Manual

• Overview
  • Download
  • Citation
  • Disclaimer
  • Last Updates
• Getting Started
  • Operating Systems
  • Working with the repository
  • User interfaces
  • High Performance Environments
• Graphical User Interface
  • Launching the Graphical User Interface
  • Menu description
• Command Line Arguments
• Global Configuration
  • Logging properties
  • PhyML binary properties
  • Hybrid shared-distributed memory execution properties
• Common Use Cases
  • Converting Alignment Files
  • Basic Model Selection
  • Loading Checkpointing Files
• Theoretical Background
  • Models of nucleotide substitution
  • Sequential Likelihood Ratio Tests (sLRT)
  • Hierarchical Likelihood Ratio Tests (hLRT)
  • Dynamical Likelihood Ratio Tests (dLRT)
  • Information Criteria
  • Model Uncertainty
  • Model Averaging
  • Model Averaged Phylogeny
  • Parameter Importance