MrBayes National Bioinformatics Infrastructure Sweden

MrBayes is a program for Bayesian phylogenetic analysis designed to perform inference and model choice across a wide range of phylogenetic and evolutionary models. It employs Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters, enabling researchers to explore complex evolutionary relationships with high precision.

Key Features:

• Versatile Data Handling: Supports nucleotide, amino acid, restriction site, and morphological data, allowing for mixed analyses combining different data types.
• Comprehensive Evolutionary Models: Includes 4x4, doublet, codon models for nucleotides, and various rate matrices for amino acids, enabling detailed exploration of sequence evolution.
• Model Flexibility: Offers the ability to link or unlink parameters across partitions, facilitating complex evolutionary scenarios.
• Positive Selection Estimation: Implements a fully hierarchical Bayesian framework for identifying positively selected sites in proteins.
• Integration with BEST Algorithms: Provides full support for the multi-species coalescent model, enhancing phylogenomic analyses.
• Relaxed-Clock Models: Estimates time-calibrated trees using both strict and relaxed-clock approaches, accommodating diverse evolutionary timescales.
• Topology Constraints: Supports complex constraints on tree topologies, including positive, negative, and backbone restrictions.
• Convergence Monitoring: Includes tools for assessing chain convergence during and after analysis, ensuring robust results.
• Posterior Summaries: Generates rich summaries of posterior samples, producing majority rule consensus trees in FigTree format.
• Stepping-Stone Methodology: Implements the stepping-stone method for accurate Bayesian model choice using Bayes factors.