Sequence analysis and data visualization tool
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Failed to load latest commit information.


Click Here to Launch the Latest Version of MicrobeTrace


Alternately, if you'd like to download the older, executable version of MicrobeTrace, click here. The old version also has a User Manual. We're working on the User manual for the new version, but it isn't ready yet. In the meanwhile, much of the functionality is very similar, so the old user manual may be instructive (if not completely accurate). Additionally, the new MicrobeTrace has an unofficial wiki that should be accurate (if not complete).

©2017-2018 Centers for Disease Control and Prevention

Developed By Tony Boyles and Eric Aslakson

If you need help using MicrobeTrace, consult our Help Wiki

If you've discovered a bug or would like to request a new feature, please check to see if it's an existing issue. If not, please file a new issue.

Accessibility and 508 Compliance

The MicrobeTrace application is not compliant with all 508 standards, and as such, it is not accessible by individuals with disabilities. However, the application complies with the 508 Accommodations stated in our Voluntary Product Accessibility Template (VPAT) form.

Public Domain

This project constitutes a work of the United States Government and is not subject to domestic copyright protection under 17 USC § 105. This project is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the CC0 1.0 Universal public domain dedication. All contributions to this project will be released under the CC0 dedication. By submitting a pull request you are agreeing to comply with this waiver of copyright interest.


The project utilizes code licensed under the terms of the Apache Software License and therefore is licensed under ASL v2 or later.

This program is free software: you can redistribute it and/or modify it under the terms of the Apache Software License version 2, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache Software License for more details.

You should have received a copy of the Apache Software License along with this program. If not, see


This project contains only non-sensitive, publicly available data and information. All material and community participation is covered by the Surveillance Platform Disclaimer and Code of Conduct. For more information about CDC's privacy policy, please visit


Anyone is encouraged to contribute to the project by forking and submitting a pull request. (If you are new to GitHub, you might start with a basic tutorial.) By contributing to this project, you grant a world-wide, royalty-free, perpetual, irrevocable, non-exclusive, transferable license to all users under the terms of the Apache Software License v2 or later.

All comments, messages, pull requests, and other submissions received through CDC including this GitHub page are subject to the Presidential Records Act and may be archived. Learn more at


This project is not a source of government records, but is a copy to increase collaboration and collaborative potential. All government records will be published through the CDC web site.


Please refer to CDC's Template Repository for more information about contributing to this repository, public domain notices and disclaimers, and code of conduct.


Thanks to 18F's open source policy and code of conduct that were very useful in setting up this GitHub organization. Thanks to CDC's Informatics Innovation Unit that was helpful in modeling the code of conduct.