PhyloSuite

PhyloSuite v2 integrates molecular dating tools, phylogenetic analysis functions, and data handling capabilities into a unified platform for phylogenetic workflows and molecular dating analysis.

Key Features:

• MDGUI: Provides a graphical interface for molecular dating analysis using MCMCtree and r8s with visual calibration point configuration.
• TimeTreeAnno: Enables visualization and annotation of timetrees.
• MCMCTracer: Performs on-demand MCMC convergence assessment and plotting.
• Automated model selection: Implements automated model selection and implementation for downstream analyses.
• Gene duplicate resolution: Resolves gene duplicates during the sequence extraction step.
• Accelerated data handling: Significantly accelerates format conversion and sequence concatenation.
• IQ-TREE integration: Incorporates the latest IQ-TREE models and functions with deeper integration.
• Workflow control: Supports one-click pause/resume functionality and multithreading acceleration.
• Multiple alignment format support: Accepts multiple alignment formats as input.

Scientific Applications:

• Molecular dating analysis: Performs Bayesian and penalized likelihood molecular dating using MCMCtree and r8s with fossil calibration.
• Timetree visualization: Generates annotated timetrees for temporal phylogenetic interpretation.
• Phylogenetic workflow integration: Streamlines complete phylogenetic analyses from sequence extraction through tree inference and dating.
• Convergence diagnostics: Assesses MCMC convergence for Bayesian phylogenetic and dating analyses.

Methodology:

PhyloSuite v2 integrates MCMCtree and r8s as plugins for molecular dating, uses visual calibration point configuration for fossil calibration setup, and implements automated model selection for downstream analyses.