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Using STAMP to identify SEED subsystems which are differentially abundant between Candidatus Accumulibacter phosphatis sequences obtained from a pair of enhanced biological phosphorus removal (EBPR) sludge metagenomes(data originally described in Parks and Beiko, 2010).

STAMP is a software package for analyzing taxonomic or metabolic profiles that promotes ‘best practices’ in choosing appropriate statistical techniques and reporting results. Statistical hypothesis tests for pairs of samples or groups of samples is support along with a wide range of exploratory plots. STAMP encourages the use of effect sizes and confidence intervals in assessing biological importance. A user friendly, graphical interface permits easy exploration of statistical results and generation of publication quality plots for inferring the biological relevance of features in a metagenomic profile. STAMP is open source, extensible via a plugin framework, and available for all major platforms.


  • June 26, 2015: STAMP v2.1.3 released. Minor bug fix to scatter plot to properly handle profiles contained a single feature.
  • June 15, 2015: STAMP v2.1.2 released. Minor enhancements to extended error bar, heatmap, and profile bar plots.
  • June 7, 2015: STAMP v2.1.1 released. Resolves issue with v2.1.0 installation.
  • June 4, 2015: STAMP v2.1.0 released. Resolves the _hierarchy_wrap issue. Requires numpy >= 1.9.1, scipy >= 0.15.1, matplotlib >= 1.4.2.
  • Previous announcements



Please uninstall previous versions of STAMP before installing a new release.

Additional Scripts

  • identify entries within a STAMP profile that are not strictly hierarchical


Citing STAMP

If you use STAMP v2+ in your research, we appreciate you citing:

STAMP v1 manuscript:

Contact Information

STAMP is in active development and we are interested in discussing all potential applications of this software. We recommend you send suggestions, comments, and bug reports to the [STAMP Google Group] so all commuity members can participate and benefit from the discussions. 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. If you need to contact the authors of STAMP privately, please email Rob Beiko (beiko [at]


The development and deployment of STAMP has been supported by several organizations: