Reconstruction Plan Spring09

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2 major programs - enhancing and testing handalign, analysis of reconstruction accuracy

flowchart (why not!)

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enhancing and testing handalign

  • parameter sampling (in progress)
  • autocorrelation (determine best rates of sampling moves to maximize mixing/time ratio)
    • rerun balibase benchmarks
    • run benchmark analysis
  • figure out a way to partition sample runs and create consensus alignments
    • want to find a way to create representative alignments for each 'peak' in distribution
    • partition sample runs by log likelihood
    • group alignments within partitions using AMA
    • create consensuses from resultant groups using CASA
  • reconstruct something (DHPS, cathelicidans, ...?)

analysis of reconstruction accuracy

  • finish mathematical analysis
  • create simulated cherries, etc. Use multiple reconstruction(/simulation?) methods. Compare to mathematical results.
  • run Tree Fam data, compare with simulated and mathematical results.
    • build 'representative' benchmark set

-- Lars Barquist - 28 Jan 2009