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Thread: clarifYDNA.com : clarifY your "next-generation" Y-DNA results

  1. #1

    Lightbulb clarifYDNA.com : clarifY your "next-generation" Y-DNA results

    I am excited to announce the launch of www.clarifYDNA.com, a service for generating comprehensive Y-trees from "next-generation" Y-DNA sequencing results.

    This service's first offering: personalised Y-tree reports produced from BigY VCF/BED data. Here is a sample. The website is now accepting orders.

    Subscribers will periodically receive personalised reports showing their position on the Y-tree relative to others in their Y-chromosomal neighbourhood. Reports build on recent versions of the ISOGG haplotree, and are able to indicate which aspects of the phylogenetic structure are robust and which are more tenuous. Sequential reports will reflect phylogenetic progress resulting from growth in our service's membership. Subscribers will have opt-in control over how much of their genetic and ancestral information is shared with their genetic neighbours.

    I originally designed the underlying phylogenetic (tree-generating) software for the purpose of handling Geno 2.0 data. The first experimental phylogeny was released in July 2013, with subsequent releases last August, September, November and February. These reports have been lauded by the genetic genealogy community and have also received some corporate and academic praise. Since November I have been adapting my software for "next-generation sequencing" results, such as Full Genome Corp.'s comprehensive Y test and FTDNA's BigY product. I have also spent time streamlining the non-phylogenetic aspects -- the parts of the process before and after the generation of the Y-tree -- a workflow for receiving and queuing data and generating and distributing personalised phylogenetic reports.

    This service is not affiliated with any Y-DNA testing company (despite having last year initiated talks to explore that option).

    I will gladly answer questions about this service, in this thread.

    Chris Morley
    www.clarifYDNA.com

  2. The Following 9 Users Say Thank You to cmorley For This Useful Post:

     AJL (06-13-2014), Clinton P (07-07-2014), DMXX (08-25-2014), Humanist (07-05-2014), J1 DYS388=13 (07-06-2014), parasar (06-13-2014), Salkin (09-25-2014), Stellaritic (06-14-2014), vettor (06-13-2014)

  3. #2
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    This post mentions the FGC comprehensive Y test, which I've had, but the clarifYDNA website doesn't -- it seems only to solicit Big Y VCF/BED files. I didn't take a Big Y test.

    I also wonder whether the very reasonably priced subscription is for a specific period, calendar year, number of updates, or... what? I couldn't tell, from the website.

    Anyway, somebody needed to ask a question, to bump the thread. (It's kind of a slow and lazy summer period, apparently. Not meaning to be northern-hemispherist, or anything.) Chris is one of the good guys, people -- let's have a little chatter.

  4. #3
    Thanks razyn.

    To answer your questions:

    (1) My focus at the moment is processing Big Y VCF/BED data. I could launch a similar service for FGC data, if there is sufficient interest. My software has already been used to process FGC variantCompare/haplogroupCompare/gtype files -- I prepared a pilot phylogeny for FGC in November. Since then, I have made further enhancements to my software. Some are BigY-specific, and some are more general. I would have to do some testing to see how these changes behave when applied to an FGC dataset. I would also have to adjust to my "backoffice" scripts (handling non-phylogenetic logistical aspects) to additionally accommodate FGC datasets.

    (2) Per https://www.clarifydna.com/productdi...ion-us-dollars (click on the "read more" button): "Subscriptions will last until at least the end of 2014." The frequency of updates will be driven by (a) my development workload, and (b) the popularity of this product.

    Chris

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     razyn (07-05-2014)

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    How does what you are selling differ from the "Morley" tab on FTDNA's BigY results matching page?

  7. #5
    Quote Originally Posted by J1 DYS388=13 View Post
    How does what you are selling differ from the "Morley" tab on FTDNA's BigY results matching page?
    The "Morley" tab you speak of gets inserted on your BigY results page by a third-party Chrome extension. I have no part in that extension, nor did I ever. I was not notified ahead of time that the extension would, for the purpose of BigY analysis, try to harness ytree.MorleyDNA.com's functionality.

    The tool at ytree.MorleyDNA.com was built for Geno 2.0 data. The online predictor and its underlying dataset haven't been modified since July or August of 2013 -- before BigY's announcement. The output of the ytree.MorleyDNA.com tool is essentially static: the classifications and lists of unplaced SNPs will not change, even as new data becomes available. I don't have any enhancements scheduled for ytree.MorleyDNA.com, but the tool will remain online, primarily as a service to those who ordered Geno 2.0. www.clarifYDNA.com is my current focus.

    BigY data is more complicated to work with. And there are known basal discrepancies between the phylogeny implied by Geno 2.0 data (or, at least, FTDNA's Geno 2.0 calls), and the one implied by "next-gen" data. Using a Geno-tuned predictor on next-gen data can produce some strange results.

    The phylogenetic algorithm underlying clarifYDNA's product is the result of several months' additional development, in order to address the added complexities of "next-gen" data. Moreover, the output (personalised reports) provided by clarifYDNA are dynamic. Our knowledge of a mutation's reliability changes as more test results becomes available. As does our knowledge of the scope or each mutation -- whether a kit's currently "novel" mutations (or at least the test subject's instances thereof -- let's not forget that mildly recurrent mutations can still be helpful) are truly localised to the test subject and his immediate patrilineal relatives; or that they are found in a whole branch of that surname; or most members of that surname; or to men sharing a MRCA around the time hereditary surnames were adopted; or to a distinctive STR cluster. As stated above,

    Subscribers will periodically receive personalised reports showing their position on the Y-tree relative to others in their Y-chromosomal neighbourhood. Reports build on recent versions of the ISOGG haplotree, and are able to indicate which aspects of the phylogenetic structure are robust and which are more tenuous. Sequential reports will reflect phylogenetic progress resulting from growth in our service's membership.
    In short: the "Morley" tab just uses a component from last year's model, and it uses that component in a way that was never intended. www.clarifYDNA.com is this year's model. A lot has changed in the last year, and a lot will continue to change.

  8. The Following 3 Users Say Thank You to cmorley For This Useful Post:

     lgmayka (07-09-2014), palamede (07-09-2014), vettor (07-09-2014)

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    Australia Italy Veneto Friuli Italy Trentino Alto Adige Italy Sweden Finns
    Quote Originally Posted by cmorley View Post
    The "Morley" tab you speak of gets inserted on your BigY results page by a third-party Chrome extension. I have no part in that extension, nor did I ever. I was not notified ahead of time that the extension would, for the purpose of BigY analysis, try to harness ytree.MorleyDNA.com's functionality.

    The tool at ytree.MorleyDNA.com was built for Geno 2.0 data. The online predictor and its underlying dataset haven't been modified since July or August of 2013 -- before BigY's announcement. The output of the ytree.MorleyDNA.com tool is essentially static: the classifications and lists of unplaced SNPs will not change, even as new data becomes available. I don't have any enhancements scheduled for ytree.MorleyDNA.com, but the tool will remain online, primarily as a service to those who ordered Geno 2.0. www.clarifYDNA.com is my current focus.

    BigY data is more complicated to work with. And there are known basal discrepancies between the phylogeny implied by Geno 2.0 data (or, at least, FTDNA's Geno 2.0 calls), and the one implied by "next-gen" data. Using a Geno-tuned predictor on next-gen data can produce some strange results.

    The phylogenetic algorithm underlying clarifYDNA's product is the result of several months' additional development, in order to address the added complexities of "next-gen" data. Moreover, the output (personalised reports) provided by clarifYDNA are dynamic. Our knowledge of a mutation's reliability changes as more test results becomes available. As does our knowledge of the scope or each mutation -- whether a kit's currently "novel" mutations (or at least the test subject's instances thereof -- let's not forget that mildly recurrent mutations can still be helpful) are truly localised to the test subject and his immediate patrilineal relatives; or that they are found in a whole branch of that surname; or most members of that surname; or to men sharing a MRCA around the time hereditary surnames were adopted; or to a distinctive STR cluster. As stated above,



    In short: the "Morley" tab just uses a component from last year's model, and it uses that component in a way that was never intended. www.clarifYDNA.com is this year's model. A lot has changed in the last year, and a lot will continue to change.
    thanks for explanation

    can you answer me then, as a T1 person with CTS8862 have you resolved this SNP , because if the answer is the same as predictor ytree.MorleyDNA then I fail to see why I need to invest in ClarifyDNA

    regards

    Father's Mothers Ydna ......R-S22778 ........Merlengo Veneto
    Father's Mtdna .....T2b35.......1735 Porcellengo Veneto Italy
    Wife's Ydna ..........R-DF99
    Sons Mtdna .....K1a4 ...........1710 Carnic Alps

    My Path = ( K-M9+, TL-P326+, T-M184+, L490+, M70+, PF5664+, L131+, L446+, CTS933+, CTS54+, CTS8862+, Z19945+, A339+ )

    The main negatives = ( M193-, P322-, P327-, Pages11- , L25- , CTS1848- )

  10. #7
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    clarifY DNA - a new Y-SNP analysis service from Chris Morley

    This is a very useful new service from Chris Morley. He is currently providing analysis of Big Y results but hopes to extend the service to cover other tests in due course:

    http://cruwys.blogspot.co.uk/2014/08...s-service.html

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    Yes, he announced his new service a few months ago, and said he's available for Q&A in the original post (see link below). Seems promising.

    http://www.anthrogenica.com/showthre...-Y-DNA-results

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    Thanks. I didn't realise there was another thread. I wonder if a moderator could merge this thread with the older one. Chris did send me the details of the new service back in June but I've only just had time to investigate it and write about it.

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    Quote Originally Posted by DebbieK View Post
    Thanks. I didn't realise there was another thread. I wonder if a moderator could merge this thread with the older one. Chris did send me the details of the new service back in June but I've only just had time to investigate it and write about it.
    Merged, as requested.

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