Applying the Thorne-Kishino-Felsenstein model to sequence evolution on a star-shaped tree

AbstractStochastic models that allow site substitutions, insertions, and deletions provide a useful framework for a statistical approach to DNA sequence evolution. Such a model, and recursions to calculate the probability of evolving two sequences, have been known for almost a decade. In this paper we show how the pairwise recursions can be generalised to a three-sequence tree, and more generally to an r-sequence star-shaped tree