Insertions, deletions, and exchangeable couplings: a Dirichlet process over TKF92 domains and sites (opens in new tab)

To introduce local heterogeneity, evolutionary models are often equipped with site-class mixtures, preserving this symmetry in the sense of de Finetti: conditional on the latent class, residues are still exchangeable. In a four-step theoretical ladder, we show how long-range structure such as couplings between distant sites can also be introduced exchangeably by using a Dirichlet process to partition sites into co-evolving classes. Our first step is a thorough analysis of TKF92 to establish s...