Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag
(A) The null model, in which an amino acid evolves independently down the tree until it reaches a leaf. (B) The alternate model, in which an amino acid evolves independently down the tree until is reaches an individual, where it is influenced by selection pressure from the predictor. The variable Hi for the ith individual represents the variable Yi had there been no influence from Xi. Only the Yi and Xi are observed. Conditional probability distributions are not shown.