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Using STAMP to identify SEED subsystems which are differentially abundant in a pair of bovine rumen microbiomes (data originally described in Brulc et al., 2009).

STAMP (Statistical Analysis of Metagenomic Profiles) is a software package for analyzing metagenomic profiles (e.g., a phylogenetic profile indicating the number of marker genes assigned to different taxonomic units or a functional profile indicating the number of sequences assigned to different biological subsystems or pathways) that promotes ‘best practices’ in choosing appropriate statistical techniques and reporting results. It 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.

STAMP v2.0.0 - BETA

STAMP v2.0.0 is in active development. It provides support for comparing multiple groups of metagenomic samples (i.e. ANOVA, post-hoc tests, t-test) along with a number of other additional features. We expect to release it by the end of August. Join the STAMP mailing list if you wish to be updated on STAMP developments.

Windows users can try out a BETA version of STAMP v2.0.0. There are still some known bugs, but the program is stable. This is also your chance to suggest new features! To get started, try out the example data in /examples/EnterotypesArumugam.

Please uninstall any previous versions of STAMP before installing the above BETA release.


Mailing list

  • Join our mailing list to keep informed about STAMP developments.




Citing STAMP

If you use STAMP in your research, please cite:

Parks, D.H. and Beiko, R.G. (2010). Identifying biologically relevant differences between metagenomic communities. Bioinformatics, 26, 715-721. (Abstract)

Contact Information

STAMP 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 Rob 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.


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