BEAST2 (http://www.beast2.org) is a free software package for Bayesian evolutionary analysis of molecular sequences using MCMC and strictly oriented toward inference using rooted, time-measured phylogenetic trees.

It estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST 2 uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each tree is weighted proportional to its posterior probability. BEAST 2 includes a graphical user-interface for setting up standard analyses and a suit of programs for analysing the results.

In this simple tutorial you will get acquainted with the basic workflow of BEAST2 and the software tools most commonly used to interpret the results of analyses. Bear in mind that this tutorial is designed only to help you get started using BEAST2. This tutorial does not discuss all the choices and concepts in detail, as they are discussed in further tutorials. Interspersed throughout the tutorial are topics for discussion. These discussion topics are optional, however if you work through them you will have a better understanding of the concepts discussed in this tutorial. Feel free to skip the discussion topics and come back to them later, while running the analysis file, or after finishing the whole tutorial.

[bioRxiv, 15 July 2024]

We introduce and apply Bayesian Reconstruction and Evolutionary Analysis of Transmission Histories (BREATH), a method to simultaneously construct phylogenetic trees and transmission trees using sequence data for a person-to-person outbreak. BREATH’s transmission process that accounts for a flexible natural history of infection (including a latent period if desired) and a separate process for sampling. It allows for unsampled individuals and for individuals to have diverse within-host infections. BREATH also accounts for the fact that an outbreak may still be ongoing at the time of analysis, using a recurrent events approach to account for right truncation. We perform a simulation study to verify our implementation, and apply BREATH to a previously-described 13-year outbreak of tuber-culosis. We find that using a transmission process to inform the phylogenetic reconstruction results in better resolution of the phylogeny (in topology, branch length and tree height) and a more precise estimate of the time of origin of the outbreak. Considerable uncertainty remains about transmission events in the outbreak, but our reconstructed transmission network resolves two major waves of transmission consistent with the previously-described epidemiology, estimates the numbers of unsampled individuals, and describes some highprobability transmission pairs.

An open source implementation of BREATH is available from:

https://github.com/rbo...

…as the BREATH package to BEAST 2.