Phred - Phrap Information

Windows and OS X users

Phred and Phrap are command line programs, intended for use from automated scripts in large-scale environments. Our experience shows that most users interested in Phred and Phrap would like a graphical user interface, as well as the ability to view and edit contigs; for those users, we offer the sequence assembly software CodonCode Aligner for Windows and Mac OS X.

CodonCode Aligner is a sequence assembly and contig editing program for Windows and Mac OS X, with the ability to run Phred and Phrap. You can download free trial versions of CodonCode Aligner. The trial version of CodonCode Aligner enables you to use Phred for base calling and Phrap for sequence assembly directly from the graphical user interface of CodonCode Aligner, without having to use the command line or scripts.

Linux/UNIX users

Running Phred-Phrap on Linux or UNIX requires that you are familiar with running programs through Perl scripts or from the command line. Academic users can obtain the software directly from the authors at the University of Washington, as described below. For users at companies and for-profit institutions, we can make time-limited evaluation versions available before purchase.

Licenses for Phred - Phrap

Academic Licenses

Users at academic and nonprofit research institutions can obtain licenses for Phred and Phrap free of charge.

  • Academic users can obtain the source code for the programs directly from the authors at the University of Washington. For details, please visit:
  • Academic users who you purchase a license for CodonCode Aligner will automatically receive a free license for the "workstation" version of Phred and Phrap that can only be used from CodonCode Aligner.

For-Profit Licenses

All users at companies and for-profit institutions, as well as users who plan to use Phred-Phrap for any commercially funded sequencing projects, need to purchase a license for Phred-Phrap. Licenses can be purchased directly from the University of Washington, or through CodonCode Corporation. Please note that CodonCode Corporation can only distribute executables; if you would like or need to obtain source code for Phred-Phrap, you need to obtain a license from the University of Washington.
Prices for site licenses obtained from CodonCode Corporation are listed at

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