BEAST 2 package for inferring transmission trees

Bayesian Reconstruction and Evolutionary Analysis of Transmission Histories (BREATH) is a BEAST 2 package for inferring transmission trees.

Using BREATH

See the tutorial on how to use BREATH.

Installing by hand

Install BEAST 2.

Download BREATH.v0.0.1.zip. Then, create a BREATH subdirectory:

for Windows in Users\<YourName>\BEAST\2.7\BREATH
for Mac in /Users/<YourName>\/Library/Application Support/BEAST/2.7/BREATH
for Linux /home/<YourName>/.beast/2.7/BREATH

Here <YourName> is the username you use. Unzip the file BREATH.v0.0.1.zip in the newly created directory.

Build from code

An alternative way to install is to build from the source code. First, get code for beast2, BeastFX and this repository. Then run

ant install

to install the package.

Reference

Caroline Colijn, Matthew David Hall, Remco Bouckaert. Taking a BREATH (Bayesian Reconstruction and Evolutionary Analysis of Transmission Histories) to simultaneously infer phylogenetic and transmission trees for partially sampled outbreaks. BioRxiv, 2024 doi:10.1101/2024.07.11.603095