Phred uses a four-phase procedure as outlined by Ewing et al. to determine a sequence of base calls from the processed DNA sequence tracing: 
# Predicted peak locations are determined, based on the assumption that fragments are relatively evenly spaced, on average, in most regions of the gel, to determine the correct number of bases and their idealized evenly spaced locations in regions where the peaks are not well resolved, noisy, or displaced (as in compressions)
# Observed peaks are identified in the trace
# Observed peaks are matched to the predicted peak locations, omitting some peaks and splitting others; as each observed peak comes from a specific array and is thus associated with 1 of the 4 bases (A, G, T, or C), the ordered list of matched observed peaks determines a base sequence for the trace.
# The unmatched observed peaks are checked for any peak that appears to represent a base but could not be assigned to a predicted peak in the third phase and if found, the corresponding base is inserted into the read sequence.
The entire procedure is rapid, usually taking less than half a second per trace. The results can be output as a PHD file, which contains base data as triples consisting of the base call, quality, and position.