Difference between revisions of "ExpressBetaDiversity"
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Express Beta Diversity (EBD) is a software package for calculating measures of taxon- or phylogenetic-based beta diversity. | Express Beta Diversity (EBD) is a software package for calculating measures of taxon- or phylogenetic-based beta diversity. | ||
| + | |||
| + | === Announcements === | ||
| + | * 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. | ||
=== Documentation === | === Documentation === | ||
| − | * [ | + | * [https://github.com/dparks1134/ExpressBetaDiversity Installation and program usage] |
* [[Supported Beta-diversity Measures|List of supported beta-diversity measures]] | * [[Supported Beta-diversity Measures|List of supported beta-diversity measures]] | ||
* [[EBD version history|Version history]] | * [[EBD version history|Version history]] | ||
=== Downloads === | === Downloads === | ||
| − | EBD is available as C++ source code under the [http://www.gnu.org/licenses/gpl.html GNU GPL v3]. A precompiled binary is provided for Windows and simple compilation instructions provided for | + | EBD is available as C++ source code under the [http://www.gnu.org/licenses/gpl.html GNU GPL v3]. A precompiled binary is provided for Windows and simple compilation instructions provided for OS X and Linux. |
| − | * [[ | + | * [https://github.com/dparks1134/ExpressBetaDiversity/releases/download/v1.0.6/ExpressBetaDiversity.exe Windows binary] |
| + | * [https://github.com/dparks1134/ExpressBetaDiversity/archive/v1.0.6.zip EBD v1.0.6 source code] | ||
| + | * [https://github.com/dparks1134/ExpressBetaDiversity Source code on GitHub] | ||
== Citing EBD == | == Citing EBD == | ||
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If you use EBD in your research, please cite: | 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''. | + | 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. ([http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej201288a.html Abstract]) |
== Contact Information == | == Contact Information == | ||
Latest revision as of 22:24, 6 October 2014
Express Beta Diversity (EBD) is a software package for calculating measures of taxon- or phylogenetic-based beta diversity.
Announcements
- 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.
Documentation
Downloads
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] 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.
