The Phred - Phrap Package: A brief description

CodonCode Corporation offers executable versions of the programs Phred, Phrap, and Cross_match for Windows, Mac OS X, Linux, and Unix. Phred, Cross_match, Phrap, Swat, and Consed 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, Phrap, Cross_match, Swat, and Consed.

This page gives a brief description of Phred, Cross_match, 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 for larger-scale projects, we offer executable versions of Phred for Mac OS X, Linux, and Unix. Our dedicated support team has extensive experience in large-scale DNA sequencing projects.

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:


CROSS_MATCH description (Crossmatch)

Cross_match: Fast DNA Sequence Comparisons and Vector Screening

Cross_match is a program for fast comparisons of DNA sequences that uses the same algorithms as Phrap. For example, the comparison of several hundred thousand bases of "raw" sequence to the sequence of an entire BAC typically takes less than one minute. Within the Phred - Phrap system, Cross_match is typically used for vector screening. Other common uses of Cross_match include:


Phred- Crossmatch - Phrap by Codoncode directory

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