Ability of pathogen genome sequences to characterise transmission between population groups

Cécile Tran-Kiem¹, Amanda C. Perofsky², Justin Lessler^3,4, Trevor Bedford^1,5.

¹ Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
^2
3 University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
⁴ Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
⁵ Howard Hughes Medical Institute, Seattle, WA, USA

Abstract

Repository organization

This repository is organized in sub-folders as follows:

• input/ contains input parameters values and data used to generate analyses. Further information is available on the folder-level README file.
• figures/ contains the figures (both from the main text and the supplementary information) associated with the manuscript.
• manuscript/ contains the manuscript.
• scripts/ contains the code used to analyse the data and reproduce the figures.
• remaster/ contains the code used to simulate the phylogenies depicted in Figure 1.
• remaster-sample-size/ contains the code used to perform the simulation study.