Supported beta-diversity Measures

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Qualitative measures requiring a rooted split system:

  • Bray-Curtis (aka: Sorensen, PhyloSor, Dice's index, pairwise Whittaker)
  • Canberra
  • Coefficient of similarity
  • Euclidean
  • Gower
  • Kulczynski (aka: Kulczynski-Cody, Sokal-Sneath)
  • Lennon compositional difference
  • Manhattan (aka: Hamming distance)
  • Soergel (aka: unweighted UniFrac, Jaccard)
  • Tamas coefficient (TC) (aka: simple matching coefficient)
  • Weighted correlation

Quantitative measures requiring a rooted split system (use -w flag):

  • Bray-Curtis (aka: normalized weighted UniFrac, percentage difference)
  • Canberra
  • Coefficient of similarity
  • Complete tree
  • Euclidean
  • Gower
  • Kulczynski
  • Lennon compositional difference
  • Manhattan (aka: weighted UniFrac)
  • Morisita-Horn
  • Soergel (aka: Ruzicka, Marczewski-Steinhaus, percentage remoteness)
  • Tamas coefficient
  • Weighted correlation
  • Yue-Clayton (aka: similarity ratio)

Root-invariant quantitative measures (use -w flag):

  • Complete tree
  • Euclidean
  • Gower
  • Manhattan (aka: weighted UniFrac)