Moore Notes 8 27 14

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Group Call

  • Participants: Katie, Jonathan, Tom, Stacia, Josh, Dongying
  • Illumina meeting Thursday
  • Dongying: How to automatically update PhyEco markers slides
    • Universal and even within a taxonomic group
    • How to pick a bit score cutoff for determining new members for each marker family?
      • Need an automated method to find drop in bit score distribution
      • Then optimize universality*evenness*single-copy-score (u*e*s)
        • Katie/Tom: Why not optimize this directly?
    • Sequences that don't get added by these criteria may belong (short branch in gene tree)
      • Automated procedure for building alignment and tree to check for membership
      • Use HMM consensus (hmmemit) to root tree, compute root to tip distance
      • Automated cutoff on root-tip depth to identify outliers (in terms of standard deviations from the mean for the family)
        • Katie: Use false positives and false negatives (or u*e*s) to pick a cutoff
    • Compared u and e of new vs. old families
  • What is a good statistic for measuring the "size" of the tree for a gene family?
    • root-tip distance
    • number of leaves
    • root-tip/leaves
    • sum of branches (normalized?)
    • density of tree calculation that Dongying developed
  • Upcoming calls:
    • Sept 3: Shotmap
    • Sept 10: Sarah?
    • Sept 17: No call