BEAST2

BEAST 2 is a cross‑platform application for Bayesian phylogenetic analysis of molecular sequence data. It infers rooted, time‑scaled trees using either strict or relaxed molecular clock models and employs Markov chain Monte Carlo sampling to average over tree space, weighting each tree by its posterior probability. The software can be used both to reconstruct phylogenies and to test evolutionary hypotheses without fixing a single topology.

The program includes a graphical user interface that guides users through setting up standard analyses, and it ships with a suite of tools for post‑processing and visualising results. Its modular architecture, introduced in the rewrite from BEAST 1.x, allows extensions through a package system, enabling a wide variety of model‑based analyses to be added without altering the core.

BEAST 2 is aimed at researchers and analysts who need robust Bayesian methods for evolutionary studies, particularly those working with DNA, RNA, or protein sequences. It runs on macOS, Windows, and Linux, and its source code is openly available on GitHub, supporting community‑driven development and customization.