EtthelWindels/tbdar_tanzania_2013-2019

Code for "Back-to-Africa introductions of Mycobacterium tuberculosis as the main cause of tuberculosis in Dar es Salaam, Tanzania" # Estimating transmission rates of different *Mtb* lineages in Tanzania using phylodynamics This repository contains the code associated with the phylodynamic analyses performed in Zwyer, Rutaihwa, Windels et al. (2023) Back-to-Africa introductions of *Mycobacterium tuberculosis* as the main cause of tuberculosis in Dar es Salaam, Tanzania. *PLOS Pathogens* 19, 4 (2023). doi.org These analyses aimed at estimating the transmission rate of different *Mycobacterium tuberculosis* lineages (introductions), by fitting a birth-death model to genomic sequencing data collected from TB patients in Dar es Salaam, Tanzania (2013-2019). The raw sequencing data used in this study are available under project accession number PRJEB49562. - The folder `analyses/` contains the XML files used for the birth-death analyses in BEAST2. - The folder `scripts/` contains R scripts used for pre-processing of the alignments and post-processing of the BEAST2 output.