VMCMC: a graphical and statistical analysis tool for Markov chain Monte Carlo traces

Area of Science:

• Computational Biology
• Bioinformatics
• Statistical Phylogenetics

Background:

• Markov chain Monte Carlo (MCMC) methods are crucial for Bayesian inference in phylogenetics.
• Challenges exist in MCMC convergence assessment and burn-in determination, particularly for large datasets.
• Current workflows often require multiple software packages for MCMC analysis and exploration.

Purpose of the Study:

• To develop a unified software solution for simplifying MCMC trace post-processing.
• To address practical difficulties in MCMC convergence assessment and burn-in estimation.
• To provide both graphical and command-line interfaces for MCMC analysis.

Main Methods:

• Development of a novel software tool named VMCMC.
• Implementation of automatic burn-in estimation algorithms.
• Integration of a graphical user interface (GUI) and a command-line interface.

Main Results:

• VMCMC simplifies the post-processing of MCMC traces.
• The software offers automatic burn-in estimation capabilities.
• VMCMC supports both interactive GUI-based exploration and automated command-line processing.

Conclusions:

• VMCMC is a free and open-source software available under the New BSD License.
• The software facilitates MCMC analysis in phylogenetics.
• VMCMC is accessible for download with source code and a tutorial manual.