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PolyPhred compares fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions. PolyPhred functions are integrated with Phred, Phrap, and Consed-Autofinish, and is not a stand alone application. PolyPhred identifies potential heterozygotes using the base-calls, base-call qualities and peak sizes provided by Phred and the sequence alignments provided by Phrap. Potential heterozygotes identified by PolyPhred are tagged (color-coded) for rapid inspection using the Consed tool.

PolyPhred is available as a site license in an executable format (Linux, SGI-IRIX, Solaris, SunOS, HP-UX Mac-OSX, AIX and DEC-Alpha). PolyPhred operation requires Phred, Phrap and Consed-Autofinish software.

You will need to license Phred, Phrap, and Consed-Autofinish before obtaining PolyPhred.

For more information:

Licensing Information

PolyPhred 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

An academic license is available to users at academic and nonprofit research institutions at no charge. Please visit the developer's site to license the software.

Commercial License


Licensing fee for Polyphred starts at $3,000 per site. This license is for internal use only prohibs distribution of the software outside of licensed site(s). 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 appropriate 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 Polyphred, contact the Express Licensing Program at


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 Descriptive and Technical Information

Deborah Nickerson
Genome Sciences
University of WashingtonHSB K-340B
Seattle, WA 98105


For Licensing Information/Customer Service

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