Moore Notes 7 14 10

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PHYLOTU group call: Pollard lab, James, Steve

  • Name: PhylOTU? PhyloTU? PHYLOTU?
  • Tom will send submit version before sending in
  • Richness underestimation issue
    • PID vs. PD distance matrices (508 full length 16S sequences)
      • Strong correlation
      • PID is bounded by 1, and most are around 0.2
      • PD is not bounded, different skew
      • Normalized PD distance matrix doesn't improve richness ratio - not a linear difference
      • What is going on in the range around the threshold? Try stratifying
    • PID vs. PD trees (fastree or NJ)
      • What matters is the comparison of branch lengths around the threshold, not rest of tree
    • Look at hierarchical clustering trees and ordered distance matrices