Computing diversity statistics

• The stats.ComputeStats class
  • Options
  • List of statistics
  • Processing data
• Computing statistics
  • Single alignment
  • Multiple alignments
  • Using individuals sites
  • Site frequency spectrum
  • Stand-alone allelic frequencies
• Structure and group labels
  • Principle
  • Group labels
  • Group labels in Fasta files
  • Creating a structure from an alignment
  • Passing labels directly
  • Simple structure
  • Fully flexible dictionary
  • Using the structure
• Missing data
  • Supporting missing data
• Linkage disequilibrium statistics
  • From ComputeStats
  • Pairwise linkage disequilibrium
  • EHH statistics
• Using VCF files
  • Short description of the format
  • Reading VCF files
  • Using default parser VCF
  • Using the fallback parser VcfParser