|Time: Apr 21, 2017 (11:00 AM)|
|Location: Parker Hall 324|
Speaker: Yujin Chung
Title: Joint distribution of tree shape and tree distance for recombination detection
Abstract: Ancestral recombination events can cause the underlying genealogy of a site to vary along the genome. To simultaneously detect recombination breakpoints in very long sequence alignments and estimate the phylogenetic tree of each block between breakpoints, I consider a Bayesian model using distance between trees in the prior distribution to favor similar trees at neighboring loci. The main hurdle in using such models is the need to calculate the normalizing function of a prior distribution on trees. I will explain how to compute the normalizing function exactly, for a distribution based on the Robinson-Foulds (RF) distance. At the core is the calculation of the joint distribution of the shape of a random tree and its RF distance to a fixed tree. I will also introduce fast approximations to the normalizing function.