Phred reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base.

Phred is required and/or recommended by some packages available on Bio-Linux such as pregap4 (Staden), stars, and trace2dbest. Phred is an integral part of the phred/phrap/consed trio of packages.

The bio-linux-phred package now comes with both the standard, tried and tested version of phred (phred_0.020425.c), as well as a beta version (phred_0.071220.c).

To run standard phred, just type

To run the beta version of phred, just type:

Please note that there are a number of differences between the two versions of phred, one of which is that the new version can handle data from additional sequencing machine types. The original version recognises these machine types:

ABI_373_377, MolDyn_MegaBACE, ABI_3700, LI-COR_4000, Beckman_CEQ_2000, ABI_3100

In addition to having some new flags and functionality, the new phred version recognises:

ABI_373_377, ABI_3700, ABI_3730, ABI_3100, ABI_3130, Beckman_CEQ_2000, LI-COR_4000, MolDyn_MegaBACE

Phred, phrap and consed are licensed software and thus are not installed by default on Bio-Linux. These programs are free to academic researchers but you must obtain a license. Further information on this is available on the official website for phred, phrap and consed.