Moore Notes 2 25 09

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PI Conference Call

  • Report approved
    • budget item breakdown needs to be modified possibly
  • postdoc candidate (Morgan Langille) visiting Eisen lab Thursday
  • Robin and Erick meeting
    • their pipeline is similar to AMPHORA
    • phylogenetic part is possibly better than just using PHYML
    • focus: individual sequence reads
    • application: classifying genes/gene families (gene function)
    • open problem: how to paste together into one tree?
  • Steve is giving a talk in MI with one method for tree building
    • building a supermatrix and building NJ tree (faster than ML)
  • Plan for Brenner meeting
    • JE idea: iterative approach (place individual reads robustly, then resolve polytomies with a different method)
    • different approach: build big joint tree (ML, Bayes, etc)
    • talk to them about computational parts, parallelization/pipeline if we knew how to do it theoretically
      • e.g. 100 gene families with 10,000 sequences each
  • How/when would we move towards DNA (versus amino acid) based analyses?
    • could be helpful for
      • polytomies that are (nearly) identical at the amino acid level
      • population genetics
    • first - need full length sequences (not trimmed) rather than HMMer output - alternative method?
      • distantly related species not used to build the HMMs will not be picked up
    • then - could do codon models for tree (after back translating)
    • What data sets do we really need? Might be trying to do too much/too hard of a problem, e.g.
      • phyloCom needs tree (doesn't have to be perfect?), diversity measures might be OK too
      • might need different pipeline for making alignments for rates of evolution - need good alignments
    • Need simulations
  • Novelty/potential DeRisi collaboration
    • evolve new trees and evolve new sequences on these trees
    • Olivier Lichtarge
    • Tim Cooper
    • There's a big DARPA project in this area
  • Need to reassess future directions