User:R. Eric Collins/MBL/Bayes

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...