BEAST2

What problem does it solve?

This Skill automates complex Bayesian phylogenetic inference using BEAST2, enabling researchers to reconstruct evolutionary histories, estimate divergence times, and test evolutionary hypotheses from molecular data.

Core Features & Use Cases

• XML Configuration: Guides users in creating and editing BEAST2 XML configuration files for various models (substitution, clock, tree priors).
• MCMC Execution & Monitoring: Provides commands to run BEAST2 analyses, resume interrupted runs, and monitor convergence using diagnostics like ESS and trace plots.
• Model Selection & Post-processing: Facilitates model comparison via Nested Sampling and aids in summarizing results using TreeAnnotator and LogCombiner.
• Use Case: A molecular biologist needs to infer the evolutionary relationships and divergence times of a viral population. They can use this Skill to configure a BEAST2 XML file, run the MCMC analysis, diagnose convergence, and generate a time-calibrated phylogenetic tree.

Quick Start

Use the BEAST2 skill to run a phylogenetic analysis with the provided 'my_data.xml' configuration file.