STAMP

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 will provide 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 mostly stable. This is also your chance to suggest new features! To get started, try out the example data in /examples/EnterotypesArumugam.

• STAMP v2.0.0 (BETA - release 10) for Windows (released August 8, 2011)

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

Announcements

• Apr. 7, 2011: Patch for STAMP v1.08 released. This patch provides improved support for converting MG-RAST v3.0 profiles into STAMP profiles.
• Mar. 14, 2011: STAMP v1.08 released. Minor update to provides support for the latest MG-RAST profiles.
• Sept. 7, 2010: STAMP v1.07 released. Improved scatter plots, enhanced annotation of COG profiles, and minor bug fixes.
• Previous announcements

Mailing list

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

Documentation

• Quick installation instructions (Microsoft Windows, Apple's Mac OS X, Linux, Command-line interface)
• User's Guide (v1.08)
• FAQs
• Version history

Downloads

• STAMP v1.08.1 patch: provides improved support for converting MG-RAST v3.0 profiles into STAMP profiles.
• STAMP v1.08 executable for Microsoft Windows (~18MB)
• STAMP v1.08 executable for Mac OS X Leopard and Snow Leopard (~73MB)
• STAMP v1.08 source code (~2MB)
• Previous versions

Examples

• Image gallery
• Example datasets

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] 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

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

• Genome Atlantic
• The Dalhousie Centre for Comparative Genomics and Evolutionary Bioinformatics, and the Tula Foundation
• The Natural Sciences and Engineering Research Council of Canada
• The Dalhousie Faculty of Computer Science