Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • #16
    New software Tool From Chris Morley:

    "Dear list,

    I have put together a process for automating the generation of a Geno
    2.0-based Y-SNP phylogeny.

    See my report "An experimental computer-generated Y-chromosomal
    phylogeny, leveraging public Geno 2.0 results and the current ISOGG
    tree" at [ http://ytree.morleydna.com/Experimen...oPhylogeny.pdf ].
    The current ISOGG tree (v. 8.61) was used as the starting point for this
    version of the experimental tree.

    Additionally, [ http://ytree.morleydna.com ] features a Y-SNP subclade
    predictor. Given a set of Y-SNP calls, it will (i) predict the subclade,
    (ii) show the phylogenetic placement (when available) of reported SNPs,
    and (iii) identify unplaced positive SNPs. It can use either the ISOGG
    tree or my experimental tree as the basis for classification. It
    accommodates FTDNA-transferred Geno 2.0 data, and also the Full Genomes
    demo data.

    It's not perfect, but it's a start. It should save some time when
    analysing kits with more than a handful of tested SNPs.

    I invite your feedback.

    Chris Morley"
    FullGenomes Kit 045DV YFull Terminal SNP Y2846 FTDNA Kit 52277 M35>V12>CTS693>CTS3346>Y2877>CTS6667>CTS8411>Y2846 MTdna U4b1a3a

    Comment


    • #17
      More information on developments on his new phylogenetic tool

      "Keep in mind that only a finite number of Y-SNPs could be selected for inclusion on the chip, and there are tradeoffs between even coverage and phylogenetic resolution. After a certain point, trying to fit an additional terminal Y-SNP on the chip comes at the expense of leaving out another one -- either a basal Y-SNP, or a phylogenetically redundant Y-SNP from another branch.

      (My next update will feature a separate proof-of-concept phylogeny built using Y-SNP calls from the two Full Genomes demo datasets.) But for those interested in experimenting, future releases of my phylogeny will be accompanied by a CSV summary file with the columns "name, parent, SNPcount, cumuSNPcount, kitCount, cumuKitCount". Expect the next version of my tree later in the week."

      Chris Morley
      FullGenomes Kit 045DV YFull Terminal SNP Y2846 FTDNA Kit 52277 M35>V12>CTS693>CTS3346>Y2877>CTS6667>CTS8411>Y2846 MTdna U4b1a3a

      Comment


      • #18
        This is the link to the latest tree from Chris Morely dated 8-Aug-2013

        Y-DNA SNP-based subclade predictor. Determine where your Genographic 2.0 or Full-Y result fits on the most extensive human Y phylogeny. Uncover novel SNPs.


        It appears that he has 75 E1b1b1 tests in this new tree and a total of 1850 Geno 2.0 tests. That is a considerable number which includes tests from other groups than just E-M35.

        He also at the end of the file has two FullGenomes sequenced demo samples using this program.

        This is a link for Geno 2.0 raw data in zip file download format with over 100 samples.

        Last edited by KerryOdair; 08-12-2013, 08:41 AM.
        FullGenomes Kit 045DV YFull Terminal SNP Y2846 FTDNA Kit 52277 M35>V12>CTS693>CTS3346>Y2877>CTS6667>CTS8411>Y2846 MTdna U4b1a3a

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Techniques and Challenges in Conservation Genomics
          by seqadmin



          The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

          Avian Conservation
          Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
          03-08-2024, 10:41 AM
        • seqadmin
          The Impact of AI in Genomic Medicine
          by seqadmin



          Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
          02-26-2024, 02:07 PM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 03-14-2024, 06:13 AM
        0 responses
        32 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-08-2024, 08:03 AM
        0 responses
        71 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-07-2024, 08:13 AM
        0 responses
        80 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-06-2024, 09:51 AM
        0 responses
        68 views
        0 likes
        Last Post seqadmin  
        Working...
        X