Configure BEAST2 XML files for Bayesian phylogenetic MCMC analyses.
npx skills add https://github.com/Neclow/claude-bioinformatics-skills --skill beast2
Please help me install this Agent Skill. Skill: BEAST2 Source: https://github.com/Neclow/claude-bioinformatics-skills/tree/main/skills/beast2 Command: npx skills add https://github.com/Neclow/claude-bioinformatics-skills --skill beast2
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.
Use the BEAST2 skill to run a phylogenetic analysis with the provided 'my_data.xml' configuration file.
High-intent search queries and answers about installing and using this skill.
To configure a BEAST2 XML file for Bayesian phylogenetic inference, you define substitution models, clock models, and tree priors. This setup allows the MCMC analysis to properly sample evolutionary histories and estimate divergence times from molecular data.
Your BEAST2 MCMC analysis fails to converge when effective sample size (ESS) values are low. You diagnose convergence by inspecting trace plots and ESS diagnostics, and can use advanced methods like CoupledMCMC or troubleshoot common configuration errors to improve sampling.
The best way to perform model selection in Bayesian phylogenetics is using Nested Sampling. This approach evaluates competing evolutionary hypotheses by calculating marginal likelihoods, allowing you to compare substitution and clock models accurately.
To summarize and post-process MCMC trees after a BEAST2 run, use TreeAnnotator and LogCombiner. These tools merge log files and tree outputs, generating a maximum clade credibility time-calibrated phylogenetic tree for evolutionary analysis.
Yes, you can resume an interrupted Bayesian phylogenetic inference run in BEAST2. The software provides specific commands to checkpoint and resume MCMC analyses, allowing you to continue evolutionary sampling without losing previous computational progress.
You need to apply calibration strategies in phylodynamics when estimating divergence times from molecular sequences. Calibration involves assigning known temporal constraints to tree priors, which is essential for generating accurate time-calibrated phylogenetic trees.
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