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Quick Intro & Lab: https://cme.h-its.org/exelixis/pubs/Krumlov2019_RAxML.pdf

Documentation:

• Installation
  • MPI version
  • Building from source
  • Building development branch
• Tutorial
  • Quick start
  • Advanced stuff
  • Parallelization
• Input data
  • Analysis type
  • Multiple sequence alignment
  • Evolutionary model
  • Starting tree
• Output files and settings
  • Prefix
  • Output files
  • Re-running the analysis
  • Log verbosity
• Tuning model optimization and tree search
  • Model and branch length optimization
  • Per-rate-category likelihood scalers
  • Tree search options
  • Bootstrapping
• Parallelization and performance
  • How many threads should I use?
  • Adaptive parallelization
  • Multithreading
  • MPI and hybrid MPI/pthreads
  • Coarse-grained parallelization
• Energy monitoring
• Advanced commands
  • Automatic model selection
  • Branch support metrics
  • Topological distance calculation
  • Consensus tree building
  • Ancestral state reconstruction
  • Disabling safety checks
  • Expert options
• Development of RAxML-NG