Enumeration and Uniform Sampling of Transmission Trees for a Known Phylogeny R package STraTUS version 1.1.2 For a single, known pathogen phylogeny, provides functions for enumeration of the set of compatible epidemic transmission trees, and for uniform sampling from that set. Optional arguments allow for incomplete sampling with a known number of missing individuals, multiple sampling, and known infection time limits. Always assumed are a complete transmission bottleneck and no superinfection or reinfection. See Hall and Colijn (2019) <doi:10.1093/molbev/msz058> for methodology. Software Depends: R (>= 3.4) Imports: ape, phangorn, igraph, gmp, ggplot2, ggtree (>= 2.0.0), RcppAlgos, stats Matthew Hall <matthew.hall@bdi.ox.ac.uk> Comprehensive R Archive Network (CRAN) Matthew Hall [aut, cre], Caroline Colijn [ctb] GPL 2020-04-04 application/tgz https://CRAN.R-project.org/package=STraTUS doi:10.32614/CRAN.package.STraTUS