phylobayesmpi

phylobayesmpi performs Bayesian phylogenetic reconstruction using finite and infinite mixture models to model across-site variation in substitution processes.

Key Features:

• Mixture models: Supports both finite and infinite mixture models to capture heterogeneity in substitution processes across sites.
• Dirichlet process mixtures: Implements Dirichlet process mixture models to represent variable equilibrium frequency profiles across sites.
• Sampling strategies: Uses partial Gibbs sampling updates for tree topology.
• Dirichlet process prior representation: Employs a truncated stick-breaking representation for the Dirichlet process prior.
• Parallelization (MPI): Leverages a message passing interface (MPI) for parallel computation and reports close to linear speed gains up to 64 cores.

Scientific Applications:

• Phylogenomics: Enables phylogenomic analyses that require explicit modeling of across-site substitution heterogeneity.
• Species relationships: Supports inference of evolutionary relationships among species.
• Lineage diversification: Assists in tracing lineage diversification using model-rich phylogenetic reconstructions.
• Molecular evolution: Facilitates studies of molecular evolution by accommodating complex substitution patterns across sites.

Methodology:

Bayesian inference using mixture models and Dirichlet process mixtures, partial Gibbs sampling for tree topology updates, a truncated stick-breaking representation for the Dirichlet process prior, and parallel execution via MPI with reported near-linear scaling to 64 cores.