ExpressBetaDiversity

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Express Beta Diversity (EBD) is a software package for calculating taxon- or phylogenetic-based beta diversity measures. EBD is available as C++ source code under the GNU GPL v3. A precompiled binary is provided for Windows users and simple compilation instructions provided for OSX and Linux. Currently EBD supports the following beta-diversity measures:

  • Bray-Curtis (aka: normalized weighted UniFrac, Sorensen, Steinhaus, Odum, percentage difference, pairwise Whittaker)
  • Canberra
  • Chi-squared
  • Coefficient o similarity
  • Complete tree
  • Euclidean
  • Fst
  • Gower
  • Hellinger
  • Kulczynski (aka: Kulczynski-Cody, Sokal-Sneath)
  • Lennon compositional difference
  • Manhattan (aka: taxicab, city-block, unnormalized weighted UniFrac)
  • Mean nearest neighbour distance (aka: comdistnn)
  • Mean phylogenetic distance (aka: comdist)
  • 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)
  • Whittaker index of association
  • Yue-Clayton (aka: similarity ratio)

Documentation

Downloads

Citing EBD

If you use EBD in your research, please cite:

Parks, D.H. and Beiko, R.G. Phylogenetic resemblance methods provides robust and complementary insights into microbial communities. 2011. (submitted to Nature Methods, December, 2011).

Contact Information

EBD is in active development and we are interested in discussing all potential applications of this software. We encourage you to send us suggestions for new features. Suggestions, comments, and bug reports can be sent to Donovan Parks (parks [at] cs.dal.ca) or Robert Beiko (beiko [at] cs.dal.ca). If reporting a bug, please provide as much information as possible and a simplified version of the data set which causes the bug. This will allow us to quickly resolve the issue.

Funding