User:R. Eric Collins/MBL/Bayes

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Paul Lewis

Bayesian Phylogenetics

  • probabilities are applied to intervals, not points
    • curve is probability density, not probability
  • gamma distribution
    • Gamma(1,1) = Exponential(1)
    • Gamma(1,2) = Exponential(1/2) in some cases
    • sometimes papers use different definition of gamma, where b = 1/b
  • dirichlet process
    • use simplified (e.g. clustered at 97% similarity) tree as dirichlet prior for treespace?

MrBayes lab

  • mrbayes only recognizes bifurcating tree
  • "not converged diagnostics"

  • database of alignment "types" e.g. those that work well, don't work well, easy, hard
  • what makes a dataset harder to converge than another? more tree islands...