Graphics: No permission is needed to reproduce a graphic produced by the Genome Browser

Permission is granted for reuse of all graphics produced by the UCSC Genome Browser website. There is no need to contact us to get permission. If your publisher, notably Elsevier, insists on getting approval, please direct them to this webpage. However, when you use the UCSC Genome Browser in your work, please cite one of our publications.

Data: No license is needed for the data files and database tables used by the Genome Browser

As far as the UCSC Genome Browser is concerned, the raw table data and binary files used to create the graphics by the browser is freely available for both public and commercial use. The README.txt file in the download directory of each assembly shows the use original restrictions pertaining to the genome sequence itself by the original authors. Conditions for individual annotation tracks, which depend on the original authors, can be found in the track description pages.

Software: Commercial use of the Genome Browser software and related tools available from our website and source code repository

As written above, when using applications from the Genome Browser tool suite, including LiftOver and BLAT, or data from the UCSC Genome Browser database in a research work that will be published in a journal or on the Internet, there is no need to get permission from us. When you use the UCSC Genome Browser in your work, please cite one of our publications.

The Genome Browser binaries and source code are freely available for academic, nonprofit, and personal use. A license is required for commercial download and installation of most Genome Browser binaries and source code, with the exception of the items in the section below, notably BLAT. To purchase a commercial license for Genome Browser source code, LiftOver, GBiB, or GBiC, please visit the Genome Browser store.

If you would like to purchase more than 20 copies of the Genome Browser source code, please follow these instructions:

1. Read and sign the licensing agreement.
2. Email a signed copy of the license agreement to the UCSC Office for IP Management (genomebrowser@ucsc. edu).
3. Follow the instructions in the license agreement for submitting the signed original copy and payment.
4. After your license application has been processed, you will receive instructions for downloading the browser software and data.

Genome Browser licensing questions should be directed to genome-www@soe.ucsc.edu. For information about commercial licensing of the Blat and In-Silico PCR tools, see the Kent Informatics website or contact kent@soe.ucsc.edu.

Software: Tools and directories freely available for all uses

The following directories are available without a license for all uses, academic, non-profit, and commercial:

• kent/src/utils (includes big* tools and C libraries, for reading and writing bigBed, bigWig and similar files)
• kent/src/lib
• kent/src/inc
• kent/src/tagStorm - tools and libraries for reading and writing hierarchical meta data files
• kent/src/parasol - a very fast cluster job scheduler
• kent/src/htslib - a third party library that we only distribute for convenience
• kent/src/hg/autoSql
• kent/src/hg/autoXml

See the LICENSE file in the top level of our source code for a listing of licenses and directories that they apply to: https://github.com/ucscGenomeBrowser/kent/blob/master/LICENSE.

When you use the UCSC Genome Browser in your work, please cite one of our publications.

Acknowledgements

This software includes software made by open-source projects:

• htslib, see Bonfield et al, 2021: Copyright (C) 2012-2020 Genome Research Ltd., see kent/src/htslib
• optimalLeaf, see Bar-Joseph et al. 2003: released into the public domain by Ziv Bar-Joseph, see kent/src/optimalLeaf.