Moore Notes 3 9 10

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Group Call

  • Steve: Did we track down the GOS PCR 16S data (Shaw et al)?
  • Steve: Is ZORRO available for masking Guillaume's alignments?
  • Every one should check that they are correctly signed up for the iSEEM Google Group
  • Dongying research update: http://bobcat.genomecenter.ucdavis.edu/dwu/DW0309.pdf
    • identifying marker genes for specific phyla
    • can combine (bottom up) to expand AMPHORA set
    • question: how to set a threshold for hits to profile HMM in a particular clade (below each node in the tree) - time consuming too
    • Martin: there is no totally reliable way to do automated identification of subfamilies
    • Tom: there are automated methods (e.g. PSYPHY) to determine cuts
    • Also working to develop a score for phylogenetic informativeness of a marker (does it produce monophyletic groups?)
      • this is essentially comparing the gene tree to the genome tree (e.g. AMPHORA)
      • other ideas:
        • entropy,
        • in exponent divide by maximum possible distance = sqrt(n*(n-1)) rather than n,
        • parsimony (e.g. number of LGT events needed to explain tree),
        • scale by number of taxa in tree
  • JG: update on Kelly's visit to U of O