Phred and consed write sequence and quality value information in
'phd' output files. A phd file contains information in a header,
the called bases, the base quality values, and the base call trace
locations.  Phd2fasta reads phd files and writes sequence and quality
value FASTA files, which phrap and cross_match need as input.
(Consed needs phd files in order to obtain the base call locations.)

WWW: http://www.phrap.org/phredphrapconsed.html