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Thursday, November 15, 2012

New add-on tool to MDLP World-22 calculator

Alex_Axe from Molgen forum announced the release of a new tool Oracle_AdMix4.
Basically, you can think of this tool as an useful add-on that extends the Oracle two-population results into four-population format.

Currently the tool support only DOS/Windows platform, and its usage is quite straightforward. The current distribution of  Oracle_AdMix4 includes the required file (data.txt) with the frequencies of 22 components in each of reference populations. The second file - input.txt - is the one you need to modify in order to use the tool on your own World-22 calculator results:

30     {Quantity of output results}
1,5    {Threshold of components to ignore noise} 
0,5    {Threshold of method to ignore noise}
2      {Power parameter for weighted method or zero for least-squares method}   
0      Pygmy
15     West-Asian
0      North-European-Mesolithic
0      Indo-Tibetan
0      Mesoamerican
0      Arctic-Amerind
0      South-America_Amerind
5      Indian
0      North-Siberean
25     Atlantic_Mediterranean_Neolithic
5      Samoedic
0      Indo-Iranian
0      East-Siberean
40     North-East-European
0      South-African
0      North-Amerind
0      Sub-Saharian
0      East-South-Asian
10     Near_East
0      Melanesian
0      Paleo-Siberian
0      Austronesian

All you need to do is to change the default values of components with your own results of World-22 calculator.

The output should appear in the following format:

1 Mordovian+Russian_South+Swedish+Swedish @ 20,749639
2 Estonian+Mordovian+Swedish+Swedish @ 23,267935
3 Finnish-North+Mordovian+Polish+Swedish @ 23,656645
4 Finnish-North+Mordovian+Russian_South+Swedish @ 23,83736
5 Estonian+Finnish-South+Mordovian+Swedish @ 24,192354
6 Mordovian+Polish+Swedish+Swedish @ 24,846391
7 Estonian+German-North+Mordovian+Swedish @ 25,176036
8 Lithuanian+Mordovian+Swedish+Swedish @ 25,511204
9 Finnish-North+Lithuanian+Mordovian+Swedish @ 25,523722
10 Finnish-South+Lithuanian_V+Mordovian+Swedish @ 25,539837

19 comments:

  1. It works! Thank you very much.

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  2. Oh, and comma (,) must be used instead of dot (.), otherwise the program falls down.

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  3. Crashes for me even using comma. Windows 7 x64

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  4. This is still an alpha version. I am working to improve the program and add some features.
    If the program does not work even using commas in input.txt, then you should try the other hand: replace all the commas with the dots in the files data.txt and input.txt
    Sometimes it helps.

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  5. Hi thanks for making this. Will there be a 64 bit version?

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  6. 097 Version: http://db.tt/634mFXL2
    However, the previous was not final. :)))

    2 Jeremy Knowles: probably not (at least not so soon)

    Also, now it's available on GEDmatch.com

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  7. Hello, how I'd like to know if you accept new members? What ethnic make-up? (I'm mixed)

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  8. Very interesting. Do you have a graph showing the different proportions among population groups/nationalities?

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  9. what is meaning of ENF in Population?

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  10. what is meaning of ENF in Population?

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  11. What do the numbers with the @ symbol in front of them mean?

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  12. Sorry I'm new at this. Can you explain how I got to this conclusion. It's pretty interesting. MDLP World-22 4-Ancestors Oracle

    This program is based on 4-Ancestors Oracle Version 0.96 by Alexandr Burnashev.
    Questions about results should be sent to him at: Alexandr.Burnashev@gmail.com
    Original concept proposed by Sergey Kozlov.
    Many thanks to Alexandr for helping us get this web version developed.

    Admix Results (sorted):

    # Population Percent
    1 Sub-Saharian 77.30
    2 Pygmy 4.27
    3 Near_East 4.01
    4 North-East-European 3.48
    5 Atlantic_Mediterranean_Neolithic 3.06
    6 North-European-Mesolithic 2.07
    7 West-Asian 1.33
    8 Austronesian 1.10


    Finished reading population data. 276 populations found.
    22 components mode.

    --------------------------------

    Least-squares method.

    Using 1 population approximation:
    1 Lemba @ 13.380752
    2 Bantu @ 16.103294
    3 Mandenka @ 23.979706
    4 Sub-Saharian @ 24.090555
    5 Yoruba @ 24.090555
    6 Biaka_Pygmies @ 27.763062
    7 Ethiopian @ 56.347858
    8 Jew-Ethiopia @ 60.162483
    9 Jew_Ethiopia @ 61.139290
    10 Lumbee @ 61.957558
    11 Moroccan @ 66.459908
    12 Australian @ 69.044312
    13 Yemen @ 71.906158
    14 Mozabite @ 72.454742
    15 Egyptian @ 76.988129
    16 Puerto-Rican @ 77.375687
    17 Ste7 @ 78.996002
    18 Miwok @ 81.768669
    19 Jordanian @ 81.774033
    20 Mexican @ 82.577103

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  13. This comment has been removed by the author.

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  14. Hello, I am fairly new to this, I was doing the MDLP World-22 Admixture, I was comparing my chromosomes to someone else's. My question is what does the top colors represent and what do the bottom colors represent.

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