STraTUS (Software for Transmission Tree Uniform Sampling)

This utility takes as input a phylogenetic tree and, interpreting it as a pathogen phylogeny, uses it to sample uniformly from the set of compatible transmission trees. The procedure is described here.

It is primarily intended for those interested in exploring the structure of transmission tree space, or in developing algorithms to do this.

The code is provided as an R package, with is also available through CRAN. Documentation is here.