TiTUS

Sampling and Summarizing Transmission Trees with Multi-strain Infections. TiTUS is a code that takes as input a timed pathogen phylogeny with leaves labelled by the host along with epidemiological data such as entry-removal times for the hosts and a contact map. It counts and uniformly samples from the set of feasbile interval vertex labelings of the timed phylogeny that satisfy the direct transmission constraint while supporting a weak transmission bottleneck.