Moore Notes 2 4 09

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Group Call (KP and JG away)

  • Here are some examples of the alignment and trees for the DeLong SSU rRNA, built with a variety of methods.
  • At this point we're hashing out mechanics and squinting to see if the sequences are reasonable.
(NJ (FastTree), parsimony (PAUP), likelihood (GARLI), Bayesian (MrBayes)).

Srijak emailed nucleotide sequences out for Delong marker genes.

  • Nucleotide sequences are aligned, trimmed and masked.
  • There are redundant sequences in nucleotide and amino acid datasets.
  • Redundant sequences have different identifiers.
  • For now, Srijak will email a list of the redundancies.


  • Should we use peptide or nucleotide data to test building approaches with simulated data?
  • What genes should we initially run simulations on?
    • recA
    • RPOB
  • What methods should we use to compare trees?
    • Robinson-Foulds
    • Quartets
    • Nodal: [1]
  • Sam will try to get initial marker gene simulation dataset be early next week.
    • Wants to use a set of genes from one gene family that are reasonably diverse.
        • Could use:
          • Amphora sequences
          • Dataset from Martin
          • Get script from Dongying that will select sequences that maximize diversity from a dataset.
  • Jess B will concurrently be working on 16s rDNA simulations.

Another Skype call tomorrow at 1.