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Phred, Phrap, and 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 below. For more information about these software please visit the Phrap home page.
Note: Repeatmasker is no longer offered
by the University of Washington.
| Academic License |
Phred, Phrap, and Consed-Autofinish are available to users at academic and nonprofit research institutions at no charge. Please click on the academic license button to access the academic license.
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| Commercial License |
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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.
Express Licensing Program
UW TechTransfer
4311 11th Avenue NE, Suite 500
Seattle, WA 98105-4608
Phone: (206) 616-9212
Fax: (206) 616-3322
Email: license@u.washington.edu
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| Authorized Distributor |
You may also obtain Phred, Phrap, and Consed-Autofinish licenses from our authorized distributor.
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CodonCode |
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: bge@u.washington.edu, website: http://www.phrap.org.
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: phg@u.washington.edu, website: http://www.phrap.org.
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 Descriptive and Technical Information, contact David Gordon, Software Engineer, Website: http://www.phrap.org/consed/consed.html
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