Difference between revisions of "Supported beta-diversity Measures"

From Bioinformatics Software
Jump to: navigation, search
(New page: Qualitative measures (require a rooted split system): * Bray-Curtis (aka: normalized weighted UniFrac, Sorensen, Steinhaus, Odum, percentage difference, pairwise Whittaker) * Canberra * Ch...)
 
 
(One intermediate revision by one user not shown)
Line 1: Line 1:
Qualitative measures (require a rooted split system):
+
Qualitative measures requiring a rooted split system:
* Bray-Curtis (aka: normalized weighted UniFrac, Sorensen, Steinhaus, Odum, percentage difference, pairwise Whittaker)
+
* Bray-Curtis (aka: Sorensen, PhyloSor, Dice's index, pairwise Whittaker)
 
* Canberra
 
* Canberra
* Chi-squared
 
 
* Coefficient of similarity
 
* Coefficient of similarity
* Complete tree
+
* Euclidean
* Fst
+
 
* Gower
 
* Gower
* Hellinger
 
 
* Kulczynski (aka: Kulczynski-Cody, Sokal-Sneath)
 
* Kulczynski (aka: Kulczynski-Cody, Sokal-Sneath)
 
* Lennon compositional difference
 
* Lennon compositional difference
* Mean nearest neighbour distance (aka: comdistnn)
+
* Manhattan (aka: Hamming distance)
* Mean phylogenetic distance (aka: comdist)
+
* Soergel (aka: unweighted UniFrac, Jaccard)
* Morisita-Horn
+
* Pearson product-moment correlation coefficient
+
* Rao's Hp
+
* Soergel (aka: Jaccard, unweighted UniFrac, Ruzicka, Marczewski-Steinhaus, percentage remoteness)
+
* Species profile
+
 
* Tamas coefficient (TC) (aka: simple matching coefficient)
 
* Tamas coefficient (TC) (aka: simple matching coefficient)
* Whittaker index of association
+
* 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)
 
* Yue-Clayton (aka: similarity ratio)
  
Quantitative measures (require a rooted split system):
+
Root-invariant quantitative measures (use -w flag):
 
+
* Complete tree
Quantitative measures (can be computed over rooted or unrooted split systems):
+
* Manhattan
+
 
* Euclidean
 
* Euclidean
 +
* Gower
 +
* Manhattan (aka: weighted UniFrac)

Latest revision as of 21:33, 10 April 2012

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)