Wednesday, December 31, 2014

Sub Project: Autosomal Tree UI

This is a sub-project for Autosomal Pedigree Creator.

This tool allows to create customized pedigree trees based on different thresholds. It is similar to Autosomal Pedigree Customization but with graphical user interface.

Prerequisites:
Usage:
Select the 'atree.txt' (output from Autosomal Pedigree Creator), adjust the parameters and click 'Generate Tree'.

Screenshot:


Download Autosomal Tree UI.zip (11.2 MB)

Source Code at GitHub.

License: MIT License.

Thursday, December 25, 2014

Parentless Phasing

Parentless Phasing is a tool that allows to do some reasonable phasing when both parents' DNA are not available, which means, each phased parent kits will still be technically unphased (as we don't know the parents), however, instead of being completely unphased, longer segments in each phased parents' kits will be phased. This is extremely helpful for people searching their immediate family since it eliminates unphased longer compound segments matches. You can add your close relative's autosomal files into the data folder, which improves accuracy. It allows to eliminate distant relatives to help find and filter closer relations. The tool supports build 37 from FTDNA, 23andMe and Ancestry autosomal files.

Prerequisites: Microsoft .Net Framework 4.0

Screenshot:

Download : Parentless Phasing.zip (300 MB)

Source Code at GitHub.

Related Blogs:


Change Log
    Version 1.0
    • Initial Release.

    Wednesday, December 24, 2014

    Pedigree Collapse Calculator

    Pedigree Collapse Calculator will tell you how much percentage of your DNA is homozygous indicating what level of relationship your parents had. The tool will tell the percentage of collapse in your pedigree. It supports FTDNA, 23andMe and Ancestry files.

    Note: Keep watch for duplicated ancestors in your pedigree if you have high RoH. The value of RoH is certainly correct but the interpretation may or may not match exactly your pedigree. e.g., a 12.5% ROH representing first cousin parents could also mean double second cousins or quadruple third cousins.. and so on.  Hence, if you have parents as double second cousins, then you could have the same RoH level as if your parents are first cousins. The accuracy of the tool diminishes beyond 3rd cousin marriages.

    Prerequisites: Microsoft .Net Framework 4.0

    Screenshot:

    Download : Pedigree Collapse Calculator.exe (389 KB)

    Source Code at GitHub.

    Change Log
    Version 1.0
    • Initial Release.

    Ancient Calculator

    Ancient Calculator will tell you how much percentage of DNA and/or compound segments is shared between an ancient DNA and the autosomal file. In other words, it tells your total percentage of shared ancestors in each others pedigree. The tool includes 59 ancient DNA which allows to compare any autosomal file with ease. It supports FTDNA, 23andMe and Ancestry files.

    Prerequisites: Microsoft .Net Framework 4.0

    Screenshot:

    Download : Ancient Calculator.exe (276 MB)

    Source Code at GitHub.

    Change Log
    Version 1.1
    • 29 Additional Ancient DNA added to the list for comparision.
    Version 1.0
    • Initial Release.

    Tuesday, December 16, 2014

    DNA Calculator

    DNA Calculator will accurately tell you how much percentage of DNA is shared between two people. The tool is meant to know the shared DNA which tells your total percentage of shared ancestors in each others pedigree. It supports FTDNA, 23andMe and Ancestry files.

    Prerequisites: Microsoft .Net Framework 4.0

    Screenshot:

    Download : DNA Calculator.exe (388 KB)

    Source Code at GitHub.

    Change Log
      Version 1.1
      • Settings customization for recent and total ancestry.
      Version 1.0
      • Initial Release.

      Monday, December 15, 2014

      Clovis Anzick Calculator


      Clovis Anzick-1 shared percentage can be calculated by using the Ancient Calculator tool. Hence, this tool is now obsolete.


      Clovis Anzick Calculator will accurately tell you how much of your DNA is from Clovis Anzick. This tool actually uses Clovis Anzick DNA to compare your autosomal file and tells your shared percentage. This is an easy way to check if you have any ancient North American ancestry. It supports FTDNA, 23andMe and Ancestry files.

      Prerequisites: Microsoft .Net Framework 4.0

      Screenshot:

      Download : Clovis Anzick Calculator.exe (7.76 MB)

      Source Code at GitHub.

      Change Log
        Version 1.0
        • Initial Release.

        Denisova Calculator


        Denisova shared percentage can be calculated by using the Ancient Calculator tool. Hence, this tool is now obsolete.


        Denisova Calculator will accurately tell you how much of your DNA is from Denisova. This tool actually uses Denisova DNA to compare your autosomal file and tells your shared percentage. It supports FTDNA, 23andMe and Ancestry files.

        Prerequisites: Microsoft .Net Framework 4.0

        Screenshot:

        Download : Denisova Calculator.exe (7.92 MB)

        Source Code at GitHub.

        Change Log
          Version 1.0
          • Initial Release.

          Neanderthal Calculator


          Neanderthal shared percentage can be calculated by using the Ancient Calculator tool. Hence, this tool is now obsolete.


          Neanderthal Calculator will accurately tell you how much of your DNA is from Neanderthal. This tool actually uses Neanderthal DNA to compare your autosomal file and tells your shared percentage. It supports FTDNA, 23andMe and Ancestry files.

          Prerequisites: Microsoft .Net Framework 4.0

          Screenshot:

          Download : Neanderthal Calculator.exe (7.93 MB)

          Source Code at GitHub.

          Change Log
            Version 1.0
            • Initial Release.

            Disease Resistance Test


            The tool is filed under factoids, which means unreliable information that is mentioned too often so that people believe it as a fact. So, please use it only for fun. Just because you have a gene or a mutation does not mean it is always expressed. Personally, I don't believe too much on this stuff because there are way too many parameters involved. Hence, use this tool to find fun facts and if you notice the result requires health attention then please visit a physician and do proper tests and confirm.


            Disease Resistance Test is a tool to find if you have resistance to several diseases including malaria, tuberculosis, bacteremia and pneumococcal disease based on your DNA. The tool supports FTDNA, 23andMe v3 & v4 and Ancestry autosomal files.

            Prerequisites:
            Usage: Browse and select the Autosomal raw file.

            Screenshot:

            Download : Disease Resistance Test.exe (410 KB)

            Source Code at GitHub.

            License: MIT License.

            Change Log
            Version 1.0
            • Initial release.

            Telomere Test


            The tool is filed under factoids, which means unreliable information that is mentioned too often so that people believe it as a fact. So, please use it only for fun. Just because you have a gene or a mutation does not mean it is always expressed. Personally, I don't believe too much on this stuff because there are way too many parameters involved. Hence, use this tool to find fun facts and if you notice the result requires health attention then please visit a physician and do proper tests and confirm.


            Telomere Test is a tool to find if you have shorter or longer telomeres based on your DNA. The tool supports FTDNA, 23andMe v3 & v4 and Ancestry autosomal files.

            Prerequisites:
            Usage: Browse and select the Autosomal raw file.

            Screenshot:

            Download : Telomere Test.exe (413 KB)

            Source Code at GitHub.

            License: MIT License.

            Change Log
            Version 1.0
            • Initial release.

            Ancestry Test


            The tool is filed under factoids, which means unreliable information that is mentioned too often so that people believe it as a fact. So, please use it only for fun. Just because you have a gene or a mutation does not mean it is always expressed. Personally, I don't believe too much on this stuff because there are way too many parameters involved. Hence, use this tool to find fun facts and if you notice the result requires health attention then please visit a physician and do proper tests and confirm.


            Ancestry Test is a tool to find your ancestry if you have European or African/Asian or Mixed based on your DNA. The tool supports FTDNA, 23andMe v3 & v4 and Ancestry autosomal files.

            Prerequisites:
            Usage: Browse and select the Autosomal raw file.

            Screenshot:

            Download : Ancestry Test.exe (421 KB)

            Source Code at GitHub.

            License: MIT License.

            Change Log
            Version 1.0
            • Initial release.

            Thursday, December 11, 2014

            Y-Tree Creator

            Y-Tree Creator allows you to automatically generate the entire Y-DNA (or a specific subclade) based on the set of Y-SNPs.

            Prerequisites:
            Usage / Tips: Extract the download and place the SNPs as a comma separated value in each file inside the data folder (SNPs format found at FTDNA projects). Execute the Y-Tree Creator executable program and build tree. Then enter the Y-SNPs in the text box and plot it. You can export or save/open the entire generated tree or the SNPs plotted on the new tree as a report. Try with a few files specific to a sub-clade and then go bigger. Currently, the data folder contains  37 files from J-Haplogroup as sample which I took from J1 Y-DNA Project. You can remove them and place your own files or just add it to the existing list of files.

            Screenshot:

             


            Download Y-Tree Creator.zip (76 KB).

            Source Code at GitHub.

            License: MIT License.

            Change Log
            Version 1.1
            • Input box text default length increased.
            Version 1.0
            • Initial release.

            mtPhyloTree Creator

            MtPhyloTree Creator allows you to automatically generate the entire mt-DNA PhyloTree (or a specific subclade) based on the set of mtDNA mutations provided.

            Prerequisites:
            Usage / Tips: Extract the download and place the mutations as a comma separated value in each file inside the data folder. Execute the MtPhyloTree Creator executable program and build tree. Then enter the mutations in the text box and plot it. You can export or save/open the entire generated tree or the mutations plotted on the new tree as a report. Try with a few files specific to a sub-clade and then go bigger. Currently, the data folder contains  13883 mtDNA files. You can remove them and place your own files or just add it to the existing list of files.

            Screenshot:
             



            Download mtPhyloTree Creator.zip (5.36 MB).

            Source Code at GitHub.

            License: MIT License.

            Change Log
            Version 1.2
            • Minor enhancement - expand/collapse tree, better error handling.
            Version 1.1
            • Opening a saved PhyloTree doesn't work - fixed.
            Version 1.0
            • Initial release.

            Monday, December 8, 2014

            Placebo Test


            The tool is filed under factoids, which means unreliable information that is mentioned too often so that people believe it as a fact. So, please use it only for fun. Just because you have a gene or a mutation does not mean it is always expressed. Personally, I don't believe too much on this stuff because there are way too many parameters involved. Hence, use this tool to find fun facts and if you notice the result requires health attention then please visit a physician and do proper tests and confirm.


            Placebo Test is a tool to find the effectiveness of placebo, investigative interest, worry, pain threshold and stress vulnerability based on your DNA. The tool supports FTDNA, 23andMe v3 & v4 and Ancestry autosomal files.

            Prerequisites:
            Usage: Browse and select the Autosomal raw file.

            Screenshot:

            Download : Placebo Test.exe (416 KB)

            Source Code at GitHub.

            License: MIT License.

            Change Log
            Version 1.0
            • Initial release.

            Personality Test


            The tool is filed under factoids, which means unreliable information that is mentioned too often so that people believe it as a fact. So, please use it only for fun. Just because you have a gene or a mutation does not mean it is always expressed. Personally, I don't believe too much on this stuff because there are way too many parameters involved. Hence, use this tool to find fun facts and if you notice the result requires health attention then please visit a physician and do proper tests and confirm.


            Personality Test is a tool to find if you are optimistic or pessimistic, empathetic and stress handling based on your DNA. The tool supports FTDNA, 23andMe v3 & v4 and Ancestry autosomal files.

            Prerequisites:
            Usage: Browse and select the Autosomal raw file.

            Screenshot:

            Download : Personality Test.exe (412 KB)

            Source Code at GitHub.

            License: MIT License.

            Change Log
            Version 1.0
            • Initial release.

            Smoking and Drinking Addiction Test


            The tool is filed under factoids, which means unreliable information that is mentioned too often so that people believe it as a fact. So, please use it only for fun. Just because you have a gene or a mutation does not mean it is always expressed. Personally, I don't believe too much on this stuff because there are way too many parameters involved. Hence, use this tool to find fun facts and if you notice the result requires health attention then please visit a physician and do proper tests and confirm.


            Smoking and Drinking Addiction Test is a tool to access the risk of having smoking and drinking addiction based on your DNA. The tool supports FTDNA, 23andMe v3 & v4 and Ancestry autosomal files.

            Prerequisites:
            Usage: Browse and select the Autosomal raw file.

            Screenshot:

            Download : SmokingDrinking Addiction Test.exe (405 KB)

            Source Code at GitHub.

            License: MIT License.

            Change Log
            Version 1.0
            • Initial release.

            Sunday, December 7, 2014

            Muscle Performance Test


            The tool is filed under factoids, which means unreliable information that is mentioned too often so that people believe it as a fact. So, please use it only for fun. Just because you have a gene or a mutation does not mean it is always expressed. Personally, I don't believe too much on this stuff because there are way too many parameters involved. Hence, use this tool to find fun facts and if you notice the result requires health attention then please visit a physician and do proper tests and confirm.


            Muscle Performance Test is a tool to identify muscle performance or endurance based on your DNA. The tool supports FTDNA, 23andMe v3 & v4 and Ancestry autosomal files.

            Prerequisites:
            Usage: Browse and select the Autosomal raw file.

            Screenshot:

            Download : Muscle Performance Test.exe (407 KB)

            Source Code at GitHub.

            License: MIT License.

            Change Log
            Version 1.1
            • Bug fix.
            Version 1.0
            • Initial release.

            Male Baldness Test


            The tool is filed under factoids, which means unreliable information that is mentioned too often so that people believe it as a fact. So, please use it only for fun. Just because you have a gene or a mutation does not mean it is always expressed. Personally, I don't believe too much on this stuff because there are way too many parameters involved. Hence, use this tool to find fun facts and if you notice the result requires health attention then please visit a physician and do proper tests and confirm.


            Male Baldness Test is a tool to test males the risk of becoming bald based on your DNA. The tool supports FTDNA, 23andMe v3 & v4 and Ancestry autosomal files.

            Prerequisites:
            Usage: Browse and select the Autosomal raw file.

            Screenshot:

            Download : Male Baldness Test.exe (409 KB)

            Source Code at GitHub.

            License: MIT License.

            Change Log
            Version 1.0
            • Initial release.

            Freckling Test


            The tool is filed under factoids, which means unreliable information that is mentioned too often so that people believe it as a fact. So, please use it only for fun. Just because you have a gene or a mutation does not mean it is always expressed. Personally, I don't believe too much on this stuff because there are way too many parameters involved. Hence, use this tool to find fun facts and if you notice the result requires health attention then please visit a physician and do proper tests and confirm.


            Freckling Test is a tool to test freckling, tanning and sun sensitivity based on your DNA. The tool supports FTDNA, 23andMe v3 & v4 and Ancestry autosomal files.

            Prerequisites:
            Usage: Browse and select the Autosomal raw file.

            Screenshot:

            Download : Freckling Test.exe (399 KB)

            Source Code at GitHub.

            License: MIT License.

            Change Log
            Version 1.0
            • Initial release.

            Back Pain Test


            The tool is filed under factoids, which means unreliable information that is mentioned too often so that people believe it as a fact. So, please use it only for fun. Just because you have a gene or a mutation does not mean it is always expressed. Personally, I don't believe too much on this stuff because there are way too many parameters involved. Hence, use this tool to find fun facts and if you notice the result requires health attention then please visit a physician and do proper tests and confirm.


            Back Pain Test is a tool to check if have the risk of lumbar disc disease (LDD) based on your DNA. The tool supports FTDNA, 23andMe v3 & v4 and Ancestry autosomal files.

            Prerequisites:
            Usage: Browse and select the Autosomal raw file.

            Screenshot:

            Download : Back-Pain-Test.exe (393 KB)

            Source Code at GitHub.

            License: MIT License.

            Change Log
            Version 1.0
            • Initial release.

            Error Avoidance Test


            The tool is filed under factoids, which means unreliable information that is mentioned too often so that people believe it as a fact. So, please use it only for fun. Just because you have a gene or a mutation does not mean it is always expressed. Personally, I don't believe too much on this stuff because there are way too many parameters involved. Hence, use this tool to find fun facts and if you notice the result requires health attention then please visit a physician and do proper tests and confirm.


            Error Avoidance Test is a tool to test if you are good or bad at avoiding errors based on your DNA. The tool supports FTDNA, 23andMe v3 & v4 and Ancestry autosomal files.

            Prerequisites:
            Usage: Browse and select the Autosomal raw file.

            Screenshot:

            Download : Error-Avoidance-Test.exe (437 KB)

            Source Code at GitHub.

            License: MIT License.

            Change Log
            Version 1.0
            • Initial release.

            HIV Immunity Test


            The tool is filed under factoids, which means unreliable information that is mentioned too often so that people believe it as a fact. So, please use it only for fun. Just because you have a gene or a mutation does not mean it is always expressed. Personally, I don't believe too much on this stuff because there are way too many parameters involved. Hence, use this tool to find fun facts and if you notice the result requires health attention then please visit a physician and do proper tests and confirm.


            HIV Immunity Test is a tool to test if you are almost immune to HIV based on your DNA. The tool supports FTDNA, 23andMe v3 & v4 and Ancestry autosomal files. Please note that this tool tests only almost complete immunity.

            Prerequisites:
            Usage: Browse and select the Autosomal raw file.

            Screenshot:

            Download : HIV Immunity Test.exe (401 KB)

            Source Code at GitHub.

            License: MIT License.

            Change Log
            Version 1.0
            • Initial release.

            Saturday, December 6, 2014

            Alcohol Flush Test


            The tool is filed under factoids, which means unreliable information that is mentioned too often so that people believe it as a fact. So, please use it only for fun. Just because you have a gene or a mutation does not mean it is always expressed. Personally, I don't believe too much on this stuff because there are way too many parameters involved. Hence, use this tool to find fun facts and if you notice the result requires health attention then please visit a physician and do proper tests and confirm.


            Alcohol Flush Test is a tool to test if you have alcohol flush based on your DNA. The tool supports FTDNA, 23andMe v3 & v4 and Ancestry autosomal files.

            Prerequisites:
            Usage: Browse and select the Autosomal raw file.

            Screenshot:

            Download : Alcohol Flush Test.exe (393 KB)

            Source Code at GitHub.

            License: MIT License.

            Change Log
            Version 1.0
            • Initial release.

            Bitter Taste Test


            The tool is filed under factoids, which means unreliable information that is mentioned too often so that people believe it as a fact. So, please use it only for fun. Just because you have a gene or a mutation does not mean it is always expressed. Personally, I don't believe too much on this stuff because there are way too many parameters involved. Hence, use this tool to find fun facts and if you notice the result requires health attention then please visit a physician and do proper tests and confirm.


            Bitter Taste Test is a tool to test if you have bitter taste based on your DNA. The tool supports FTDNA, 23andMe v3 & v4 and Ancestry autosomal files.

            Prerequisites:
            Usage: Browse and select the Autosomal raw file.

            Screenshot:

            Download : Bitter Taste Test.exe (420 KB)

            Source Code at GitHub.

            License: MIT License.

            Change Log
            Version 1.0
            • Initial release.

            Longevity Test


            The tool is filed under factoids, which means unreliable information that is mentioned too often so that people believe it as a fact. So, please use it only for fun. Just because you have a gene or a mutation does not mean it is always expressed. Personally, I don't believe too much on this stuff because there are way too many parameters involved. Hence, use this tool to find fun facts and if you notice the result requires health attention then please visit a physician and do proper tests and confirm.


            Longevity Test is a tool to test how long can you live based on your DNA. The tool supports FTDNA, 23andMe v3 & v4 and Ancestry autosomal files.

            Prerequisites:
            Usage: Browse and select the Autosomal raw file.

            Screenshot:

            Download : Longevity Test.exe (459 KB)

            Source Code at GitHub.

            License: MIT License.

            Change Log
            Version 1.1
            • Minor bug-fix.
            Version 1.0
            • Initial release.

            Friday, December 5, 2014

            Earwax Test


            The tool is filed under factoids, which means unreliable information that is mentioned too often so that people believe it as a fact. So, please use it only for fun. Just because you have a gene or a mutation does not mean it is always expressed. Personally, I don't believe too much on this stuff because there are way too many parameters involved. Hence, use this tool to find fun facts and if you notice the result requires health attention then please visit a physician and do proper tests and confirm.


            Earwax Test is a tool to test if you have "dry" or "wet" earwax. The tool supports FTDNA, 23andMe v3 & v4 and Ancestry autosomal files.

            Prerequisites:
            Usage: Browse and select the Autosomal raw file.

            Screenshot:


            Download : Earwax Test.exe (388 KB)

            Source Code at GitHub.

            License: MIT License.

            Change Log
            Version 1.1
            • Minor bug-fix.
            Version 1.0
            • Initial release.

            Thursday, December 4, 2014

            Caffeine Metabolism Test


            The tool is filed under factoids, which means unreliable information that is mentioned too often so that people believe it as a fact. So, please use it only for fun. Just because you have a gene or a mutation does not mean it is always expressed. Personally, I don't believe too much on this stuff because there are way too many parameters involved. Hence, use this tool to find fun facts and if you notice the result requires health attention then please visit a physician and do proper tests and confirm.


            Caffeine Metabolism Test is a tool to test if you have "fast" or "slow" caffeine metabolism. The tool supports FTDNA, 23andMe v3 & v4 and Ancestry autosomal files.

            Prerequisites:
            Usage: Browse and select the Autosomal raw file.

            Screenshot:


            Download : Caffeine Metabolism Test.exe (387 KB)

            Source Code at GitHub.

            License: MIT License.

            Change Log
            Version 1.1
            • Minor bug-fix.
            Version 1.0
            • Initial release.

            Tuesday, December 2, 2014

            BRCA1 Test


            The tool is filed under factoids, which means unreliable information that is mentioned too often so that people believe it as a fact. So, please use it only for fun. Just because you have a gene or a mutation does not mean it is always expressed. Personally, I don't believe too much on this stuff because there are way too many parameters involved. Hence, use this tool to find fun facts and if you notice the result requires health attention then please visit a physician and do proper tests and confirm.


            BRCA1 Test is a tool to test if you are positive for BRCA1 mutation. Hence, positive means, it's mostly positive but negative means, it is only negative for the mentioned particular type of BRCA1 mutation. The tool supports FTDNA, 23andMe v3 and Ancestry but not 23andMe v4. The only way to confirm is by doing an actual test.

            Prerequisites:
            Usage: Browse and select the Autosomal raw file.

            Screenshot:


            Download : BRCA1 Test.exe (393 KB)

            Source Code at GitHub.

            License: MIT License.

            Change Log
            Version 1.5
            • Improved accuracy of detection because of additional volunteer sending her autosomal DNA who was tested positive for BRAC1. Mutation name added in v1.3 removed to avoid confusion.
            Version 1.4
            • Improved accuracy of detection.
            Version 1.3
            • Mutation name added in result.
            Version 1.2
            • Minor bug-fix
            Version 1.1
            • Improved accuracy of detection.
            Version 1.0
            • Initial release.
            Related Blogs

            Monday, December 1, 2014

            Warrior Gene Test


            The tool is filed under factoids, which means unreliable information that is mentioned too often so that people believe it as a fact. So, please use it only for fun. Just because you have a gene or a mutation does not mean it is always expressed. Personally, I don't believe too much on this stuff because there are way too many parameters involved. Hence, use this tool to find fun facts and if you notice the result requires health attention then please visit a physician and do proper tests and confirm.


            Warrior Gene Test is a tool to test if you have the 3 repeats warrior gene. The tool supports FTDNA, 23andMe and Ancestry autosomal files. The tool is designed to work only on male X-Chromosomes.

            Prerequisites:
            Usage: Browse and select the Autosomal or X-Chromosome raw file.

            Screenshot:


            Download : Warrior Gene Test.exe (385 KB)

            Source Code at GitHub.

            License: MIT License.

            Change Log
            Version 1.3
            • Improved Accuracy.
            Version 1.2
            • Minor bug-fix.
            Version 1.1
            • Improved Accuracy.
            Version 1.0
            • Initial release.
            Related Blogs

            Sunday, November 30, 2014

            Sub Project: Autosomal Pedigree Customization

            This is a sub-project for Autosomal Pedigree Creator.

            This tool allows to create customized pedigree trees based on different thresholds.

            Prerequisites:
            Usage:

            Copy atree.txt (found in tmp folder after the execution of Autosomal Pedigree Creator) into the root folder of atree2gv and execute the below command from console / command prompt.

            atree2gv [-d=<distant-bp-threshold>] [-c=<close-bp-threshold>] [-s=<individual-segment-bp-threshold>] [-g=<large|small>]

            E.g.,
            atree2gv -d=1000000 -c=1500000000 -s=5000000 -g=large

            • -d=<value>, where value is the threshold in base-pairs for defining distant cousins.
            • -c=<value>, where value is the threshold in base-pairs for defining close relations, usually parent/child. If there are no parent child but only 2nd or third cousins, then you need to enter the value in base-pairs that could be shared by those relations. Parent/child shares 50% of 3.2 billion base pairs. So, the default value is 1500000000.
            • -s=<value>, where value is the threshold in base-pairs for defining individual segments.

            Download atree2gv.zip (11.9 MB)

            Source Code at GitHub.

            License: MIT License.

            Sunday, November 23, 2014

            Autosomal Pedigree Creator

            A tool that automatically creates a pedigree tree based on segment matches from a set of autosomal files. This tool will also let you know how a segment match of an unrelated genetic match is related and through whom. Supports FTDNA, 23andMe and Ancestry files.

            Prerequisites:
            Usage:
            1. Rename autosomal filenames to have meaningful names like their actual names or Father, Mother etc. No numbers just alphabets.
            2. Copy all the renamed files to a folder.
            3. Browse and select the that folder.
            4. Pedigree created. Enjoy!
            Note: To get best results, make sure you have the kit along with the parents’ kits as well. If you don’t have any parents and you got a blank pedigree or you got some individuals omitted, try dump all option.

            Screenshots:
            Tool in action

            Generated Output


            Download Autosomal Pedigree Creator.zip (792 KB)

            Documentation: Autosomal Pedigree Creator.pdf (1.04 MB) (Online Version)

            Source Code at GitHub.

            License: MIT License.

            Sub Projects: 
            FAQ:
            Tool hangs at 90%: It means the pedigree is either too large or unable to handle. In this case, just copy the atree.txt result, close the application and use the sub-project Autosomal Pedigree Customization.

            Change Log
            Version 1.6
            • Hung at 90% bug fixed.
            Version 1.5
            • Supports Ancestry files.
            Version 1.4
            • Allows alphanumeric names for kits.
            Version 1.3
            • Minor bug-fix to provide more accurate pedigree.
            Version 1.2
            • Dump-all option for remotely/unrelated autosomal files.
            Version 1.1
            • Minor bug-fix.
            Version 1.0
            • Initial release.

            Related Blogs

            Wednesday, November 19, 2014

            Ancient Ancestry

            Ancient Ancestry is a tool to compare an autosomal DNA with already triangulated ancient DNA segments. The tool will also provide a hierarchical view of how each segment flows through ancients. and allows you to export into an excel friendly format for further analysis. The tool supports FTDNA, 23andMe and Ancestry with build 37 autosomal files.

            Prerequisites:
            Usage: Open an autosomal file and the tool will automatically plot the matching segments.

            Screenshots:




            Download Ancient Ancestry.exe (7.66 MB).

            Source Code at GitHub.

            License: MIT License.

            Change Log
            Version 1.1
            • 29 Additional Ancient DNA added
            • Incorrect percentage value - bug fixed.
            Version 1.0
            • Initial release.

            Ancient Hungarian Neolithic genome - NE1

            The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. The authors had analysed a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (~22 × ) and seven to ~1 × coverage, to investigate the impact of these on Europe’s genetic landscape. I converted the raw data of NE1 from Polgár-Ferenci-hát site in Hungary into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry and uploaded to GEDmatch as kit# F999937.

            Download: 
            Reference:
            Cristina Gamba, Eppie R. Jones, Matthew D. Teasdale, Russell L. McLaughlin, Gloria Gonzalez-Fortes, Valeria Mattiangeli, László Domboróczki, Ivett Kővári, Ildikó Pap, Alexandra Anders, Alasdair Whittle, János Dani, Pál Raczky, Thomas F. G. Higham, Michael Hofreiter, Daniel G. Bradley & Ron Pinhasi "Genome flux and stasis in a five millennium transect of European prehistory" doi:10.1038/ncomms6257.

            Data Used

            Saturday, November 15, 2014

            Neanderthal Vi33.26 DNA

            Authors had provided Neanderthal genomes with their publications. I converted the raw data of Vi33.26 sample into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found this ancient DNA has less SNPs that are common with them. Hence, I did not upload this to GEDMatch. However, complete SNPs are available for download.

            Download: 
            Reference:
            Green, Richard E., Johannes Krause, Adrian W. Briggs, Tomislav Maricic, Udo Stenzel, Martin Kircher, Nick Patterson et al. "A draft sequence of the Neandertal genome." science 328, no. 5979 (2010): 710-722.

            Data Used

            Neanderthal Vi33.25 DNA

            Authors had provided Neanderthal genomes with their publications. I converted the raw data of Vi33.25 sample into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found this ancient DNA has less SNPs that are common with them. Hence, I did not upload this to GEDMatch. However, complete SNPs are available for download.

            Download: 
            Reference:
            Green, Richard E., Johannes Krause, Adrian W. Briggs, Tomislav Maricic, Udo Stenzel, Martin Kircher, Nick Patterson et al. "A draft sequence of the Neandertal genome." science 328, no. 5979 (2010): 710-722.

            Data Used

            Neanderthal Vi33.16 DNA

            Authors had provided Neanderthal genomes with their publications. I converted the raw data of Vi33.16 sample into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found this ancient DNA has less SNPs that are common with them. Hence, I did not upload this to GEDMatch. However, complete SNPs and filtered SNPs are available for download.

            Download: 
            Reference:
            Green, Richard E., Johannes Krause, Adrian W. Briggs, Tomislav Maricic, Udo Stenzel, Martin Kircher, Nick Patterson et al. "A draft sequence of the Neandertal genome." science 328, no. 5979 (2010): 710-722.

            Data Used

            Friday, November 14, 2014

            Neanderthal Sid1253 DNA

            Authors had provided Neanderthal genomes with their publications. I converted the raw data of Sid1253 sample into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found this ancient DNA has less SNPs that are common with them. Hence, I did not upload this to GEDMatch. However, complete SNPs are available for download.

            Download: 
            Reference:
            Green, Richard E., Johannes Krause, Adrian W. Briggs, Tomislav Maricic, Udo Stenzel, Martin Kircher, Nick Patterson et al. "A draft sequence of the Neandertal genome." science 328, no. 5979 (2010): 710-722.

            Data Used

            Neanderthal Feld1 DNA

            Authors had provided Neanderthal genomes with their publications. I converted the raw data of Feld1 sample into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found this ancient DNA has less SNPs that are common with them. Hence, I did not upload this to GEDMatch. However, complete SNPs are available for download.

            Download: 
            Reference:
            Green, Richard E., Johannes Krause, Adrian W. Briggs, Tomislav Maricic, Udo Stenzel, Martin Kircher, Nick Patterson et al. "A draft sequence of the Neandertal genome." science 328, no. 5979 (2010): 710-722.

            Data Used