This is a modified version of TransPhylo, a software package that can reconstruct infectious disease transmission chains using genomic data. This version allows for the estimation of the Generation time parameter if the sampling proportion (π) is known. It is now many commits behind the main TransPhylo package and should be used with care.
For a description of TransPhylo, see the following article:
Didelot, Fraser, Gardy and Colijn (2017) Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks http://dx.doi.org/10.1093/molbev/msw275
You can install TransPhylo mod in R using the following command:
devtools::install_github("gtonkinhill/TransPhylo_mod")
The TransPhylo tutorial can be downloaded here. This tutorial is also available within the R package as a vignette. The TransPhylo reference manual can be downloaded here.