Statistics and plotting

• Diversity & divergence
• F-statistics
• Hardy-Weinberg equilibrium
• Linkage disequilibrium
• Site frequency spectra
• Pairwise distance and ordination
• Principal components analysis
• Admixture
• Selection
  • Integrated haplotype score (IHS)
  • Cross-population extended haplotype homozygosity (XPEHH)
  • Number of segregating sites by length (NSL)
  • Haplotype diversity, Garud’s H statistics
  • Population branching statistic (PBS)
  • Delta Tajima’s D
  • Utilities and plotting functions
• Mendelian inheritance
• Runs of homozygosity (ROH)
• Window utilities
• Preprocessing utilities
• Miscellanea