PPanGGOLiN Version 1 Documentation

• Introduction
• Installation instructions
• Basic usage and practical information
• step by step pangenome analysis
  • Annotation
  • Cluster
  • Graph
  • Partition
• Regions of Genome Plasticity
  • RGP
  • Spots of insertion
• Conserved modules
• Align
• Genomic context
• Output
  • Draw
    • Ushaped plot
    • Tile plot
    • Spot plots
  • Rarefaction
  • Write
    • organisms statistics
    • GEXF files
    • JSON
    • gene presence absence
    • matrix
    • mean persistent duplication
    • partitions
    • projection
    • gene families
    • plastic regions
    • spots
    • summarize spots
    • borders
    • Modules
    • Spot modules
  • Fasta
    • Genes
    • Protein families
    • Genes families
    • Regions
  • MSA
    • partitions
    • source
    • phylo
  • Info
  • Metrics