  The reconstruction of transmission trees for epidemics from genetic data has
been the subject of some recent interest. It has been demonstrated that the
transmission tree structure can be investigated by augmenting internal nodes of
a phylogenetic tree constructed using pathogen sequences from the epidemic with
information about the host that held the corresponding lineage. In this paper,
we note that this augmentation is equivalent to a correspondence between
transmission trees and partitions of the phylogenetic tree into connected
subtrees each containing one tip, and provide a framework for Markov Chain
Monte Carlo inference of phylogenies that are partitioned in this way, giving a
new method to co-estimate both trees. The procedure is integrated in the
existing phylogenetic inference package BEAST.
