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