July 26, 2011

DIY Dodecad

It's been more than 3 years that I started the non-commercial autosomal ancestry analysis field with the release of EURO-DNA-CALC. Today, I am releasing DIY Dodecad 1.0, the next generation of ancestry self-analysis.

Back in 2008, personal genome services using microarrays had just recently started, and it was a great opportunity to bring together the published data about human populations in the scientific literature with the new flood of data from customers of the new companies. I thought, that these were either underserved by the simple European-Asian-African model in the more reputable companies, or fed fairytales by the less reputable ones.

Of course, EURO-DNA-CALC was rudimentary by today's standards, as it used only a few hundred ancestry informative SNPs. Nonetheless, it did manage to be of some use before it was retired.

Almost a year ago, I decided to take up the mantle of genome blogger once again, with the goal of updating and improving EURO-DNA-CALC with the new wealth of population data that had since become available. Two reasons made me deviate from my original plan:
  • ADMIXTURE only runs on Linux or MacOS, while my favorite R is quite underpowered to do the job; hence, the vast majority of regular PC users would not/could not try a new tool that upped both the number of SNPs, and the number of ancestral populations substantially.
  • I realized the value of not only providing a tool to the community based on published data, but on collecting data myself; this would ensure that the tool would take into account several regions of the world that are "black holes" as far as publicly accessible data are concerned.
Thus began the Dodecad Ancestry Project, based on the idea of providing the community with results in exchange for data that could then create better results, and so on, in a virtuous circle.

Nonetheless, I always kept thinking of how I could encompass the Dodecad Project's main admixture analysis in a DIY tool; I explain the reasons why in my post introducing the new software, but they all boil down to one:

  • Interest in the Project has been huge, and I always felt bad when I had to turn down someone's relatives, or people of mixed ancestry, or the n-th member of a well-represented group. With all the automation in place, it still takes me a couple of minutes to process a sample, and the task of doing it myself for potentially thousands is daunting.

I learned that the hard way when I briefly opened submission to everybody; I had to close it in less than 12 hours, because of the overwhelming demand.

The new tool allows everyone to calculate their Dodecad v3 results. It did take me a few hours to write a couple hundred lines of code for it, but it will both make Dodecad analysis accessible to nearly everyone and save me a lot of time, some of which will, hopefully, be spent on experimenting with new interesting ideas for the Project beyond Clusters Galore, concordance ratios, zombies, the Dodecad Oracle, etc.

So, if you have a PC or Linux machine and 23andMe or Family Finder data, give it a try!

18 comments:

  1. Would people recommend 23andMe or Family Finder?

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  2. I am DOD618, these are my results with DIY Dodecad V1:
    West European = 51,82%
    Mediterranean = 38,99%
    West Asian = 4,23%
    East european = 2,06%
    North-West African = 1,80%
    South Asian = 0,69%
    South-West Asian = 0,41%
    South-East Asian = 0,01%
    Neo African = 0,00%
    North-East Asian = 0,00%
    East African = 0,00%
    Palaeo African = 0,00%

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  3. Hi Dienekes,
    although I am a fan of your blog, I m' afraid your political views are too far right-wing for me to follow. I think that posting articles written by Breivik 's Greek comrades-in-arms, of course does not make you responsible for the Utoya Island incident, but surely puts you in the same picture with the Norwegian Aryan. Perhaps it is an opportunity to get rid of your anti-immigration, anti-leftist and anti-multicultural political agenda,
    sincerely yours

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  4. Prof.Steve:

    1. You are off-topic
    2. What "articles" are you referring to and by what "Greek comrades-in-arms?"?
    3. I'm happily opposed to the ideology of multiculturalism and to left-wing ideology in general; some murderous Norwegian nutcase's opinions are irrelevant to me and would certainly not sway me one way or another in my political views.

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  5. The Norwegian nationalist in his Manifesto,among others, is referring to :
    1.Laikos Orthodoxos Synagermos(LAOS)
    2.Hellenic Front. The leader of this organization is Makis Voridis, a former nazi activist who is now an elected m.p. in Greek Parliament. He is amember of LAOS party,where one can find many nazis in cover, like this Plevris guy, who is the son of a notorious anti-semite and admirer of Hitler and the "aryan" race .I see that, you have posted an article written by Mr Voridis in your greek blog,even today.

    Anyway, if some anarchists burn down a building with three people in it, we do not say they are insane, we blame their ideology,right? So, when a nationalist kills a hundred people, how could you say that his racist ideology has nothing to do with it? And why do you grant him an indulgence for the remission of his horrible crimes, stating that he is just an insane person?

    The fact that Breivik shares political views with Mr Voridis and others(and you) does not mean anything?

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  6. I never posted an article by Mr. Voridis, I have his FEED on my blogroll, together with feeds of some politicians I respect from several other center-right parties of Greece.

    If you were not an ill-informed busybody, you would realize that I have been one of the most vocal opponents of LAOS on my blog. But, that does not mean that I don't respect certain LAOS politicians, and Mr. Voridis is certainly quite worthy of respect for many of his political positions.

    Anyway, if some anarchists burn down a building with three people in it, we do not say they are insane, we blame their ideology,right? So, when a nationalist kills a hundred people, how could you say that his racist ideology has nothing to do with it? And why do you grant him an indulgence for the remission of his horrible crimes, stating that he is just an insane person?

    Your sense of proportion is horribly misplaced. There have been criminals professing literally every sort of ideology or belief system: anarchists, nationalists, socialists, communists, Christians, atheists, and so on and so forth.

    Going by your irrational "argument" one ought to distance themselves from every set of ideas known to man, because every set of ideas has been at one time or another been misused by a criminal.

    The fact that Breivik shares political views with Mr Voridis and others(and you) does not mean anything?

    No, it does not mean anything. I'll judge Mr. Voridis's views on my own, and a Norwegian psychopath's opinions of them is irrelevant.

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  7. "Prof. Steve" is bang out of order!

    When radical muslims let off bombs, did he say to muslims, "will you now renounce your muslim ideology"?

    The leftists are beyond contempt that they would try to use the Norway incident to further their plans to flood Europe will mass coloured immigration.

    Mass immigration amounts to genocide, the destruction of the indigenous people.

    These leftists expect our peoples to willingly disappear as soon as possible in order to satisfy the leftists that we are "good" people. Well no, we are not going to do that!

    The national ethnic groups of Europe will survive and we will keep our homelands and we are not going to apologise to anyone for that!

    We have a right to our own home countries and we will never surrender!

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  8. " There have been criminals professing literally every sort of ideology or belief system: anarchists, nationalists, socialists, communists, Christians, atheists, and so on and so forth."

    Exactly.

    "Going by your irrational "argument" one ought to distance themselves from every set of ideas known to man, because every set of ideas has been at one time or another been misused by a criminal."

    In some cases though, some sets of ideas are advocating crimes against humanity.For example:
    -Believing that some race is "better" than the others.
    -Believing that human races should never mix.
    -believing that the various ...cultures should never mix.

    Under the issue about not mixing civilizations, one can find easily traces of irrational thoughts, even a certain amount of stupidity. Right now, we are communicating using an alphabet given to British by the Romans, who borrowed it from Greeks who created it using the Semitic alphabet as a basis,and were using numbers given to us by the Arabs who took it from the Indians. We listen to rhythmical patterns brought to the States by negro slaves from Africa and melodies composed by Jewish composers, who used instruments based on an invention of Mesopotamians, using a theory formed by Europeans, who were using another possible Greek invention,a polyphonic instrument, called organ. We are all living in modern states with laws and armies, Levantine prehistoric inventions, etc, etc, etc. This is what we have learned at school. And this is what we realize reading your own articles.

    As a Greek you should bare in mind that classical Greece is a fine example of mixing of civilizations,(even acculturation, if you wish). I am referring to Greek tribes from the eastern neolithic revolution mixing with PIE speaking tribes who came from the north (or Caspian Sea) thousands of years later.

    Personally, I'd wish to have some real multi-culti atmosphere in Europe today. But it is not the case. Do you know many Greeks improvising ragas or dancing Bharata Natyam?(frankly,I know only one :-). Do you think that the English scene is ready to accept one of the many Greek, Byzantine and eastern musical scales? No such luck.

    What we have here is the cremation of all cultures of the planet before the statue of Moloch, whose real name is Money. Or Capital. Or huge music companies crazy about earning money, but not about any spiritual needs of humanity.

    It's worth mentioning that modern Greek culture has been created mostly by Leftists, communists, or former communists,gay and Jewish, Armenian, Arberesh and others.

    If you exclude them from modern Greek culture, you won't have many great things left. Except maybe from the nazi speeches of Mr. Vorides, a possible Breivik accomplice...

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  9. It's worth mentioning that modern Greek culture has been created mostly by Leftists, communists, or former communists,gay and Jewish, Armenian, Arberesh and others.

    If you exclude them from modern Greek culture, you won't have many great things left.


    You profess to be a non-racist and yet you ascribe a remarkable degree of cultural infertility to the majority of the Greek people who are not communist, gay, Jewish, Armenian, or Arberesh.

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  10. I've been dipping into this site for a few years now but I must have missed all Dienekes facist rants.
    Prof, I'm on the far left but can't say I've noticed anyone here advocating Greek racial purity, or any other racial purity for that matter.Dienekes may be a raving Nazi but if he is he hides it well!

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  11. "Prof. Steve" sounds like a genocidal imperialist. He argues that we would have a higher "culture" if the indigenous ethnic homelands of Europe are obliterated under a flood of mass coloured immigration. That is exactly the sort of argument that was used by the classical Liberal philosophers to justify the extermination of the indigenous peoples and cultures of the American and Australian continents.

    The Liberal-Leftist multiculti-maniacs now want to exterminate all of the indigenous peoples of Europe. We can see clearly that they have declared war on all of our peoples and we must never surrender to them under any circumstances whatsoever. We must all come together and liberate Europe from the multi-culti exterminationists.

    Europe has the highest culture that the world has ever known and we dont need to be replaced by other ethnic groups. What "Prof. Steve" doesnt seem to grasp is that we want our OWN culture in our OWN homelands for our OWN people. Every ethnic group in history has been willing to fight for that right and we will surrender our homelands under NO condition.

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  12. I downloaded your DYIDodecadWin and found it a little hard to get used to but the results were rewarding. I have myself and three siblings in my 23andMe account. However, I am the only one in your project. I computed the values for the three other siblings and computed a composite profile for the family. There are only minor variations in the four major components for the four of us. I believe this confirms the validity of the methods to some degree and was surprisingly close. I fit the data to a mixture of:

    Population Admixture
    Orkney_1KG 69.51%
    N_Italian_D 20.78%
    Russian_D 7.19%
    Lezgins 1.78%
    Kalash 0.75%
    RMSD 0.0410

    As you can see from the RMSD (root mean square deviation) for the fit is only 0.041 which I consider a very good fit. The data:
    East European West European Mediterranean Neo African West Asian South Asian Northeast Asian Southeast Asian East African Southwest Asian Northwest African Palaeo African
    SmiserComposite 12.44 49.17 27.13 0.00 9.23 0.85 0.32 0.00 0.01 0.83 0.02 0.00
    Mixture as below 12.42 49.17 27.12 0.00 9.23 0.85 0.43 0.14 0.00 0.88 0.09 0.00
    Differences -0.01 0.00 0.00 0.00 -0.01 0.00 0.12 0.14 -0.01 0.05 0.07 0.00

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  13. I still can't figure this out, does anyone want to do my results for me please :-)

    Denise

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  14. I didn't succeed in making working my downloaded Dodecad software.
    There will be skillful persons who did succeed.

    May I ask if one of them would be so kind to investigate my genome that was tested at 23andme ?
    My ancestors in the fifth generation, 32 persons, were all born within a circle of 30 kilometers round Maastricht in the South of the Netherlands.

    If granted I send the text file by e-mail.

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  15. @Apostate

    I have accounts at both. 23 and me has a much bigger database, is more professional, better value for money and has more extras.

    Folk at Family Finder are more likely to respond to correspondence and share with you. The also have the associated STR Surname projects.

    But the size of the 23and Me database is the clincher.

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  16. Wonderful program, it worked for me, no issues.

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  17. Pffff ! Succes!

    East_European 10.15%
    West_European 48.71%
    Mediterranean 26.26%
    Neo_African 0.08%
    West_Asian 11.73%
    Southeast_Asian 0.17%
    Southwest_Asian 2.08%
    Northwest_African 0.81%

    Thanks Dienekes

    ReplyDelete

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