Welcome to the AvP wiki!

• Setting up
  • Create environment with conda
  • Download and format the database
  • Config files
• Usage
  • Prepare input files
  • AvP prepare - Extract the candidates, prepare the groups, and perform MSA
  • AvP detect - Perform tree inference and detect HGT candidates
  • Downstream analyses
    • AvP classify - Classify genes in specific taxonomic categories
    • AvP evaluate - Evaluate alternative topology
    • hgt local score - Calculate a score to identify possible contaminants
• Tutorial