https://github.com/aaboyles/microbetrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
https://github.com/aaboyles/microbetrace
bioinformatics cdc epidemiology genomic-data-analysis genomics genomics-visualization hiv network-analysis network-graph network-visualization pathogens phylogenetic-trees phylogenetics phylogenomics phylogeny sequence-alignment
Last synced: 3 months ago
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The Visualization Multitool for Molecular Epidemiology and Bioinformatics
- Host: GitHub
- URL: https://github.com/aaboyles/microbetrace
- Owner: AABoyles
- License: apache-2.0
- Created: 2018-02-16T19:45:18.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2024-09-13T09:17:28.000Z (8 months ago)
- Last Synced: 2025-01-01T17:21:25.243Z (5 months ago)
- Topics: bioinformatics, cdc, epidemiology, genomic-data-analysis, genomics, genomics-visualization, hiv, network-analysis, network-graph, network-visualization, pathogens, phylogenetic-trees, phylogenetics, phylogenomics, phylogeny, sequence-alignment
- Language: HTML
- Homepage: https://aaboyles.github.io/MicrobeTrace/
- Size: 68.5 MB
- Stars: 11
- Watchers: 3
- Forks: 40
- Open Issues: 16
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Security: SECURITY.md
Awesome Lists containing this project
README
[](https://microbetrace.cdc.gov/MicrobeTrace/)
# MicrobeTrace [](https://doi.org/10.1101/2020.07.22.216275)
*The Visualization Multitool for Molecular Epidemiology and Bioinformatics*
Developed By ([some folks](https://github.com/CDCgov/MicrobeTrace/blob/master/humans.txt) at) CDC.
## To Use MicrobeTrace:
* **[Launch MicrobeTrace](https://microbetrace.cdc.gov/MicrobeTrace/)**
* [Download Sample Data](https://github.com/CDCgov/MicrobeTrace/raw/master/demo/MicrobetraceDemoData.zip)
* [Download Sample COVID Data](https://github.com/CDCgov/MicrobeTrace/raw/master/demo/COVID%20Dummy%20Data.zip)
* [View the Help Wiki](https://github.com/CDCgov/MicrobeTrace/wiki)
* [Read the Latest Manual](https://github.com/CDCgov/MicrobeTrace/raw/master/docs/MicrobeTrace_Manual.pdf)
* [Watch and follow along with the webinar](https://www.youtube.com/watch?v=5E-_Kb7yvHU)
* [Watch how to use MicrobeTrace for COVID-19](https://www.youtube.com/watch?v=he0Yq5yvToc)
* [Cite MicrobeTrace](https://github.com/CDCgov/MicrobeTrace/wiki/Cite-MicrobeTrace)
## To Spread the Word:
* [View the MicrobeTrace Flyer](https://github.com/CDCgov/MicrobeTrace/blob/master/docs/MicrobeTrace%20Flyer_Sept_2019.pdf)
* [Read our Reports](https://medium.com/microbetrace-reports/latest)
* [Connect with our User Community](https://www.reddit.com/r/MicrobeTrace/)
## To Help Us Build:
* [Report Bugs or Request Features](https://github.com/CDCgov/MicrobeTrace/issues)
* [Request Access to Our Slack](mailto:[email protected]?subject=Slack%20Request&body=Hello!%0AI'd%20like%20an%20invitation%20to%20join%20the%20MicrobeTrace%20Slack%20Channel%2C%20please.%0AThank%20you!)
* [Deploy Your Own Instance of MicrobeTrace](https://github.com/CDCgov/MicrobeTrace/wiki/z-Deployment)
* [Help us Develop MicrobeTrace](https://github.com/CDCgov/MicrobeTrace/wiki/z-Development)
## 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](https://creativecommons.org/publicdomain/zero/1.0/).
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.
## License
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 http://www.apache.org/licenses/LICENSE-2.0.html
## Privacy
This project contains only non-sensitive, publicly available data and
information. All material and community participation is covered by the
Surveillance Platform [Disclaimer](https://github.com/CDCgov/template/blob/master/DISCLAIMER.md)
and [Code of Conduct](https://github.com/CDCgov/template/blob/master/code-of-conduct.md).
For more information about CDC's privacy policy, please visit [http://www.cdc.gov/privacy.html](http://www.cdc.gov/privacy.html).
## Contributing
Anyone is encouraged to contribute to the project by [forking](https://help.github.com/articles/fork-a-repo)
and submitting a pull request. (If you are new to GitHub, you might start with a
[basic tutorial](https://help.github.com/articles/set-up-git).) 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](http://www.apache.org/licenses/LICENSE-2.0.html) or
later.
Before you get started, please read the [Developer's Guide to MicrobeTrace.](https://github.com/CDCgov/MicrobeTrace/wiki/z-Development)
All comments, messages, pull requests, and other submissions received through
CDC including this GitHub page are subject to the [Presidential Records Act](http://www.archives.gov/about/laws/presidential-records.html)
and may be archived. Learn more at [http://www.cdc.gov/other/privacy.html](http://www.cdc.gov/other/privacy.html).
## Records
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](http://www.cdc.gov).
## Notices
Please refer to [CDC's Template Repository](https://github.com/CDCgov/template)
for more information about [contributing to this repository](https://github.com/CDCgov/template/blob/master/CONTRIBUTING.md),
[public domain notices and disclaimers](https://github.com/CDCgov/template/blob/master/DISCLAIMER.md),
and [code of conduct](https://github.com/CDCgov/template/blob/master/code-of-conduct.md).