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Express Beta Diversity (EBD) is a software package for calculating measures of taxon- or phylogenetic-based beta diversity.


  • Oct. 7, 2014: EBD v1.0.6 release. Improved support for taxon-based beta diversity calculators. Fixed compiler errors under GCC >= 4.6.8.
  • June 27, 2014: EBD v1.0.5 release. Improved support for parsing Newick trees with missing branch length information.
  • May 24, 2013: EBD v1.0.4 release. Added support for generating jackknife values and hierarchical cluster trees.
  • Feb. 5, 2013: EBD v1.0.3 release. Added functionality to project (prune) a tree to a specific set of taxa.
  • Feb. 1, 2013: EBD v1.0.2 release. Now contains functionality for generating hierarchical cluster trees and a script for converting UniFrac formatted sample data into the EBD format.



EBD is available as C++ source code under the GNU GPL v3. A precompiled binary is provided for Windows and simple compilation instructions provided for OS X and Linux.

Citing EBD

If you use EBD in your research, please cite:

Parks, D.H. and Beiko, R.G. Measures of phylogenetic differentiation provide robust and complementary insights into microbial communities. Advance online publication, August 2, 2012. (Abstract)

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] or Robert Beiko (beiko [at] 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.