS00ODNmLWE5ZGQtMDJmM2Y5YTNi NzA0&hl=en_US)
Download the MDLP K=7 by Vadim Verenich here (https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=0B6n7iMc2P-yQMWYwODYwMjctYWVmNS00YTlmLWJmYTctYTc5Mjc3NWI4NWY3&hl=en_US)

Download the Dodecad Oracle v1 calculator here (https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=0B7JDEoCgzRKeM2RiYjVlYTYtZTVmYy00OGVjLTk1YTY tMWY5OWM1NDg1ODhj&hl=en_US)

The Dodecad Oracle v1 tool allows you to view your closest population matches and for those with unknown mixed ancestry it lists mixed population matches.

Dodecad software is provided free of charge for non-commercial use by Dienekes Pontikos @ http://dodecad.blogspot.com

If you are having trouble using the program I would be happy to help if I can.

Knovas
04-11-11, 16:34
You should add the recent Eurasia7, if you check the post you'll see there's also a Calculator for it (several individuals were not included).

Also, there was a Calculator for the Eurogenes K=14, but Davidski removed the post. I don't know if the link is available somewhere, but I have the ZIP. If someone wants to calculate it, I could upload the file. I think it's better than the K=10 in some aspects.

Another interesting point, is that I recently wrote to Dienekes' proposing him to provide tools for the calculation of samples from data source (HGDP, Behar, etc.) using DIY. That will allow people to compare personal results, not only with known people joining the projects, also with those anonimous individuals whose results are only visible sometimes in the population portraits (Dodecad v3) and the Eurogenes project. Just note in the Euro7, Eurasia7, Weac, etc., they are listed as average, but not individually. Then, if Dienekes' finally finds the way to convert this files into a compatible format for DIY, we could see exactly their admixture proportions in the different tests.

For the moment he is busy and told me it can't be done easily, but I'm sure he'll try to do so :)

Dorianfinder
06-11-11, 22:12
The Eurasia7 by Dodecad and the Eurogenes K=14 by Davidski have been added to the list.

Knovas
06-11-11, 23:36
I uploaded the K=14 here: https://docs.google.com/open?id=0B8-Sh-LdY4_HYTkxYTAxMzEtNzRlOS00ODNmLWE5ZGQtMDJmM2Y5YTNi NzA0

You can list the link together with the others, Dorian.

The components are:
- Northeast Euro (peaks in Russians)
- West Euro (Basques & Irish)
- East Mediterranean (Cypriots)
- Volga-Ural (Chuvashs)
- West Asian (Lezgins)
- Middle Eastern (Saudis)
- Berber (Mozabite Berbers)
- South Asian (South Indians)
- North Asian (Nganassans)
- South Siberian (Evenks)
- East Siberian (Koryaks)
- East Asian (Japanese)
- Southeast Asian (Southern Chinese)
- Sub-Saharan (Western Africans)

Enjoy!

UPDATE: To run the K=14 the word "test" instead "dv3" is required. That's all.

Knovas
07-11-11, 14:52
I also uploaded the last version of the Euro-DNA-Calc here: https://docs.google.com/open?id=0B8-Sh-LdY4_HYjc5ODZiMjktOGExYy00ZWQyLWE0YTItMWZjZjg0NjY1 ZTBl

It can be added at the beggining too :)

Components:
- Northwest Euro
- Southeast Euro
- Ashkenazi Jewish

It's very simple and must be taken with caution, since sometimes the reports don't make any sense. Keep in mind that Northwest Euro can include plain Western European allele frequencies (I know that because I got 75% there being Iberian), and having some West Asian admixture could report Ashkenazi Jewish here. Just this, be carefull with the interpretations, and pay attention to the major percents.

Dorianfinder
07-11-11, 15:43
Thanks! The Euro-DNA-Calc software is compatible with 23andMe and deCODEme genotype data whereas the other calculators found in the list in post #2 are all compatible with FTDNA, 23andMe and deCODEme genotype data.

MarTyro
08-11-11, 15:25
calculate your autosomal admixture percentages using the following calculators
Thank you very much for this useful list/links and thread; also Knovas for his additions.

Dorianfinder
23-11-11, 20:14
ADVANCED ANALYSIS

All 22 chromosomes can be analyzed using the 'bychr' mode instead of the 'genomewide' mode in the dv3.par file found in all dodecad calculators mentioned above. Similarly, ancestry percentages for individual segments of an individual's genome can be calculated using the 'byseg' mode.

The accuracy of analysis increases when viewing all 22 chromosomes. Also, one can study the individual chromosomes and create a graphic representation of each chromosome's ancestral admixture.

If you have used this software please feel free to post your experience here.

Dorianfinder
28-11-11, 13:31
SNP Map (http://snpmap.blogspot.com/2011/06/snpmap-version-102-introduction.html)

This tool allows you to browse your individual snp frequencies, and allows you to compare your particular snp to its frequency within other population groups.

The program is downloaded onto your pc and you upload your raw data files from either Relative Finder or Family Finder onto the program. It's user-interface is a no-frills database but it does the job well. It allows you to analyze your individual snps with full confidentiality and it's free.

Knovas
28-11-11, 22:22
I already checked it quickly with different raw data's from people I know: 1 mixed Iberian (different regions), 1 mostly Catalan (me) a Basque individual and an Angloamerican of mostly English/Irish descent.

I looked at Chromosome X in all cases to see it under similar conditions, and it basically shows there's apreciable shared ancestry between populations. Not all markers are informative in ancestral terms, some of them are related to health or something like this, but I'm not a professional to distinguish them. However, I did not see huge differences between this 4 individuals, it's not rare for example to find a genotype present in 90% of African population and, lets say, only 20% in Europe. At least, I could apreciate it in all the individuals, but perhaps the "sample size" it's too low.

Well, there are a lot of markers one could check with different interpretations. There's nothing more I could say considering my knowledge, just some observations. Other people much versed in allele frequencies would be of greater help.

Dorianfinder
29-11-11, 09:28
I did not see huge differences between this 4 individuals, it's not rare for example to find a genotype present in 90% of African population and, lets say, only 20% in Europe. At least, I could apreciate it in all the individuals, but perhaps the "sample size" it's too low.

The 20% found in Europe and Africa refers to shared admixture (convergence). If you want to decrease this overlap you can increase reliability from 80% to 95%. The Relative Finder X-chromosome data file has many non-ancestral markers, unlike the FTDNA Family Finder data file which is ancestral in its entirety.

Allele frequencies can be considered reliable when a particular admixture component is found in progressive strands spanning more than 1mil, if it's unbroken over 6mil then ancestry is certain.

Many people don't know what to do with the X-chromosome data file they get from RF and FF. In fact, it's much better than an mtdna test and the best indication of maternal ancestry. The X-chromosome is passed onto men by their mothers and includes all maternal great-grandmothers, so it's amazingly useful for individuals from the USA and South Africa who think they may have a great-grandmother who may have had possible Amerindian or slave ancestry.

5383

Knovas
29-11-11, 11:22
Thanks. All the raw data's I checked are from 23andme, which of course have many non ancestral markers. Anyways, I'll consider your suggestions and continue exploring similarities.

I think the idea of the program it's quite good, and it could be helpfull for the design of new analysis. Possibly both Dienekes' and Davidski used it for something.

Dorianfinder
19-12-11, 18:02
Download the K12a calculator here (https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=0B7JDEoCgzRKeZTljNzFlMGMtZGFiOC00NzU3LTgxMjM tNjg1NDk1YzY2ZDk0&hl=en_US)
Download the world9 calculator here (https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=0B7AJcY18g2GaZDUzZGNlY2YtZTMyOS00OGNmLTkwOTA tYjIyZDZjMmExNDJk&hl=en_US)

Download the Dodecad Oracle (K12a version) here (https://docs.google.com/leaf?id=0B7AJcY18g2GaNzFmYTM3YmItYzY4OC00YzYzLThkM jktNWU3Y2UwZjc2MTk4&hl=en_US) (left click 'file' to download)

Knovas
19-12-11, 19:11
Thanks Dorian, I was about to miss the World9. Interesting this one, I'm going to start a thread for comparison with the previous Eurasia7.

aaliy06
14-01-12, 01:36
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

Knovas
14-01-12, 14:55
You must create a new folder and call it "working directory", that's what it means. Then, extract the analysis components into this one and continue following the instructions. You need to add the DIY archive and your transformed genotype data (in a format understood by DIY).

Note that previously you must download the latest version of DIY and the R program. I'm assuming you did.

aaliy06
14-01-12, 20:39
Yes I downloaded the latest version, does it matter where you put the working directory folder at? I mean can you put it in your documents or does it have to be on your C: drive? and do you have to have the quotation marks?

Thanks
aaliy06

aaliy06
14-01-12, 21:01
One more thing, what is the format that DIY understands?

Knovas
14-01-12, 21:35
I think it doesn't matter where you create the folder. If it doesn't work, just change the position. Mine are in my documents (I have many working directories for the different calculators) and there's no problem.

The format that DIY understands is the transformation you'll have to do on your raw data following the instructions. Unzip your data inside the working directory, follow the preliminary steps, and an archive called "genotype" will emerge inside the working directory. This one will be valid for all calculators designed for DIY; the only one which DIY is able to read and extract admixture proportions.

Carlos
15-01-12, 00:03
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.

Dorianfinder
15-01-12, 00:41
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 (http://www.adlsoft.net/). 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 (http://www.r-project.org/). 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.

aaliy06
15-01-12, 08:33
Thank you, I will give it a try

Knovas
15-01-12, 15:43
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.

aaliy06
16-01-12, 06:05
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

Dorianfinder
16-01-12, 07:46
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.

aaliy06
16-01-12, 11:12
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.

Carlos
16-01-12, 16:32
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?

Dorianfinder
16-01-12, 21:56
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 (http://dodecad.blogspot.com/2011/09/do-it-yourself-dodecad-v-21.html) [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.

Carlos
16-01-12, 23:24
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.

Dorianfinder
01-02-12, 03:58
Download the K7b calculator here (https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=0B7AJcY18g2GaZGVlMDJiNWItMDdmMy00YWYxLTljNTA tMzcyNzRkMzc1MTRj&hl=en_US).
Download the K12b calculator here (https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=0B7AJcY18g2GaZWFhZTYxOTUtNDI2Yi00M2VlLWEzZGY tODIyNzUxNWJlZTdl&hl=en_US).

Download the new Dodecad Oracle for K12b here (https://docs.google.com/leaf?id=0B7AJcY18g2GaYWNiZjI3ZGYtM2EwYy00OTdjLTgwN jUtMWZkODFhNDQ5NjFi&hl=en_US).

Dorianfinder
03-07-12, 00:08
There are two more calculators from Dienekes aka the Dodecad Ancestry Project.

Download the weac2 calculator files here (https://docs.google.com/file/d/0B7AJcY18g2GaZWZYbC1zVEF4RlE/edit?pli=1).
Download the K10a calculator here (https://docs.google.com/file/d/0B7AJcY18g2Gab05oMjJlQmpjb0U/edit?pli=1).

zanipolo
23-07-13, 08:34
It seems that aDna sites are still using this mixture................is it still correct for STRs?

http://www2.gslt.hum.gu.se/~leifg/jh/Roewer%2BCroucher%2Bal_on_Ystr%2BHistory_2005.pdf

Dorianfinder
06-02-14, 22:57
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!

Sile
07-02-14, 07:44
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
http://imageshack.com/scaled/medium/819/k09h.jpg (http://imageshack.com/photo/my-images/819/k09h.jpg/) 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)
(http://imageshack.com)

Dorianfinder
20-03-14, 09:57
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.

LeBrok
20-03-14, 17:02
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.

Ernesto Grandi
20-03-14, 21:51
is it possible to run your raw data on DODECAD outside GEDmatch platform? some other websites?

Ernesto Grandi
20-03-14, 21:52
previus DODECAD calculators will still available?

Sile
21-03-14, 08:07
Why isn't the french admixture split in many admixture tests?

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