The Phred - Phrap Package: A brief description

CodonCode Corporation offers the programs Phred and Phrap for Windows and Mac OS X. Phred and Phrap were developed by Dr. Phil Green and co-workers at the University of Washington in Seattle. CodonCode Corporation has acquired the distribution rights for Phred and Phrap.

This page gives a brief description of Phred and Phrap. The Phred-Phrap programs were developed for use by automated scripts, and therefore do not have a graphical user interface. For scientists who prefer to use Phred and Phrap from a graphical user interface on OS X or Windows, we offer the sequence assembly and editing software CodonCode Aligner. CodonCode Aligner makes basecalling with Phred and sequence assembly with Phrap easy, and also offers functions for contig editing and mutation detection.

PHRED description.

Phred: Better Base Calling

Phred is a base-calling program for DNA sequence traces. The program was developed by Drs. Phil Green and Brent Ewing, and is copyrighted by the University of Washington. It is widely used by the largest academic and commercial sequencing laboratories. Two major reasons why Phred is used by leading sequencers are:

Phred was developed for the Human Genome Project, were large amounts of sequence data were processed by automated scripts; therefore, Phred's processing options are set by command line parameters. For Windows and OS X users who would like to use Phred through an easy-to-use graphical user interface, we have developed the sequence analysis software CodonCode Aligner. CodonCode Aligner greatly simplifies using Phred for base calling and Phrap for sequence assembly, and also offers a number of additional functions often needed in DNA sequencing projects, for example contig alignment and editing, reference sequence alignments, and mutation detection.

For corporate users who wish to use Phred-Phrap, purchasing Phred and / or Phrap licenses together with CodonCode Aligner, allows use of Phred and Phrap througha graphical user interface. Purchasing information for CodonCode Aligner can be found here.

Academic users who plan to use Phred from scripts or the command line can obtain source code for Phred-Phrap free of charge directly from the authors. For academic users who prefer a graphical user interface and purchase licenses for CodonCode Aligner, use of the workstation versions of Phred and Phrap that are included with CodonCode Aligner is free of charge.

To learn more about how Phred works or about Phred quality values, visit our PHRED page.

A description of PHRAP.

Phrap: Better Sequence Assemblies

Phrap is a leading program for DNA sequence assembly. Phrap is routinely used in some of the largest sequencing projects in the Human Genome Sequencing Project and in the biotech industry. Some of Phrap's feature include:


Phred- Crossmatch - Phrap by Codoncode directory

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