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Phred, Phrap, Consed-Autofinish

Phred, Phrap, and Consed-Autofinish are standard bioinformatics tools used by over 250 commercial sites and thousands of academic labs. These three software tools can be licensed together or separately, but the combination is recommended because of the benefits of the integration of these programs. Information on licensing for one or all of these programs can be found more


Phred reads DNA sequencer trace data, calls bases, assigns quality values to the bases, and writes the base calls and quality values to output files. Phred is available in a source code format as a site license.

For Descriptive and Technical Information for Phred, contact Brent Ewing, Software Engineer, email:


Phrap is a package of programs for assembling shotgun DNA sequence data. Its key features include

  • allows use of entire read (not just trimmed high quality part)
  • uses a combination of user-supplied and internally computed data quality information to improve accuracy of assembly in the presence of repeats
  • constructs contig sequence as a mosaic of the highest quality parts of reads (rather than a consensus)
  • provides extensive information about assembly (including quality values for contig sequence) to assist troubleshooting
  • handles very large datasets.

Phrap is available in a source code format as a site license and includes Phrap, Cross_Match, and Swat.

For Descriptive and Technical Information, contact Phil Green, Professor, email:


Consed-Autofinish is a Unix-based graphical editor for Phrap sequence assemblies. Consed includes Autofinish, which automatically chooses finishing reads. Consed is tightly integrated with Phrap and is the optimal editor for use with Phrap.

Consed is available as a site license in an executable format (Sun Solaris, HP-UX, DEC-Alpha, Linux) and includes Consed and Autofinish.

For more information:

Licensing Information

Phred, Phrap, Consed-Autofinish is one of the many software programs and tools created at the University of Washington available through our Express Licensing Program. These agreements have standard terms and conditions that allow for rapid licensing by companies, organizations, or individuals.

Academic License

Phred, Phrap, and Consed-Autofinish are available to users at academic and nonprofit research institutions at no charge. To obtain an academic license, read and follow the instructions available on the website.

Commercial License

This license agreement applies to one or all of the Phred, Phrap, and Consed-Autofinish programs. This license is required for use of these software by commercial entities and is for internal use only. Redistribution of software outside licensed site(s) is not permitted.

Licensing fee for Phrap starts at $5,000 per site. Licensing fee for Phred and Consed starts at $2,500 per software per site. The conditions and financial terms of this license apply only to those who sign and return it "as is." This license may be modified for an additional cost.

Download the Express License (PDF file), sign it, and return it to the University of Washington according to the instructions on the license. For questions about licensing Phred, Phrap and Consed-Autofinish, contact the Express Licensing Program.



You may also obtain Phred, Phrap, and Consed-Autofinish licenses from our authorized distributor, CodonCode.

The conditions and financial terms of this license apply only to those who download the license, sign it and return it "as is" to UW CoMotion. Some Express Licenses may be modified for an additional cost. Other licensing arrangements may be available.

For Licensing Information/Customer Service

Express Licensing Program
UW CoMotion
4545 Roosevelt Way NE, Suite 400
Phone: (206) 543-3970
Fax: (206) 616-3322